Methods, systems and related machine learning tools for accelerated plant productivity and atmospheric carbon sequestration

Abstract

Systems and methods for accelerating plant biomass growth and plant-mediated sequestration of atmospheric carbon, in particular, for selection of microbial drivers thereof from naturally occurring fungal species and / or strains are disclosed. The systems or methods may facilitate identification and propagation of a growth-promoting fungal consortium from a natural fungal microbiome. Sampling kits to collect soil samples are provided. Sample nucleic acid material may be extracted from the soil to generate a fungal microbiome dataset comprising of nucleic acid sequences. A machine learning tool, trained on high productivity ecosystems data, may processes the microbiome dataset to identify the growth-promoting fungal consortium. Propagation may include introducing a soil sample portion into a forest bioreactor to cultivate the growth-promoting fungal consortium, followed by inoculum preparation and application onto plants at a geographic location. Monitoring plant productivity post-inoculation may be achieved using an array of sensors to assess the efficacy of the fungal consortium.

Description

FUNGA.001WO PATENT METHODS, SYSTEMS AND RELATED MACHINE LEARNING TOOLS FOR ACCELERATED PLANT PRODUCTIVITY AND ATMOSPHERIC CARBON SEQUESTRATION CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is related to U.S. Provisional Patent Application No. 63 / 571140, filed March 28, 2024, entitled “METHODS, SYSTEMS AND RELATED MACHINE LEARNING TOOLS FOR ACCELERATED PLANT PRODUCTIVITY AND ATMOSPHERIC CARBON SEQUESTRATION,” the disclosure of which is incorporated herein by reference in its entirety. BACKGROUND Field of the Disclosure

[0002] This application relates generally to improved methods and systems of accelerating plant biomass growth and plant-mediated sequestration of atmospheric carbon, in particular, for automating selection of microbial drivers thereof from naturally occurring plant rhizospheres. Background

[0003] Commercial applications for soil microbiome melioration have been slow to develop, particularly in scenarios where harnessing the benefits of an entire native community is sought. Several factors contribute to this slow development, such as uncertain methods for identifying the appropriate microbial biodiversity, and due to difficulties in scaling inoculum production and fungal establishment.

[0004] The vast majority of plant species form symbioses with fungi, which significantly influence their access to growth-limiting resources. Recent research has shown, however, that functional characteristics of the soil fungal microbiome as a whole can influence the growth of an entire forest. For example, there is a strong correlation between the fungal microbiome’s functional characteristics and overall forest productivity. Thus, soil fungibiodiversity serves as a strong bio-indicator of underlying plant growth and health. Additionally, recent research has shown that certain, location-specific, fungal species are linked to forest performance, measured in terms of tree growth rate and ability to sequester atmospheric carbon.

[0005] Therefore, it is critical to take a holistic and natural approach in developing systems and methods of forest management and regeneration, especially in commercial contexts where biomass productivity is tightly linked to economic profitability. While commercial microbial inoculants are widely available, cross-laboratory studies have shown that many fungal inoculant products are ineffective at increasing tree growth rate, biomass productivity and atmospheric carbon uptake, especially in the long-term. Most commercial inoculants are ineffective for several reasons, most notably due to the limited number of species they contain, most of which can be ill-suited for geographically wide-spread inoculation across a variety of ecological regions.

[0006] Consequently, there is an urgent need to adopt a holistic and natural approach in the development of soil fungi microbiome inoculants, aimed at enhancing plant growth, resilience, adaptability and carbon uptake in commercial applications. Specifically, identifying and propagating consortia of locally adapted soil fungi species is crucial for ensuring the ecological compatibility and sustainability of fungal rhizosphere inoculants, thereby accelerating plant productivity. There is a need to identify solutions that facilitate the integration of local microbiota to preserve biodiversity, restore natural ecosystem functions, and mitigate the risk of introducing potentially invasive species, thereby ensuring commercial production of plant biomass is aligned with ongoing sustainability efforts. SUMMARY

[0007] For purposes of summarizing the disclosure and describing certain advantages that may be achieved, certain objects have been described. Of course, it is to be understood that not necessarily all such objects or advantages may be achieved in accordance with any particular embodiment of the disclosure. Thus, for example, those skilled in the art will recognize that the disclosure may be embodied or carried out in a manner that achieves or optimizes one advantage or group of advantages as taught herein without necessarily achieving other objects or advantages as may be taught or suggested herein.

[0008] In a first aspect, a method of accelerating plant productivity and atmospheric carbon sequestration is provided. The method can include, for example, identifying a growth-promoting fungal consortium from a natural fungal microbiome, including: providing at least one sampling kit to a subject at a geographic location, the at least one sampling kit including a sample container configured to receive a soil sample from the geographic location; receiving the at least one sampling kit, including the soil sample, from the geographic location; extracting nucleic acid material from a first portion of the soil sample; generating a fungal microbiome dataset based on sequencing the nucleic acid material present in the first portion of the soil sample, wherein sequencing further includes a plurality of reagents that enrich for fungal-derived nucleic acids; providing a machine learning tool, wherein the machine learning tool includes a training database, the training database including biotic and abiotic data associated with a plurality of high productivity ecosystems; and inputting the fungal microbiome dataset into machine learning tool, whereby the machine learning tool identifies the growth-promoting fungal consortium including a subset of fungal species present in the first portion of the soil sample and associated with the plurality of high productivity ecosystems; propagating the growth-promoting fungal consortium, including: providing a second portion of the soil sample to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth-promoting fungal consortium to reproduce and outcompete other organisms present in the second portion of the soil sample; colonizing the feedstock with fungal species and / or strains including the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including the feedstock and the growth-promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; and inoculating a plurality of plants present at the geographic location with the inoculum slurry; and monitoring productivity of each of the plurality of plants after each of the plurality of plants has been inoculated with the inoculum slurry, wherein monitoring includes utilizing a plurality of sensors.

[0009] In some embodiments, the growth-promoting fungal consortium includes a plurality of fungal species and / or strains native to the geographic location; and wherein the geographic location is a natural ecosystem.

[0010] In some embodiments, the monitoring includes observing.

[0011] In some embodiments, the plant productivity includes metrics selected from the group including biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0012] In some embodiments, the plurality of sensors includes at least a plant growth rate sensor and a plant photosynthesis rate sensor.

[0013] In some embodiments, the plant photosynthesis rate sensor includes a tool for measuring a rate of atmospheric carbon sequestration.

[0014] In some embodiments, the method further includes sequencing utilizing the plurality of reagents that enrich for fungal-derived nucleic acids, wherein the plurality of reagents includes at least a plurality of primers targeting an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha) genomic region, a Beta-Tubulin( -tubulin) genomic region, an RNA Polymerase II (RPB1 and / or RPB2) genomic region,and / or a Calmodulin (CaM) genomic region.

[0015] In some embodiments, each of the plurality of high productivity ecosystems includes an ecosystem including photosynthesizing organisms with a high rate of atmospheric carbon sequestration and / or biomass production.

[0016] In some embodiments, the forest bioreactor is a sealed environment or an unsealed environment, and the method further includes the optimal environment of a temperature, an oxygen content, a salinity, and / or a pH.

[0017] In some embodiments, propagating includes sexual and asexual reproduction of each fungal species and / or strain including the growth-promoting fungal consortium.

[0018] In some embodiments, each of the plurality of plants includes a tree.

[0019] In another aspect, a system for accelerating plant productivity and atmospheric carbon sequestration is disclosed. The system can include, for example, at least one sampling kit, wherein the at least one sampling kit is configured to be sent to and from a geographic location and includes a sample container, the sample container configured toreceive a soil sample; a soil sample processing system configured to extract nucleic acid material from a first portion of the soil sample; a nucleic acid sequencing platform configured to sequence the nucleic acid material present in the first portion of the soil sample and configured to generate a fungal microbiome dataset, wherein the nucleic acid sequencing platform further includes a plurality of reagents adapted to enrich for fungal-derived nucleic acids; a machine learning tool, wherein the machine learning tool includes a training database, the training database included of biotic and abiotic data associated with a plurality of high productivity ecosystems, and wherein the machine learning tool is configured to identify a growth-promoting fungal consortium including a subset of fungal species present in the first portion of the soil sample and associated with the plurality of high productivity ecosystems; a forest bioreactor configured to receive a second portion of the soil sample and to propagate the growth-promoting fungal consortium, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are adapted to promote colonization of the feedstock by the growth-promoting fungal consortium such as to outcompete other organisms present in the soil sample; an inoculum slurry including a mixture of water and a growth-promoting fungal consortium inoculum, wherein the growth- promoting fungal consortium inoculum includes the feedstock substantially colonized by the growth-promoting fungal consortium; a plurality of plants, wherein each of the plurality of plants is inoculated with the inoculum slurry; and a plurality of sensors configured to monitor plant productivity of each of the plurality of plants inoculated with the inoculum slurry.

[0020] In some embodiments, the growth-promoting fungal consortium includes a plurality of fungal species and / or strains native to the geographic location.

[0021] In some embodiments, the geographic location is a natural ecosystem.

[0022] In some embodiments, the system is configured to maximize plant productivity utilizing metrics selected from the group consisting of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0023] In some embodiments, the plurality of sensors includes at least one of a plant growth rate sensor and a plant photosynthesis rate sensor.

[0024] In some embodiments, the plant photosynthesis rate sensor includes a tool for measuring a rate of atmospheric carbon sequestration.

[0025] In some embodiments, the plurality of reagents adapted to enrich for fungal- derived nucleic acids includes at least a plurality of primers configured to target an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha) genomic region,a Beta-Tubulin ( -tubulin) genomic region, an RNA Polymerase II (RPB1 and / or RPB2)genomic region, and / or a Calmodulin (CaM) genomic region.

[0026] In some embodiments, each of the plurality of high productivity ecosystems includes an ecosystem including photosynthesizing organisms with a high rate of atmospheric carbon sequestration and / or biomass production.

[0027] In some embodiments, the forest bioreactor is a sealed environment or an unsealed environment, further including the optimal environment included of a temperature, an oxygen content, a salinity, and / or a pH.

[0028] In some embodiments, colonization of the feedstock includes sexual reproduction and asexual reproduction of each fungal species and / or strain including the growth-promoting fungal consortium.

[0029] In some embodiments, each of the plurality of plants includes a tree.

[0030] In another aspect, a method of producing a fungal inoculum is disclosed. The method may include, for example, providing a forest bioreactor; isolating a growth- promoting fungal consortium; providing the growth-promoting fungal consortium to the forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth-promoting fungal consortium to grow and to reproduce; colonizing the feedstock with fungal species and / or strains including the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including the feedstock and the growth-promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; and harvesting the inoculum slurry.

[0031] In some embodiments, the growth-promoting fungal consortium includes a plurality of fungal species and / or fungal strains native to a geographic location.

[0032] In some embodiments, the geographic location is a natural ecosystem.

[0033] In some embodiments, the geographic location includes a high productivity ecosystem, wherein the high productivity ecosystem includes photosynthesizing organisms with a high rate of atmospheric carbon sequestration and / or biomass production.

[0034] In some embodiments, the growth-promoting fungal consortium is adapted to maximize plant productivity utilizing metrics selected from the group consisting of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0035] In some embodiments, the growth-promoting fungal consortium is identified using a plurality of reagents adapted to enrich for fungal-derived nucleic acids, the plurality of reagents including at least a plurality of primers configured to target an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha) genomic region,a Beta-Tubulin ( -tubulin) genomic region, an RNA Polymerase II (RPB1 and / or RPB2)genomic region, and / or a Calmodulin (CaM) genomic region.

[0036] In some embodiments, the forest bioreactor is a sealed environment or an unsealed environment, further including the optimal environment including a temperature, an oxygen content, a salinity, and / or a pH.

[0037] In some embodiments, colonizing the feedstock includes sexual reproduction and asexual reproduction of each fungal species and / or strain including the growth-promoting fungal consortium.

[0038] In some embodiments, the growth-promoting fungal consortium inoculum is applied to at least one plant.

[0039] In some embodiments, the at least one plant is a tree.

[0040] In another aspect, a method of increasing plant productivity with reduced plant fertilizer utilization is disclosed. The method may include, for example, isolating a growth-promoting fungal consortium; providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth-promoting fungal consortium to grow and to reproduce; colonizing the feedstock with fungal species and / or strains including the growth-promoting fungal consortium for a periodof time sufficient to create a growth-promoting fungal consortium inoculum including the feedstock and the growth-promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; and inoculating a plurality of plants with the inoculum slurry, wherein the fungal species and / or strains including the growth-promoting fungal consortium enhances nutrient bioavailability without the need for chemical fertilizers.

[0041] In some embodiments, the growth-promoting fungal consortium includes a plurality of fungal species and / or strains native to a geographic location.

[0042] In some embodiments, the geographic location is a natural ecosystem.

[0043] In some embodiments, plant productivity includes metrics selected from the group consisting of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0044] In some embodiments, the method further includes harvesting the growth- promoting fungal consortium from a high productivity ecosystem, the high productivity ecosystem including a plurality of photosynthesizing organisms with a high rate of atmospheric carbon sequestration and / or biomass production.

[0045] In some embodiments, each of the plurality of plants includes a tree.

[0046] In another aspect, a method of generating biodiversity credits is provided. The method includes, for example, isolating a growth-promoting fungal consortium, wherein the growth-promoting fungal consortium includes native fungal species and / or strains; providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth-promoting fungal consortium to grow and to reproduce; colonizing the feedstock with the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including the feedstock and the growth-promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; inoculating a plurality of plants with the inoculum slurry; and establishing a community of the native fungal species and / or strains including the growth-promoting fungal consortium,in symbiosis with the plurality of plants, wherein the biodiversity credits increase in positive correlation to a diversity of the community of the native fungal species and / or strains.

[0047] In another aspect, a method of improving water quality is provided. The method may include, for example, inoculating a plurality of plants with an inoculum slurry, wherein the inoculum slurry includes a mixture of water and a growth-promoting fungal consortium inoculum including a feedstock and a growth-promoting fungal consortium; and establishing a community of the native fungi including the growth-promoting fungal consortium in symbiosis with the plurality of plants, wherein the growth-promoting fungal consortium inoculum includes a plurality of native fungal species and / or strains, and wherein each of the plurality of native fungal species and / or strains is adapted to filter contaminants from a volume of water, thereby improving quality of the volume of water.

[0048] In another aspect, a method of improving water quality is provided. The method may include, for example, inoculating a plurality of plants with an inoculum slurry, wherein the inoculum slurry includes a mixture of water and a growth-promoting fungal consortium inoculum including a feedstock and a growth-promoting fungal consortium; and establishing a community of native fungal species or strains , the native fungal species or strains being in symbiosis with the plurality of plants, wherein the growth-promoting fungal consortium inoculum comprises the native fungal species or strains, and wherein the native fungal species or strains are adapted to filter contaminants from a volume of water, thereby improving quality of the volume of water.

[0049] In some embodiments, the contaminants include at least a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, and / or agricultural runoff.

[0050] In some embodiments, the volume of water is a naturally occurring volume of water or an artificially formed volume of water.

[0051] In another aspect, a method of remediating soil is provided. The method may include, for example, isolating a growth-promoting fungal consortium; forming a growth- promoting fungal consortium inoculum including a feedstock and the growth-promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; inoculating a volume of soil with theinoculum slurry; and maturing the inoculum slurry within the volume of soil such as to substantially colonize the volume of soil with the growth-promoting fungal consortium.

[0052] In some embodiments, the volume of soil is selected from the group consisting of in situ soil, ex situ soil, translocated soil, and artificial soil.

[0053] In some embodiments, the volume of soil includes nutritive materials, the nutritive material providing a nutritive substrate for the growth-promoting fungal consortium to grow and substantially colonize the volume of soil.

[0054] In some embodiments, the volume of soil contains at least one contaminant.

[0055] In some embodiments, the at least one contaminant is substantially removed from the volume of soil and absorbed by at least one fungus including the growth-promoting fungal consortium.

[0056] In some embodiments, the at least one contaminant includes a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, and / or agricultural runoff. BRIEF DESCRIPTION OF THE DRAWINGS

[0057] The features and advantages of the methods and systems described herein will become more fully apparent from the following description and appended claims, taken in conjunction with the accompanying drawings. These drawings depict only several embodiments in accordance with the disclosure and are not to be considered limiting of their scope. In the drawings, similar reference numbers or symbols typically identify similar components, unless context dictates otherwise. In some instances, the drawings may not be drawn to scale.

[0058] Fig. 1 illustrates an example embodiment of a method of developing a training dataset for a machine learning tool for accelerated plant productivity and atmospheric carbon sequestration.

[0059] Fig. 2 illustrates an embodiment of a method of accelerating plant productivity and atmospheric carbon sequestration.

[0060] Fig. 3 illustrates an embodiment of a system for accelerating plant productivity and atmospheric carbon sequestration.

[0061] Fig. 4 illustrates a method of producing a fungal inoculum with a forest bioreactor.

[0062] Fig. 5 illustrates a method of increasing plant productivity with reduced plant fertilizer utilization.

[0063] Fig.6 illustrates a method of generating biodiversity credits.

[0064] Fig.7 illustrates a method of improving water quality.

[0065] Fig.8 illustrates a method of remediating soil. DEFINITIONS

[0066] As used herein, “plant productivity” refers to the rate at which plants in an ecosystem synthesize organic matter through photosynthesis. For example, plant productivity can refer to the rate of biomass increase of a plant and / or the rate of atmospheric carbon sequestration by a plant. In some embodiments, plant productivity can be measured at the level of an individual plant, a plurality of plants, a whole ecosystem (e.g., a forest), and other like groupings of plants of the same or different species. In some embodiments, plant productivity can be quantified as the amount of carbon fixed per unit area per period of time, which can be expressed in terms of mass (e.g., grams of carbon per square meter per year). In some embodiments, plant productivity can be divided into subcategories, including, but not limited to, (1) gross primary productivity (GPP), which is the total rate of photosynthesis inclusive of oxygen produced and carbon dioxide consumed by photosynthesis, and (2) net primary productivity (NPP), which is carbon dioxide respired by a plant or group of plants subtracted from the GPP. In some embodiments, NPP can represent the rate of new biomass production available for consumption by heterotrophic organisms (such as animals, fungi, and bacteria) or for accumulation in the form of standing biomass. In some embodiments, plant productivity can be further quantified in terms of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0067] As used herein, “carbon sequestration” refers to the process of capturing and storing atmospheric carbon dioxide (CO2) in a stable form. For example, carbon sequestration can be achieved through physical, chemical, or biological processes that remove CO2from the atmosphere and secure it in natural (e.g., forests) or artificial reservoirs.

[0068] In some embodiments, carbon sequestration can occur through photosynthesis of plants and other photosynthesizing organisms. As used herein, carbon sequestration can refer to the biological conversion of atmospheric CO2 into organic carbon compounds and biomass through the process of photosynthesis. In some embodiments, plant photosynthesis can include a process whereby plants utilize specialized enzymes to catalyze the fixation of CO2into organic molecules (e.g., glucose, cellulose, lignin, etc.). In some embodiments, plant photosynthesis can be an effective means of transferring carbon from the atmosphere and stably storing it in living tissue. Advantageously, the stored organic material can contribute to nutrient cycling in ecosystem, for example, when plants die and decompose, sequestered atmospheric carbon can be transferred and recycled in non-gaseous form through carbon pools. In some embodiments, carbon sequestration by natural ecosystems can be a means of mitigating anthropogenically driven levels of CO2 in the atmosphere that, e.g., can contribute to climate change. In some embodiments, carbon sequestration by plants can be enhanced by selecting plant species with high growth rates and long lifespans and through managing forests for increased density and longevity.

[0069] As used herein, “growth-promoting fungal consortium” refers to a pool of fungal species and / or strains that increase the plant productivity of an individual plant, and ecosystem, or any subset therebetween. In some embodiments, a growth-promoting fungal consortium refers to a subset of a fungal microbiome. For example, a fungal microbiome can include pathogenic, parasitic, commensal species, in addition to mutualistic species, wherein pathogenic and / or commensal species may not be species best suited to accelerate plant growth and / or increase atmospheric carbon sequestration.

[0070] As used herein, “geographic location” refers to any location, point or area that can be defined by latitudinal and longitudinal coordinates. In some embodiments, the geographic location is a natural ecosystem. For example, a natural ecosystem can be an old growth forest, a native grassland, a rainforest, or any other ecosystem that has not been substantially affected by human activities. In some alternative embodiments, a geographic location can be a location involving substantial human activities. For example, farmlands, orchards, gardens, plantations and other locations where plants grow as the direct result of human activities.

[0071] As used herein, “nucleic acid material” refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, these terms include single-, double-, or multi-stranded DNA or RNA. Examples of polynucleotides include a gene or gene fragment, whole genomic DNA, genomic DNA, epigenomic, genomic DNA fragment, exon, intron, messenger RNA (mRNA), regulatory RNA, transfer RNA, ribosomal RNA, non-coding RNA (ncRNA) such as PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), and long non-coding RNA (lncRNA), small hairpin (shRNA), small nuclear RNA (snRNA), micro RNA (miRNA), small nucleolar RNA (snoRNA) and viral RNA, ribozyme, cDNA, recombinant polynucleotide, branched polynucleotide, plasmid, vector, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probe, primer or amplified copy of any of the foregoing. A polynucleotide can include modified nucleotides, such as methylated nucleotides and nucleotide analogs including nucleotides with non-natural bases, nucleotides with modified natural bases such as aza- or deaza-purines. A polynucleotide can be composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); and thymine (T). Uracil (U) can also be present, for example, as a natural replacement for thymine when the polynucleotide is RNA. Uracil can also be used in DNA. The term “nucleic acid sequence” can refer to the alphabetical representation of a polynucleotide or any nucleic acid molecule, including natural and non-natural bases.

[0072] As used herein, “reagents” refers to a selection of chemicals, enzymes, and buffers designed to lyse cells, denature proteins, and solubilize nucleic acid material, facilitating its purification from biological samples. The term “reagents that enrich for fungal- derived nucleic acids” can include reagents that can be collectively referred to as “primer.” As used herein, a primer refers to a short, synthetic oligonucleotide sequences designed to anneal to complementary regions of a target nucleic acid molecule, providing the starting point for enzymatic amplification and subsequent determination of the nucleotide sequence. For example, in the context of identifying fungi found in an environmental sample, a primer can be designed to target an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha(TEF1-alpha) genomic region, a Beta-Tubulin ( -tubulin) genomic region, an RNAPolymerase II (RPB1 and / or RPB2) genomic region, a Calmodulin (CaM) genomic region, orany other genomic regions that is used in the relevant art to identify fungal species and / or strains. In some embodiments, the primers used can be those as described by Tedersoo et al. (2018), New Phytologist, 217(3), pg. 1370-1385, which is incorporated by reference herein in its entirety.

[0073] As used herein, “machine learning” refers to an algorithmic application of artificial intelligence (AI) that provides systems the ability to learn and improve performance without ample or significant human input. Human input may be part of the learning for such tools (or models applied through such tools). Such tools may encompass predictive modeling using both historical and real time data, which allows software to become more accurate in predicting outcomes without being explicitly programmed. Such tools often implement models important for optimizing computational methods at a large scale or with a large quantity of data. “Training database” as used herein refers to a subset of data used to train a machine learning tool by iteratively adjusting the machine learning tool’s parameters based on the input- output pairs provided, aiming to minimize the difference between predicted and actual outcomes.

[0074] As used herein, “forest bioreactor” refers to a sealed or unsealed tool that is used to propagate the growth-promoting fungal consortium. For example, the forest bioreactor can include a feedstock and / or a plurality of conditions favoring the growth of fungal species and / or strains comprising the growth-promoting fungal consortium. In some further embodiments, the bioreactor can be configured such as to suppress growth of undesirable species present in a microbiome sample, such as species that do not include the growth- promoting fungal consortium.

[0075] As used herein, “feedstock” refers to a material or surface thereof, from or on which an organism lives, grows, and / or obtains its nourishment. In some embodiments, a substrate provides sufficient nutrition to the organism under target growth conditions such that the organism can live and grow without providing the organism a further source of nutrients. In some embodiments, the substrate is a natural substrate. Non-limiting examples of a natural substrate include a lignocellulosic substrate, a cellulosic substrate, or a lignin-free substrate. The materials can have a variety of particle sizes and occur in a variety of forms, including shavings, pellets, chips, flakes, or flour, or can be in monolithic form.

[0076] As used herein, “optimal environment” refers to an environment that supports the growth of mycelia, as would be readily understood by a person of ordinary skill in the art in the mycelial cultivation industry, which includes a gaseous environment of carbon dioxide (CO2), oxygen (O2), and other atmospheric gases including nitrogen (N2), and which is further characterized as having a temperature, a relative humidity, a salinity, and a pH.

[0077] As used herein, “inoculum” refers to a solid or liquid composition of any living organism or part thereof, including, but not limited to fungi and other living material present in a microbiome. “Inoculum slurry” as used herein refers to a liquid inoculum comprising a mixture of the fungal colonized feedstock with water or any other suitable liquid and / or nutrient amendments.

[0078] As used herein, “fungi,” “fungal species” and / or “fungal strain” refers to an organism classified as Basidiomycota, Ascomycota, and the phylum formerly referred to as Zygomycota. In some embodiments, fungi include all species classified as Cryptomycota, Microsporidia, Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Mucoromycota, Glomeromycota, Ascomycota and Basidiomycota. In some embodiments, fungi can include a mold, a yeast, and / or a filamentous fungus. For example, a filamentous fungus can include a mycelium, the mycelium further comprising a network of hyphae. In some embodiments a fungal strain can refer a genetic variant or subtype of a fungal species, characterized by distinct morphological, physiological, or genetic traits that differentiate the strain. In some embodiments, a fungal strain can result from mutations, genetic recombination, or adaptation. For example, a fungal strain can result from adaptation to a specific environmental condition. In some embodiments a strain can result from laboratory experimentation, mutagenesis and / or breeding. In some embodiments, a fungal strain can be characterized as a morphological variant, a life history variant, a genetic variant, an epigenetic variant, and / or like variations of a type specimen of a fungal species. For example, a fungal strain comprising a genetic variant can be characterized by genetic differences thereof to at least part of the genome of the type fungal species whose at least partial genome is known and / or has been sequenced. In some embodiments, a fungal strain can be characterized as a fungus exhibiting differences in characteristics such as growth rate, pathogenicity, enzyme production, and resistance to antimicrobial agents, from a type sample of the species.

[0079] As used herein, “plant” refers to photosynthetic eukaryotes belonging to the kingdom Plantae, characterized by the presence of chloroplasts containing chlorophyll and cell walls composed of cellulose. In some embodiments, plants can include eukaryotic organisms whose cells contain chloroplasts containing chlorophyll a and chlorophyll b. As used herein, “tree” refers to its plain language meaning. In some embodiments, a tree can refer to any plant that would be understood as a tree by a skilled artisan. In some embodiments, a tree can include any large plant. In some embodiments, a tree can include a plant with a woody structure. For example, a tree can include a plant with a woody structure and whose cells include cellulose and / or lignin.

[0080] As used herein, “establish,” “established” and / or “establishing” refers to the successful introduction, colonization, and subsequent growth and proliferation. In some embodiments, one of more fungi can be established in a volume of soil. For example, fungal mycelium, cells, spores, and other like fungal structures can be added to a volume of soil, a feedstock, a substrate, and / or like media, wherein such fungal structures reproduce asexually and / or asexually, thereby increasing the biomass of such fungi. In some embodiments, one or more plants can be established. For example, a seed, a transplanted seedling, or a transplanted plant can be said to have established when the plant has successfully developed a robust root system to support growth, nutrient uptake, water absorption, and like plant physiological processes, without supplemental support beyond normal care. In some embodiments, an established plant has acclimated to a new environment and demonstrates healthy growth, including, but not limited to, new foliage, root development, and like morphological growth. In some embodiments, a growth-promoting fungal consortium can be established. For example, growth-promoting fungal consortium can substantially colonize, fully colonize, and / or fully consume the medium to / on which it is added. In some embodiments, established can refer to growth-promoting fungal consortium inoculum becoming fully associated in symbiosis with a plant. For example, an organism can be qualified as established when the organism persists in a stable and self-sustaining equilibrium. DETAILED DESCRIPTION

[0081] The figures and the following description relate to various example embodiments by way of illustration only. It should be noted that from the following discussion,example embodiments of the structures, methods, systems, and associated models disclosed herein will be readily recognized as viable alternatives that may be employed without departing from the principles of what is claimed. Reference will now be made in detail to several embodiments, examples of which are illustrated in the accompanying figures. It is noted that wherever practicable, similar or like reference numbers may be used in the figures and may indicate similar or like functionality. The figures depict embodiments of the disclosed methods or systems (with select equipment for purposes of illustration) and one skilled in the art will readily appreciate from the following description that various example embodiments of the structures, systems, methods and equipment described herein may be employed without departing from the principles described herein.

[0082] Described herein are embodiments of systems and methods to accelerate plant productivity and atmospheric carbon sequestration. The growth-promoting fungal consortium inoculum that is identified and propagated can be used in various commercial contexts, including, but not limited to, forestry, crop agriculture, horticulture, ecosystem conservation and / or habitat remediation, and like contexts.

[0083] It is an object of the present disclosure to provide a method of identifying a growth-promoting fungal consortium from a natural fungal microbiome. In some embodiments, the method can include providing a sampling kit comprising a sampling vessel configured to receive a soil sample from a geographic location. In some embodiments, the sampling kit, including the soil sample, can be received from the geographic location. For example, the soil sample can be taken from a forest in a remote geographic location and the soil sample can thereafter be transported by any suitable means to a central laboratory. In some embodiments the geographic location can be a natural ecosystem. In some embodiments, once the soil sample is received, the nucleic acid material content of a first portion of the soil sample can be extracted. In some embodiments, the extracted nucleic acid material can then be sequenced, wherein sequencing reagents can be selected for their ability to enrich for fungal- derived nucleic acids. For example, the plurality of reagents that enrich for fungal-derived nucleic acids can include one or more primers targeting an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha) genomic region, a Beta-Tubulin( -tubulin) genomic region, an RNA Polymerase II (RPB1 and / or RPB2) genomic region, aCalmodulin (CaM) genomic region, and / or any other suitable taxonomic barcodes for identifying fungi from their nucleic acid material. In some embodiments, sequencing results in a fungal microbiome dataset. In some embodiments, a machine learning tool can be used, wherein the machine learning tool can include a training database including biotic and abiotic data associated with a plurality of high productivity ecosystems. For example, the machine learning tool can be trained with data from a training dataset that includes a library of DNA taxonomic barcode sequences that correlate with fungal taxonomic nomenclature, in addition to ecosystem metrics associated with high productivity ecosystems, such as species richness, nutrient content, rainfall, biomass accumulation, yield, growth rate, and other suitable metrics. In some embodiments, the plurality of high productivity ecosystems can include ecosystems with a large number or high biodiversity of photosynthesizing organisms, and with a high rate of atmospheric carbon sequestration and / or biomass production. In some embodiments, plant productivity can include metrics including, but not limited tom, biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, photosynthesis rate, and other suitable metrics. In some embodiments, the fungal microbiome dataset can be input into the trained machine learning tool to identify the species present in the soil sample such as to identify a growth-promoting fungal consortium, which can include of a subset of fungal taxa present in the soil sample and that are determined by the machine learning tool to promote plant productivity.

[0084] It is yet another object of the present disclosure to provide a method of propagating the growth-promoting fungal consortium. In some embodiments, the growth- promoting fungal consortium can include a plurality of fungal species and / or strains native to the geographic location. In some embodiments, a second portion of the soil sample can be provided to a forest bioreactor. For example, the forest bioreactor can be prepared to such as to provide an optimal environment for the growth-promoting fungal consortium to reproduce sexually and asexually and to outcompete other, undesired fungi that are present in the soil sample and are not plant growth-promoting. In some embodiments, the forest bioreactor can include a feedstock, wherein the feedstock can be selected to provide a nutritive source for the growth-promoting fungal consortium such that they more reproduce sexually and / or asexually. In some embodiments, the forest bioreactor can be sealed or unsealed. In some embodiments,the forest bioreactor can additionally include a temperature, an oxygen content, a salinity, a pH and any other suitable condition favoring rapid fungal growth and reproduction. In some further embodiments, the method can include colonizing the feedstock in the forest bioreactor for a time sufficient to create a growth-promoting fungal consortium inoculum. For example, the growth-promoting fungal consortium inoculum can include or can consist essentially of the feedstock and the growth-promoting fungal consortium. In some embodiments, the growth- promoting fungal consortium inoculum includes the feedstock and the growth-promoting fungal consortium. In some further embodiments, the growth-promoting fungal consortium inoculum can be mixed with water to create an inoculum slurry. In some embodiments, the method can include harvesting the inoculum slurry and thereafter inoculating a plurality of plants at the geographic location from which the soil sample was initially taken, with the inoculum slurry.

[0085] It is yet another object of the present disclosure to provide a method of monitoring the productivity of each of the plurality of plants after they have been inoculated with the inoculum slurry. In some embodiments, monitoring includes, for example, utilizing a plurality of sensors. For example, the plurality of plants can be monitored for their growth rate and their rate of photosynthesis using sensors configured to measure for either or both. In some embodiments, the plant photosynthesis rate sensor includes a tool for measuring a rate of atmospheric carbon sequestration.

[0086] It is another object of the present disclosure to provide a system for accelerating plant productivity and atmospheric carbon sequestration. In some embodiments, the system includes at least one sampling kit, wherein the at least one sampling kit can be configured to be sent to and from a geographic location. In some further embodiments, the geographic location is a natural ecosystem. In some embodiments, the at least one sample kit includes a sample container, and the sample container can be configured to receive a soil sample.

[0087] It is a further object of the present disclosure to provide a system comprising a processing system configured to extract nucleic acid material from a first portion of the soil sample. In some further embodiments, the system includes a nucleic acid sequencing platform. For example, the nucleic acid sequencing platform can be configured to sequence the nucleic acid material present in the first portion of the soil sample and can be configured to generate afungal microbiome dataset. In some embodiments, the nucleic acid sequencing platform can further include a plurality of reagents that can be adapted to enrich for fungal-derived nucleic acids. For example, the plurality of reagents can include primers, including, but not limited to, primers targeting an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha(TEF1-alpha) genomic region, a Beta-Tubulin ( -tubulin) genomic region, an RNAPolymerase II (RPB1 and / or RPB2) genomic region, a Calmodulin (CaM) genomic region, and / or other suitable taxonomic barcode regions for fungi.

[0088] It is yet a further object of the present disclosure to provide a system comprising a machine learning tool. In some embodiments, the machine learning tool can include a training database, the training database may further include biotic and abiotic data associated with a plurality of high productivity ecosystems. For example, the plurality of high productivity ecosystems can include ecosystems with a large number and / or high diversity of photosynthesizing organisms, additionally including a high rate of atmospheric carbon sequestration and / or biomass production. In some further embodiments, the machine learning tool can be configured to identify a growth-promoting fungal consortium that can include a subset of fungal species present in the first portion of the soil sample and can be associated with the plurality of high productivity ecosystems.

[0089] It is a further object of the present disclosure to provide a forest bioreactor. In some embodiments, the forest bioreactor can be configured to receive a second portion of the soil sample and to propagate the growth-promoting fungal consortium. For example, the forest bioreactor can include a sealed or unsealed controlled environment in which the growth- promoting fungal consortium can grow in an optimal environment, including, but not limited to, a temperature, an oxygen content, a salinity, and / or a pH. In some further embodiments, the forest bioreactor can include a feedstock. For example, the feedstock and the optimal environment can be such as to promote colonization of the feedstock by, and / or asexual and sexual reproduction of, the growth-promoting fungal consortium in order to outcompete other organisms present in the soil sample.

[0090] It is yet a further object of the present disclosure to provide an inoculum slurry. In some embodiments, the inoculum slurry can include a mixture of water and a growth-promoting fungal consortium inoculum. In some further embodiments, the growth-promoting fungal consortium inoculum can include the feedstock substantially colonized by the growth- promoting fungal consortium.

[0091] It is a further object of the present disclosure to provide a plurality of plants. In some embodiments, the plurality of plants can be inoculated with the inoculum slurry. In some further embodiments, the plurality of plants can include a single species. In some alternative embodiments, the plurality of plants can include a plurality of species. In some embodiments the plurality of plants can include one or more tree species. In some alternative embodiments, the plurality of plants can include, for example, a mixture of woody and herbaceous species. For example, a tiered-cropping system can be implemented according to the present disclosure, wherein plants of two or more different height can be grown together, with the uppermost layer including the tallest-growing species and the lowermost layer including the shortest-growing species.

[0092] It is yet a further object of the present disclosure to provide a plurality of sensors. In some embodiments, the plurality of sensors can be configured to monitor plant productivity of each of the plurality of plants inoculated with the inoculum slurry. For example, plant productivity can be monitored and / or measured with respect to biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, photosynthesis rate, and any other metric suitable for measuring plant productivity. In some further embodiments, the plurality of sensors can include at least one of a plant growth rate sensor and a plant photosynthesis rate sensor. For example, the plant photosynthesis rate sensor can include a tool for measuring a rate of atmospheric carbon sequestration.

[0093] It is another object of the present disclosure to provide a method of producing a fungal inoculum with a forest bioreactor. In some embodiments, the method can include providing a forest bioreactor. For example, the forest bioreactor can be prepared such as to provide an optimal environment for the growth-promoting fungal consortium to reproduce sexually and asexually and to outcompete other, undesired fungi that are present in a soil sample and are not plant growth-promoting. In some embodiments, the forest bioreactor includes a feedstock, wherein the feedstock can be selected to provide a nutritive source for the growth-promoting fungal consortium such that the fungal species and / or strains includedtherein reproduce sexually and / or asexually. In some embodiments, the forest bioreactor can be sealed or unsealed. In some embodiments, the forest bioreactor can additionally include a temperature, an oxygen content, a salinity, a pH and any other suitable condition favoring rapid fungal growth and reproduction. In some further embodiments, the method includes colonizing the feedstock in the forest bioreactor for a time sufficient to create a growth-promoting fungal consortium inoculum. For example, the growth-promoting fungal consortium inoculum can include or can consist essentially of the feedstock and the growth-promoting fungal consortium. In some further embodiments, the growth-promoting fungal consortium inoculum can be mixed with water to create an inoculum slurry. In some embodiments, the method can include harvesting the inoculum slurry and thereafter inoculating a plurality of plants at the geographic location from which the soil sample was initially taken, with the inoculum slurry. In some further embodiments, producing a fungal inoculum with a forest bioreactor can include isolating a growth-promoting fungal consortium. In yet some further embodiments, the producing a fungal inoculum with a forest bioreactor can include providing the growth- promoting fungal consortium to the forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment can be selected to cause the growth-promoting fungal consortium to grow and to reproduce. In some further embodiments, producing a fungal inoculum with a forest bioreactor can include colonizing the feedstock with fungal species and / or strains comprising the growth- promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including or consisting essentially of the feedstock and the growth-promoting fungal consortium. In some further embodiments, producing a fungal inoculum with a forest bioreactor can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry. In some further embodiments, producing a fungal inoculum with a forest bioreactor can include harvesting the inoculum slurry. For example, the inoculum slurry can include the growth-promoting fungal consortium, the growth-promoting fungal consortium including one or more fungal species and / or strains that increase plant productivity.

[0094] It is yet a further object of the present disclosure to provide a growth- promoting fungal consortium that includes a plurality of fungal species and / or fungal strains native to a geographic location. For example, a native fungal species and / or strain can includea species and / or strain that is naturally present in a geographic location. In some embodiments, the geographic location can include a geographic area, e.g., bound by a length and width. In some embodiments, a geographic location includes a volume. For example, a fungal species and / or strain can be native to a circumscribed geographic area, including up to a depth in the soil or up to a certain height or elevation.

[0095] It is yet a further object of the present disclosure to provide a method of producing a fungal inoculum with a forest bioreactor using fungal species and / or strains from a geographic location that is a natural ecosystem. In some embodiments, the geographic location can include a high productivity ecosystem. For example, the high productivity ecosystem can include photosynthesizing organisms with a high rate of atmospheric carbon sequestration and / or biomass production. In some embodiments, the growth-promoting fungal consortium can be adapted to maximize plant productivity utilizing metrics including, but not limited to, biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0096] It is yet a further object of the present disclosure to provide a method of producing a fungal inoculum with a forest bioreactor for which the growth-promoting fungal consortium can be identified using a plurality of reagents. In some embodiments, the plurality of reagents is adapted to enrich for fungal-derived nucleic acids. For example, the plurality of reagents can include, but are not limited to, at least a plurality of primers configured to target an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha)genomic region, a Beta-Tubulin ( -tubulin) genomic region, an RNA Polymerase II (RPB1and / or RPB2) genomic region, and / or a Calmodulin (CaM) genomic region.

[0097] It is yet a further object of the present disclosure to provide a method of producing a fungal inoculum with a forest bioreactor that can include a sealed environment or an unsealed environment. In some embodiments, the bioreactor can be configured to simulate an optimal environment. For example, the optimal environment can include a temperature, an oxygen content, a salinity, and / or a pH.

[0098] It is yet a further object of the present disclosure to provide a method of producing a fungal inoculum with a forest bioreactor that includes colonizing. In someembodiments, colonizing can include colonizing a feedstock. In some embodiments, colonizing a feedstock includes sexual reproduction and asexual reproduction of each fungal species and / or strain comprising the growth-promoting fungal consortium.

[0099] It is yet a further object of the present disclosure to provide a method of producing a fungal inoculum with a forest bioreactor wherein the growth-promoting fungal consortium inoculum is applied to at least one plant. In some embodiments, the plant includes a plurality of plants. In some further embodiments, the plurality of plants can include a single species. In some alternative embodiments, the plurality of plants can include a plurality of species. In some embodiments the plurality of plants can include one or more tree species. In some alternative embodiments, the plurality of plants includes a mixture of woody species and herbaceous species. For example, a tiered-cropping system can be implemented according to the present disclosure, wherein plants of two or more different height can be grown together, with the uppermost layer including the tallest-growing species and the lowermost layer including the shortest-growing species.

[0100] It is another object of the present disclosure to provide a method of increasing plant productivity with reduced plant fertilizer utilization. In some embodiments, increasing plant productivity with reduced plant fertilizer utilization can include isolating a growth-promoting fungal consortium. In some embodiments, increasing plant productivity with reduced plant fertilizer utilization can include providing the growth-promoting fungal consortium to a forest bioreactor. For example, the forest bioreactor can be configured to provide a feedstock and an optimal environment. By way of further example, the feedstock and the optimal environment can be selected to cause the growth-promoting fungal consortium to grow and to reproduce. In some embodiments, increasing plant productivity with reduced plant fertilizer utilization can include colonizing the feedstock with fungal species and / or strains comprising the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including or consisting essentially of the feedstock and the growth-promoting fungal consortium. In some embodiments, increasing plant productivity with reduced plant fertilizer utilization can include, mixing the growth- promoting fungal consortium inoculum with water to form an inoculum slurry. In some embodiments, increasing plant productivity with reduced plant fertilizer utilization can include, harvesting the inoculum slurry. In some embodiments, increasing plant productivitywith reduced plant fertilizer utilization can include inoculating a plurality of plants with the inoculum slurry. For example, the fungal species and / or strains comprising the growth- promoting fungal consortium can enhance nutrient bioavailability without the need for chemical fertilizers.

[0101] It is another object of the present disclosure to provide a method of generating biodiversity credits. For example, a biodiversity credit can include a market-based method of quantifying conservation and / or restoration efforts. By way of further example, quantifying conservation and / or restoration efforts can include tradable units that correspond to a quantifiable improvement in biodiversity due to conservation efforts, habitat restoration, or sustainable management practices. By way of yet a further example, biodiversity credits can be bought and sold. In some embodiments, generating biodiversity credits can include isolating a growth-promoting fungal consortium. For example, the growth-promoting fungal consortium can include native fungal species and / or strains. In some embodiments, generating biodiversity credits can include providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment. For example, the feedstock and the optimal environment can be selected to cause the growth- promoting fungal consortium to grow and to reproduce. In some embodiments, generating biodiversity credits can include colonizing the feedstock with the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including or consisting essentially of the feedstock and the growth-promoting fungal consortium. In some embodiments, generating biodiversity credits can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry. In some embodiments, generating biodiversity credits can include harvesting the inoculum slurry. In some embodiments, generating biodiversity credits can include inoculating a plurality of plants with the inoculum slurry. In some embodiments, generating biodiversity credits can include establishing a community of the native fungal species and / or strains comprising the growth- promoting fungal consortium, in symbiosis with the plurality of plants. For example, generating biodiversity credits can include increasing an entity’s biodiversity credits in positive correlation to a diversity of the community of the native fungal species and / or strains. In some embodiments, the biodiversity credits can be carbon credits as would be readily understood by the skilled artisan.

[0102] It is another object of the present disclosure to provide a method of improving water quality. In some embodiments, improving water quality can include inoculating a plurality of plants with an inoculum slurry. For example, the inoculum slurry can include a mixture of water and a growth-promoting fungal consortium inoculum including or consisting essentially of a feedstock and a growth-promoting fungal consortium. In some embodiments, improving water quality can include establishing a community of native fungi including the growth-promoting fungal consortium in symbiosis with the plurality of plants. For example, the growth-promoting fungal consortium inoculum can include a plurality of native fungal species and / or strains. By way of further example, each of the plurality of native fungal species and / or strains can be adapted to filter contaminants from a volume of water, thereby improving quality of the volume of water. In some embodiments, improving water quality can include establishing a community of native fungal species or strains, the native fungal species or strains being in symbiosis with the plurality of plants. For example, the growth-promoting fungal consortium inoculum can include native fungal species and / or strains. By way of further example, the native fungal species and / or strains can be adapted to filter contaminants from a volume of water, thereby improving quality of the volume of water. It is a further object of the present disclosure to provide a method of improving water quality by removing at least one contaminant from a volume of water. In some embodiments, the contaminants include, but are not limited to, a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, and / or agricultural runoff.

[0103] It is another object of the present disclosure to provide a method of improving water quality of a volume of water. In some embodiments, the volume of water is a naturally occurring volume of water or an artificially formed volume of water. For example, a naturally occurring volume of water can include, but is not limited to, a lake, a pond, a lagoon, an estuary, a bog, a swamp, a marsh, and / or a wetland. By way of further example, a natural body of water can also include, but is not limited to an aquifer and / or groundwater that has permeated soil. In some embodiments, the volume of water is an artificial body of water, a reservoir, a water tank, an artificial lake, a sump, a cesspool, a cistern, or any other like artificial body of water. By way of further example, an artificial volume of water can also include, water that has artificially saturated a body of earth, soil gravel or any like material.

[0104] It is another object of the present disclosure to provide a method of remediating soil. In some embodiments, remediating soil can include isolating a growth- promoting fungal consortium. In some embodiments, remediating soil can include forming a growth-promoting fungal consortium inoculum including or consisting essentially of a feedstock and the growth-promoting fungal consortium. In some embodiments, remediating soil can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry. In some embodiments, remediating soil can include harvesting the inoculum slurry. In some embodiments, remediating soil can include inoculating a volume of soil with the inoculum slurry. In some further embodiments, remediating soil can include maturing the inoculum slurry within the volume of soil such as to substantially colonize the volume of soil with the growth-promoting fungal consortium.

[0105] It is a further object of the present disclosure to provide a method of remediating soil by selecting a volume of soil. In some embodiments, the volume of soil can be selected from, but not limited to, in situ soil, ex situ soil, translocated soil, and artificial soil. For example, in situ soil can include soil that is naturally present in an ecosystem, ex situ soil can include soil collected from a natural ecosystem and placed in a different geographic location, translocated soil can include soil moved within a natural or artificial system, and artificial soil can include man-made blend of various components designed to simulate natural soil properties. In some further embodiments, the volume of soil can include nutritive materials. For example, the nutritive material can provide a nutritive substrate for a growth- promoting fungal consortium to grow and substantially colonize the volume of soil. In some embodiments, the volume of soil can contain at least one contaminant. In some embodiments, remediating a volume of soil that includes a contaminant can include substantially removing the contaminant from the soil. For example, removing can include absorbing from the volume of soil one or more contaminants by at least one fungus of the growth-promoting fungal consortium. In some further embodiments, the at least one contaminant can include a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, and / or agricultural runoff.

[0106] Fig. 1 illustrates an example embodiment of a method of developing a training dataset for a machine learning tool for accelerated plant productivity and atmosphericcarbon sequestration 100. FIG. 1 illustrates an example embodiment by which the training database is compiled for use with the machine learning tool. The method 100 outlines a three- step process for understanding the relationship between growth rates of a natural ecosystem and fungal microbiome comprising the natural ecosystem.

[0107] In some embodiments, developing the training database can begin with sampling a plurality of natural ecosystem to measure the fungal microbiome and plant growth rates step 110. For example, extensive sampling can ensure a robust training dataset, which can enable the machine learning tool to comprehensively assess a fungal microbiome dataset input. In some embodiments, step 110 can further include collecting data for the training database on the health and productivity of natural ecosystems, as well as the diversity and role of fungal species within differing natural ecosystems.

[0108] In some embodiments, developing the training data base includes pairing the data collected in step 110 with climate and soil maps step 120. Step 120 can control for environmental variation, allowing for more accurate selection of fungal species and / or strains in the growth-promoting fungal consortium decoupled from other environmental factors, such as soil type, temperature, precipitation, and other climatic conditions.

[0109] Step 130 describes an embodiment where data from step 110 and analysis from step 120 are combined to construct a machine learning tool 130. For example, the machine learning tool 130 can be used to understand the specific needs of the forest as influenced by the soil fungal microbiome, e.g., in terms of nutrient cycling, disease resistance, and growth optimization.

[0110] Fig. 2 illustrates an embodiment of a method of accelerating plant productivity and atmospheric carbon sequestration 200. In some embodiments, the method of accelerating plant productivity and atmospheric carbon sequestration 200 can begin with the overarching goal of identifying a growth-promoting fungal consortium from a natural fungal microbiome 201. In some embodiments, the method of accelerating plant productivity and atmospheric carbon sequestration 200 can include providing a sampling kit comprising a sampling vessel configured to receive a soil sample from a geographic location 202. In some embodiments, the sampling kit, including the soil sample, can be received from the geographic location 203. In some embodiments, once the soil sample is received, the nucleic acid material content of a first portion of the soil sample can be extracted 204. In some embodiments, theextracted nucleic acid material can then be sequenced 205. For example, sequencing reagents can be selected for their ability to enrich for fungal-derived nucleic acids. In some embodiments, sequencing results in a fungal microbiome dataset 205. In some embodiments, a machine learning tool can be used, wherein the machine learning tool includes a training database including biotic and abiotic data associated with a plurality of high productivity ecosystems 206. In some embodiments, the fungal microbiome dataset can be input into the trained machine learning tool to identify the species present in the soil sample such as to identify a growth-promoting fungal consortium, which includes a subset of fungal taxa present in the soil sample and that are determined by the machine learning tool to promote plant productivity 207.

[0111] In some further embodiments, after the growth-promoting fungal consortium can be identified 210, the next overarching goal is to propagate the fungal species and / or strains that can be included in the growth-promoting fungal consortium 220. In some embodiments, a second portion of the soil sample can be provided to a forest bioreactor 221. For example, the forest bioreactor can be prepared to such as to provide an optimal environment for the growth-promoting fungal consortium to reproduce sexually and asexually and to outcompete other, undesired fungi that are present in the soil sample and are not plant growth-promoting. In some embodiments, the forest bioreactor includes a feedstock, wherein the feedstock can be selected to provide a nutritive source for the growth-promoting fungal consortium such that they more reproduce sexually and / or asexually. In some embodiments, the forest bioreactor can be sealed or unsealed. In some embodiments, the forest bioreactor can additionally include a temperature, an oxygen content, a salinity, a pH and any other suitable condition favoring rapid fungal growth and reproduction. In some further embodiments, the method includes colonizing the feedstock in the forest bioreactor for a time sufficient to create a growth-promoting fungal consortium inoculum 222. For example, the growth-promoting fungal consortium inoculum 222 includes or consists essentially of the feedstock and the growth-promoting fungal consortium. In other embodiments, the growth-promoting fungal consortium inoculum 222 includes the feedstock and the growth-promoting fungal consortium. In some further embodiments, the growth-promoting fungal consortium inoculum can be mixed with water to create an inoculum slurry 223. In some embodiments, the method can include harvesting the inoculum slurry 224 and thereafter inoculating a plurality of plants atthe geographic location from which the soil sample was initially taken, with the inoculum slurry 225.

[0112] In yet some further embodiments, the method 200 includes monitoring the productivity of each of the plurality of plants 230 after they have been inoculated with the inoculum slurry. In some embodiments, monitoring includes utilizing a plurality of sensors. For example, the plurality of plants can be monitored for their growth rate and their rate of photosynthesis using sensors configured to measure for either or both. In some embodiments, the plant photosynthesis rate sensor includes a tool for measuring a rate of atmospheric carbon sequestration.

[0113] Fig. 3 illustrates an embodiment of a system for accelerating plant productivity and atmospheric carbon sequestration 300. In some embodiments, the system includes at least one kit. For example, the kit can include a sampling kit that can contain a sample container into which a sample of soil is placed. In some further embodiments, no kit is required. For example, a sample of soil can be harvested from a geographic location and subsequently analyzed for the purpose of accelerating plant productivity and atmospheric carbon sequestration. In some embodiments, the system can include a soil sample processing system configured to extract nucleic acid material from the soil sample. For example, the soil sample can be divided into portions for various analyses or applications, such as a first portion of the soil sample from which nucleic acid material is extracted. In some embodiments, the system can further include a nucleic acid sequencing platform 301. For example, nucleic acid sequencing platform 301 can include a place-specific or geographic location-specific data analysis pipeline. In some embodiments, the system can include nucleic acid sequencing platform 301 that is configured to sequence the nucleic acid material present in the first portion of the soil sample. In some further embodiments, nucleic acid sequencing platform 301 can be configured to generate a fungal microbiome dataset. For example, nucleic acid sequencing platform 301 can include a data analysis pipeline that is configured to receive the nucleic acid material and / or extract the nucleic acid material, and thereafter sequence the nucleic acid material. In some embodiments, the nucleic acid sequencing platform 301 can further include a plurality of reagents adapted to enrich for fungal-derived nucleic acids. In some embodiments, nucleic acid sequencing platform 301 can include a data analysis pipeline that is a machine learning tool. For example, the machine learning tool can include a place-specificor geographic locations-specific training database, the training database being carefully curated to include biotic and abiotic data associated with a plurality of high productivity ecosystems. By way of further example, the machine learning tool can identify a growth-promoting fungal consortium present in the first portion of the soil sample and / or from the nucleic acid material extracted therefrom. For example, the data analysis platform comprising the nucleic acid sequencing platform 301 can be configured to identify a subset of fungal species present in the first portion of the soil sample and associated with the plurality of high productivity ecosystems. In some further embodiments, nucleic acid sequencing platform 301 can be configured to generate place-specific or geographic-location-specific fungal inoculants with the data analysis pipeline. For example, the data analysis pipeline can be configured to receive the fungal microbiome dataset, which can serve as a training set for, the data analysis pipeline including a machine learning tool. By way of further example, the machine learning tool can identify the growth-promoting fungal consortium that includes a subset of fungal species present in the first portion of the soil sample and associated with the plurality of high productivity ecosystems.

[0114] In some further embodiments, the system can include propagation of the growth-promoting fungal consortium 302. For example, a forest bioreactor can be configured to receive a second portion of the soil sample and to propagate the growth-promoting fungal consortium. In some embodiments, the forest bioreactor can be configured to provide a feedstock and an optimal environment. For example, the feedstock and the optimal environment can be adapted to promote colonization of the feedstock by the growth-promoting fungal consortium such as to outcompete other organisms present in the soil sample. In some embodiments, propagation of the growth-promoting fungal consortium 302 can include a nursery of plant-growing subsystem in which plant seedlings are established by inoculating each of the plant seedlings with the growth-promoting fungal consortium 302. In some further embodiments, the plant seedlings can be established by inoculating each with an inoculum slurry. In some embodiments, the inoculum slurry can include a mixture of water and a growth- promoting fungal consortium inoculum. For example, the growth-promoting fungal consortium inoculum can include the feedstock that is substantially colonized by the growth- promoting fungal consortium.

[0115] In yet some further embodiments, the system includes one or more sensors that can be configured to monitor plant productivity 303 of each of the plurality of plants inoculated with the inoculum slurry. For example, to monitor plant productivity 303 can include to work with existing commercial plant growers, including, but not limited to, persons working in forestry, crop agriculture, horticulture, ecosystem conservation and / or habitat remediation, and like contexts or infrastructure to deploy the established seedlings that have been inoculated with the inoculum slurry, in the field, including, but not limited to, a natural ecosystem or an artificial planting system. For example, an artificial planting system can include a farm, an orchard, a commercial forest, and like contexts. In some embodiments, the one or more sensors can automate monitoring plant productivity 303. For example, the one or more sensors can automatically measure plant productivity with metrics including, but not limited to, biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

[0116] In yet some further embodiments, the system can also include tracking plant productivity among inoculated plants relative to non-inoculated plants 304. For example, inoculated plants can be tracked for added growth or plant productivity relative to a control group of plants, the control group of plants including plants that have not been inoculated with the growth-promotion fungal consortium inoculum.

[0117] In yet some further embodiments, the system can be configured to operate in tandem with a method of generating biodiversity credits 305. For example, the increase in plant productivity generated by inoculating plants with the growth-promoting fungal consortium can generate revenue through sales of verified carbon credits, while also increasing revenue for land partners by increasing crop, biomass, and the like, yield. In some embodiments, accelerated plant growth, for example, tree growth in a forestry context, can be translated into carbon credits 306, which can be bought or sold. In some further embodiments, the system can increase plant productivity, which can correlate with increased biomass volume 307. For example, in a forestry context, the increase in tree growth can result in an increase the quantity of commercial product associated with tree biomass.

[0118] Fig. 4 illustrates a method of producing a fungal inoculum with a forest bioreactor 400. In some embodiments, the method of producing a fungal inoculum with a forest bioreactor 400 can include one or more inputs 401. In some embodiments, the method ofproducing a fungal inoculum with a forest bioreactor 400 can include providing a forest bioreactor 410. For example, the forest bioreactor can include feedstock and an optimal environment, wherein the feedstock and the optimal environment can be adapted to promote colonization of the feedstock by the growth-promoting fungal consortium such as to outcompete other organisms present in the soil sample. In some further embodiments, the method of producing a fungal inoculum with a forest bioreactor 400 can include isolating a growth-promoting fungal consortium 420. In yet some further embodiments, the method of producing a fungal inoculum with a forest bioreactor 400 can include providing the growth- promoting fungal consortium to the forest bioreactor 430. For example, the forest bioreactor can include the feedstock and the optimal environment that are preconfigured to cause the growth-promoting fungal consortium to grow and to reproduce. In some embodiments, the method of producing a fungal inoculum with a forest bioreactor 400 can include colonizing the feedstock with fungal species and / or strains comprising the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum 440. For example, growth-promoting fungal consortium inoculum can include the feedstock and the growth-promoting fungal consortium. In some embodiments, the feedstock can be entirely consumed by the growth-promoting fungal consortium, resulting in a growth- promoting fungal inoculum consisting of or consisting essentially of or comprising fungal biomass. In some embodiments, the method of producing a fungal inoculum with a forest bioreactor 400 can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry 450. In some embodiments, the method of producing a fungal inoculum with a forest bioreactor 400 can include harvesting the inoculum slurry 460.

[0119] Fig. 5 illustrates a method of increasing plant productivity with reduced plant fertilizer utilization 500. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include one or more inputs 501. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include isolating a growth-promoting fungal consortium 510. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment 520. For example, the feedstock and the optimal environment can be selected to cause the growth-promoting fungal consortiumto grow and to reproduce. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include colonizing the feedstock with fungal species and / or strains that can include the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum including the feedstock and the growth-promoting fungal consortium 530. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry 540. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include harvesting the inoculum slurry 550. In some embodiments, the method of increasing plant productivity with reduced fertilizer utilization 500 can include inoculating a plurality of plants with the inoculum slurry 560. For example, the fungal species and / or strains that can be included in the growth-promoting fungal consortium can enhance nutrient bioavailability without the need for chemical fertilizers. In some further embodiments, the growth-promoting fungal consortium can include a plurality of fungal species and / or strains native to a geographic location. For example, the geographic location can be a natural ecosystem. In some embodiments, plant productivity can be measured with metrics including, but not limited to, biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, photosynthesis rate, and other like metrics of plant productivity. In some further embodiments, method of increasing plant productivity with reduced fertilizer utilization 500 can include harvesting the growth-promoting fungal consortium from a high productivity ecosystem, the high productivity ecosystem including a plurality of photosynthesizing organisms with a high rate of atmospheric carbon sequestration and / or biomass production.

[0120] Fig. 6 illustrates a method of generating biodiversity credits 600. In some embodiments, the method of generating biodiversity credits 600 can include one or more inputs 610. In some embodiments, the method of generating biodiversity credits 600 can include isolating a growth-promoting fungal consortium 620. For example, the growth-promoting fungal consortium can include native fungal species and / or strains. In some embodiments, the method of generating biodiversity credits 600 can include providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment 630. For example, the feedstock and the optimal environment canbe selected to cause the growth-promoting fungal consortium to grow and to reproduce. In some embodiments, the method of generating biodiversity credits 600 can include colonizing the feedstock with the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum the feedstock and the growth- promoting fungal consortium 640. In some embodiments, the method of generating biodiversity credits 600 can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry 650. In some embodiments, the method of generating biodiversity credits 600 can include harvesting the inoculum slurry 660. In some embodiments, the method of generating biodiversity credits 600 can include inoculating a plurality of plants with the inoculum slurry 670. In some embodiments, the method of generating biodiversity credits 600 can include establishing a community of the native fungal species and / or strains including the growth-promoting fungal consortium in symbiosis with the plurality of plants. For example, the biodiversity credits can increase in positive correlation to a diversity of the community of the native fungal species and / or strains.

[0121] Fig. 7 illustrates a method of improving water quality 700. In some embodiments, the method of improving water quality 700 can include one or more inputs 710. In some embodiments, the method of improving water quality 700 can include inoculating a plurality of plants with an inoculum slurry 720. For example, the inoculum slurry can include a mixture of water and a growth-promoting fungal consortium inoculum a feedstock and a growth-promoting fungal consortium. In some embodiments, the method of improving water quality 700 can include establishing a community of the native fungi including the growth- promoting fungal consortium in symbiosis with the plurality of plants 740. For example, the growth-promoting fungal consortium inoculum can include a plurality of native fungal species and / or strains. By way of further example, each of the plurality of native fungal species and / or strains can be adapted to filter contaminants from a volume of water, thereby improving quality of the volume of water. In some embodiments, the method of improving water quality 700 can include the contaminants, which can include, but are not limited to, a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, and / or agricultural runoff. In some embodiments, the method of improving water quality 700 can include thevolume of water, the volume of water including, but not limited to, a naturally occurring volume of water or an artificially formed volume of water.

[0122] Fig. 8 illustrates a method of remediating soil 800. In some embodiments, the method of remediating soil 800 can include one or more inputs 810. In some embodiments, the method of remediating soil 800 can include isolating a growth-promoting fungal consortium 820. In some embodiments, the method of remediating soil 800 can include forming a growth-promoting fungal consortium inoculum a feedstock and the growth- promoting fungal consortium 830. In some embodiments, the method of remediating soil 800 can include mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry 840. In some embodiments, the method of remediating soil 800 can include harvesting the inoculum slurry 850. In some embodiments, the method of remediating soil 800 can include inoculating a volume of soil with the inoculum slurry 860. In some embodiments, the method of remediating soil 800 can include maturing the inoculum slurry within the volume of soil such as to substantially colonize the volume of soil with the growth-promoting fungal consortium 870. In some embodiments, the method of remediating soil 800 can include the volume of soil, the volume of soil can be in situ soil, ex situ soil, translocated soil, artificial soil and / or any like medium capable of remediation by a growth-promoting fungal consortium. In some further embodiments, the method of remediating soil 800 can include the volume of soil including nutritive materials, the nutritive material providing a nutritive substrate for the growth-promoting fungal consortium to grow and substantially colonize the volume of soil. In some embodiments, the method of remediating soil 800 can include the volume of soil including at least one contaminant. In some embodiments, the method of remediating soil 800 can include the at least one contaminant substantially removed from the volume of soil and absorbed by at least one fungus comprising the growth-promoting fungal consortium. In some embodiments, the method of remediating soil 800 can include the at least one contaminant, the at least one contaminant including, but not limited to, a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, agricultural runoff and / or any like contaminant.

[0123] Various modifications to the implementations described in this disclosure may be readily apparent to those skilled in the art, and the generic principles defined hereinmay be applied to other implementations without departing from the spirit or scope of this disclosure. Thus, the claims are not intended to be limited to the implementations shown herein, but are to be accorded the widest scope consistent with this disclosure, the principles and the novel features disclosed herein. Additionally, a person having ordinary skill in the art will readily appreciate, the terms “upper” and “lower” are sometimes used for ease of describing the figures, and indicate relative positions corresponding to the orientation of the figure on a properly oriented page, and may not reflect the proper orientation of a feature as implemented.

[0124] While certain embodiments have been described, these embodiments have been presented by way of example only and are not intended to limit the scope of the disclosure. Indeed, the novel methods and systems described herein may be embodied in a variety of other forms. Furthermore, various omissions, substitutions and changes in the systems and methods described herein may be made without departing from the spirit of the disclosure. The accompanying claims and their equivalents are intended to cover such forms or modifications as would fall within the scope and spirit of the disclosure.

[0125] Features, materials, characteristics, or groups described in conjunction with a particular aspect, embodiment, or example are to be understood to be applicable to any other aspect, embodiment or example described in this section or elsewhere in this specification unless incompatible therewith. All of the features disclosed in this specification (including any accompanying claims, abstract and drawings), and / or all of the steps of any method or process so disclosed, may be combined in any combination, except combinations where at least some of such features and / or steps are mutually exclusive. The protection is not restricted to the details of any foregoing embodiments. The protection extends to any novel one, or any novel combination, of the features disclosed in this specification (including any accompanying claims, abstract and drawings), or to any novel one, or any novel combination, of the steps of any method or process so disclosed.

[0126] The word “exemplary” is used herein to mean “serving as an example, instance, or illustration.” Any aspect or embodiment described herein as “exemplary” is not necessarily to be construed as preferred or advantageous over other aspects or embodiments. Various aspects of the novel systems and methods are described more fully hereinafter with reference to the accompanying drawings. This disclosure may, however, be embodied in manydifferent forms and should not be construed as limited to any specific structure or function presented throughout this disclosure. Rather, these aspects are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the disclosure to those skilled in the art. Based on the teachings herein one skilled in the art should appreciate that the scope of the disclosure is intended to cover any aspect of the novel systems and methods disclosed herein, whether implemented independently of, or combined with, any other aspect described. For example, a method may be practiced using any number of the aspects set forth herein. In addition, the scope of the disclosure is intended to cover such a method which is practiced using other structure, functionality, or structure and functionality in addition to or other than the various aspects of the disclosures set forth herein. It should be understood that any aspect disclosed herein may be embodied by one or more elements of a claim.

[0127] Furthermore, certain features that are described in this disclosure in the context of separate implementations can also be implemented in combination in a single implementation. Conversely, various features that are described in the context of a single implementation can also be implemented in multiple implementations separately or in any suitable subcombination. Although features may be described above as acting in certain combinations, one or more features from a claimed combination can, in some cases, be excised from the combination, and the combination may be claimed as a subcombination or variation of a subcombination.

[0128] The features and attributes of the specific embodiments disclosed above may be combined in different ways to form additional embodiments, all of which fall within the scope of the present disclosure. Also, the separation of various system components in the implementations described above should not be understood as requiring such separation in all implementations, and it should be understood that the described components and systems can generally be integrated together in a single product or packaged into multiple products.

[0129] Moreover, while operations may be depicted in the drawings or described in the specification in a particular order, such operations need not be performed in the particular order shown or in sequential order, or that all operations be performed, to achieve desirable results. Other operations that are not depicted or described can be incorporated in the example methods and processes. For example, one or more additional operations can be performed before, after, simultaneously, or between any of the described operations. Further, theoperations may be rearranged or reordered in other implementations. Those skilled in the art will appreciate that in some embodiments, the actual steps taken in the processes illustrated and / or disclosed may differ from those shown in the figures. Depending on the embodiment, certain of the steps described above may be removed, others may be added. Furthermore, the features and attributes of the specific embodiments disclosed above may be combined in different ways to form additional embodiments, all of which fall within the scope of the present disclosure.

[0130] For purposes of this disclosure, certain aspects, advantages, and novel features are described herein. Not necessarily all such advantages may be achieved in accordance with any particular embodiment. Thus, for example, those skilled in the art will recognize that the disclosure may be embodied or carried out in a manner that achieves one advantage or a group of advantages as taught herein without necessarily achieving other advantages as may be taught or suggested herein.

[0131] Conditional language, such as “can,” “could,” “might,” or “may,” unless specifically stated otherwise, or otherwise understood within the context as used, is generally intended to convey that certain embodiments include, while other embodiments do not include, certain features, elements, and / or steps. Thus, such conditional language is not generally intended to imply that features, elements, and / or steps are in any way required for one or more embodiments or that one or more embodiments necessarily include logic for deciding, with or without user input or prompting, whether these features, elements, and / or steps are included or are to be performed in any particular embodiment.

[0132] Conjunctive language such as the phrase “at least one of X, Y, and Z,” unless specifically stated otherwise, is otherwise understood with the context as used in general to convey that an item, term, etc. may be either X, Y, or Z. Thus, such conjunctive language is not generally intended to imply that certain embodiments require the presence of at least one of X, at least one of Y, and at least one of Z. Thus, as used herein, a phrase referring to “at least one of X, Y, and Z” is intended to cover: X, Y, Z, X and Y, X and Z, Y and Z, and X, Y and Z.

[0133] The headings provided herein, if any, are for convenience only and do not necessarily affect the scope or meaning of the devices and methods disclosed herein.

[0134] Language of degree used herein, such as the terms “approximately,” “about,” “generally,” and “substantially” as used herein represent a value, amount, or characteristic close to the stated value, amount, or characteristic that still performs a desired function or achieves a desired result. For example, the terms “approximately”, “about”, “generally,” and “substantially” may refer to an amount that is within less than 10% of, within less than 5% of, within less than 1% of, within less than 0.1% of, and within less than 0.01% of the stated amount.

[0135] The scope of the present disclosure is not intended to be limited by the specific disclosures of embodiments in this section or elsewhere in this specification and may be defined by claims as presented in this section or elsewhere in this specification or as presented in the future. The language of the claims is to be interpreted broadly based on the language employed in the claims and not limited to the examples described in the present specification or during the prosecution of the application, which examples are to be construed as non-exclusive.

[0136] Any and all cited references are incorporated by reference herein in their entirety.

Claims

WHAT IS CLAIMED IS:

1. A method of accelerating plant productivity and atmospheric carbon sequestration, comprising: identifying a growth-promoting fungal consortium from a natural fungal microbiome, comprising: providing at least one sampling kit to a subject at a geographic location, the at least one sampling kit comprising a sample container configured to receive a soil sample from the geographic location; receiving the at least one sampling kit, including the soil sample, from the geographic location; extracting nucleic acid material from a first portion of the soil sample; generating a fungal microbiome dataset based on sequencing the nucleic acid material present in the first portion of the soil sample, wherein sequencing further comprises a plurality of reagents that enrich for fungal-derived nucleic acids; providing a machine learning tool, wherein the machine learning tool comprises a training database, the training database comprising biotic and abiotic data associated with a plurality of high productivity ecosystems; and inputting the fungal microbiome dataset into machine learning tool, whereby the machine learning tool identifies the growth-promoting fungal consortium comprising a subset of fungal species present in the first portion of the soil sample and associated with the plurality of high productivity ecosystems; propagating the growth-promoting fungal consortium, comprising: providing a second portion of the soil sample to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth-promoting fungal consortium to reproduce and outcompete other organisms present in the second portion of the soil sample; colonizing the feedstock with fungal species or strains comprising the growth-promoting fungal consortium for a period of time sufficient to create agrowth-promoting fungal consortium inoculum comprising the feedstock and the growth-promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; and inoculating a plurality of plants present at the geographic location with the inoculum slurry; and monitoring productivity of each of the plurality of plants after each of the plurality of plants has been inoculated with the inoculum slurry, wherein monitoring comprises utilizing a plurality of sensors.

2. The method of Claim 1, wherein the growth-promoting fungal consortium comprises a plurality of fungal species or strains native to the geographic location; and wherein the geographic location is a natural ecosystem.

3. The method of Claims 1, wherein monitoring comprises observing.

4. The method of Claim 1, wherein plant productivity comprises metrics selected from the group consisting of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

5. The method of Claim 1, wherein the plurality of sensors comprises at least a plant growth rate sensor and a plant photosynthesis rate sensor.

6. The method of Claims 5, wherein a plant photosynthesis rate sensor comprises a tool for measuring a rate of atmospheric carbon sequestration.

7. The method of Claims 1-6, further comprising sequencing utilizing the plurality of reagents that enrich for fungal-derived nucleic acids, wherein the plurality of reagents comprises at least a plurality of primers targeting an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, aTranslation Elongation Factor 1-alpha (TEF1-alpha) genomic region, a Beta-Tubulin ( -tubulin) genomic region, an RNA Polymerase II (RPB1 or RPB2) genomic region, or a Calmodulin (CaM) genomic region.

8. The method of Claims 1-7, wherein each of the plurality of high productivity ecosystems comprises an ecosystem comprising photosynthesizing organisms with a high rate of atmospheric carbon sequestration or biomass production.

9. The method of Claims 1-8, wherein the forest bioreactor is a sealed environment or an unsealed environment, further comprising the optimal environment comprised of a temperature, an oxygen content, a salinity, or a pH.

10. The method of Claims 1-9, wherein propagating comprises sexual and asexual reproduction of each fungal species or strain comprising the growth-promoting fungal consortium.

11. The method of Claim 1, wherein each of the plurality of plants comprises a tree.

12. A system for accelerating plant productivity and atmospheric carbon sequestration, comprising: at least one sampling kit, wherein the at least one sampling kit is configured to be sent to and from a geographic location and comprises a sample container, the sample container configured to receive a soil sample; a soil sample processing system configured to extract nucleic acid material from a first portion of the soil sample; a nucleic acid sequencing platform configured to sequence the nucleic acid material present in the first portion of the soil sample and configured to generate a fungal microbiome dataset, wherein the nucleic acid sequencing platform further comprises a plurality of reagents adapted to enrich for fungal-derived nucleic acids; a machine learning tool, wherein the machine learning tool comprises a training database, the training database comprised of biotic and abiotic data associated with a plurality of high productivity ecosystems, and wherein the machine learning tool is configured to identify a growth-promoting fungal consortium comprising a subset of fungal species present in the first portion of the soil sample and associated with the plurality of high productivity ecosystems; a forest bioreactor configured to receive a second portion of the soil sample and to propagate the growth-promoting fungal consortium, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are adapted to promote colonization of the feedstock by thegrowth-promoting fungal consortium such as to outcompete other organisms present in the soil sample; an inoculum slurry comprising a mixture of water and a growth-promoting fungal consortium inoculum, wherein the growth-promoting fungal consortium inoculum comprises the feedstock substantially colonized by the growth-promoting fungal consortium; a plurality of plants, wherein each of the plurality of plants is inoculated with the inoculum slurry; and a plurality of sensors configured to monitor plant productivity of each of the plurality of plants inoculated with the inoculum slurry.

13. The system of Claim 12, wherein the growth-promoting fungal consortium comprises a plurality of fungal species or strains native to the geographic location.

14. The system of Claims 13, wherein the geographic location is a natural ecosystem.

15. The system of Claim 12, wherein the system is configured to maximize plant productivity utilizing metrics selected from the group consisting of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

16. The system of Claim 12, wherein the plurality of sensors comprises at least one of a plant growth rate sensor and a plant photosynthesis rate sensor.

17. The system of Claim 16, wherein a plant photosynthesis rate sensor comprises a tool for measuring a rate of atmospheric carbon sequestration.

18. The system of Claims 12-17, wherein the plurality of reagents adapted to enrich for fungal-derived nucleic acids comprises at least a plurality of primers configured to target an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha) genomicregion, a Beta-Tubulin ( -tubulin) genomic region, an RNA Polymerase II (RPB1 or RPB2)genomic region, or a Calmodulin (CaM) genomic region.

19. The system of Claims 12-18, wherein each of the plurality of high productivity ecosystems comprises an ecosystem comprising photosynthesizing organisms with a high rate of atmospheric carbon sequestration or biomass production.

20. The system of Claims 12-19, wherein the forest bioreactor is a sealed environment or an unsealed environment, further comprising the optimal environment comprised of a temperature, an oxygen content, a salinity, or a pH.

21. The system of Claims 12-20, wherein colonization of the feedstock comprises sexual reproduction and asexual reproduction of each fungal species or strain comprising the growth-promoting fungal consortium.

22. The system of Claim 12, wherein each of the plurality of plants comprises a tree.

23. A method of producing a fungal inoculum, comprising: providing a forest bioreactor; isolating a growth-promoting fungal consortium; providing the growth-promoting fungal consortium to the forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth- promoting fungal consortium to grow and to reproduce; colonizing the feedstock with fungal species or strains comprising the growth- promoting fungal consortium for a period of time sufficient to create a growth- promoting fungal consortium inoculum comprising the feedstock and the growth- promoting fungal consortium; mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; and harvesting the inoculum slurry.

24. The method of Claim 23, wherein the growth-promoting fungal consortium comprises a plurality of fungal species or fungal strains native to a geographic location.

25. The method of Claim 24, wherein the geographic location is a natural ecosystem.

26. The method of Claims 24-25, wherein the geographic location comprises a high productivity ecosystem, wherein the high productivity ecosystem comprises photosynthesizing organisms with a high rate of atmospheric carbon sequestration or biomass production.

27. The method of Claim 23, wherein the growth-promoting fungal consortium is adapted to maximize plant productivity utilizing metrics selected from the group consisting ofbiomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

28. The method of Claims 23-27, wherein the growth-promoting fungal consortium is identified using a plurality of reagents adapted to enrich for fungal-derived nucleic acids, the plurality of reagents comprising at least a plurality of primers configured to target an Internal Transcribed Spacer genomic region (ITS), an ITS1 genomic region, an ITS2 genomic region, a Large Subunit rRNA (LSU) genomic region, a small subunit rRNA (SSU) genomic region, an 18S genomic region, a Translation Elongation Factor 1-alpha (TEF1-alpha) genomic region,a Beta-Tubulin ( -tubulin) genomic region, an RNA Polymerase II (RPB1 or RPB2) genomicregion, or a Calmodulin (CaM) genomic region.

29. The method of Claims 23-28, wherein the forest bioreactor is a sealed environment or an unsealed environment, further comprising the optimal environment comprising a temperature, an oxygen content, a salinity, or a pH.

30. The method of Claims 23-29, wherein colonizing the feedstock comprises sexual reproduction and asexual reproduction of each fungal species or strain comprising the growth- promoting fungal consortium.

31. The method of Claim 23, wherein the growth-promoting fungal consortium inoculum is applied to at least one plant.

32. The method of Claim 31, wherein the at least one plant is a tree.

33. A method of increasing plant productivity with reduced plant fertilizer utilization, comprising: isolating a growth-promoting fungal consortium; providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth- promoting fungal consortium to grow and to reproduce; colonizing the feedstock with fungal species or strains comprising the growth- promoting fungal consortium for a period of time sufficient to create a growth- promoting fungal consortium inoculum comprising the feedstock and the growth- promoting fungal consortium;mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; and inoculating a plurality of plants with the inoculum slurry, wherein the fungal species or strains comprising the growth-promoting fungal consortium enhances nutrient bioavailability without need for chemical fertilizers.

34. The method of Claim 33, wherein the growth-promoting fungal consortium comprises a plurality of fungal species or strains native to a geographic location.

35. The method of Claims 33-34, wherein the geographic location is a natural ecosystem.

36. The method of Claim 33, wherein plant productivity comprises metrics selected from the group consisting of biomass accumulation, leaf area index (LEA), growth rate, plant height, yield, net assimilation rate, water use efficiency, nutrient use efficiency, and photosynthesis rate.

37. The method of Claims 33-36, further comprising harvesting the growth-promoting fungal consortium from a high productivity ecosystem, the high productivity ecosystem comprising a plurality of photosynthesizing organisms with a high rate of atmospheric carbon sequestration or biomass production.

38. The method of Claim 33, wherein each of the plurality of plants comprises a tree.

39. A method of generating biodiversity credits, comprising: isolating a growth-promoting fungal consortium, wherein the growth-promoting fungal consortium comprises native fungal species or strains; providing the growth-promoting fungal consortium to a forest bioreactor, the forest bioreactor configured to provide a feedstock and an optimal environment, wherein the feedstock and the optimal environment are selected to cause the growth- promoting fungal consortium to grow and to reproduce; colonizing the feedstock with the growth-promoting fungal consortium for a period of time sufficient to create a growth-promoting fungal consortium inoculum comprising the feedstock and the growth-promoting fungal consortium;mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; inoculating a plurality of plants with the inoculum slurry; and establishing a community of the native fungal species or strains comprising the growth-promoting fungal consortium, in symbiosis with the plurality of plants, wherein the biodiversity credits increase in positive correlation to a diversity of the community of the native fungal species or strains.

40. A method of improving water quality, comprising: inoculating a plurality of plants with an inoculum slurry, wherein the inoculum slurry comprises a mixture of water and a growth- promoting fungal consortium inoculum comprising a feedstock and a growth- promoting fungal consortium; and establishing a community of native fungal species or strains , the native fungal species or strains being in symbiosis with the plurality of plants, wherein the growth-promoting fungal consortium inoculum comprises the native fungal species or strains, and wherein the native fungal species or strains are adapted to filter contaminants from a volume of water, thereby improving quality of the volume of water.

41. The method of Claim 40, wherein the contaminants comprise at least a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, or agricultural runoff.

42. The method of Claims 40-41, wherein the volume of water is a naturally occurring volume of water or an artificially formed volume of water.

43. A method of remediating soil, comprising: isolating a growth-promoting fungal consortium; forming a growth-promoting fungal consortium inoculum comprising a feedstock and the growth-promoting fungal consortium;mixing the growth-promoting fungal consortium inoculum with water to form an inoculum slurry; harvesting the inoculum slurry; inoculating a volume of soil with the inoculum slurry; and maturing the inoculum slurry within the volume of soil such as to substantially colonize the volume of soil with the growth-promoting fungal consortium.

44. The method of Claims 43, wherein the volume of soil is selected from the group consisting of in situ soil, ex situ soil, translocated soil, and artificial soil.

45. The method of Claims 43-44, wherein the volume of soil comprises nutritive materials, the nutritive materials providing a nutritive substrate for the growth-promoting fungal consortium to grow and substantially colonize the volume of soil.

46. The method of Claim 43, wherein the volume of soil contains at least one contaminant.

47. The method of Claim 46, wherein the at least one contaminant is substantially removed from the volume of soil and absorbed by at least one fungus comprising the growth- promoting fungal consortium.

48. The method of Claims 46-47, wherein the at least one contaminant comprises a heavy metal, an organic molecule, an inorganic molecule, a pharmaceutical, a nutrient, a plastic, a sediment, a radioactive molecule, a pesticide, an herbicide, a detergent, industrial waste, or agricultural runoff.

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