WO2025136827A1 - Compositions and methods for biological production and harvest of copper, nickel, cobalt, and mixtures thereof - Google Patents

Abstract

An isolated bacillus cuprevida strain deposited at the Agricultural Research Service Culture Collection under the Accession number NRRL No. B-68290 according to the Budapest Treaty. Compositions comprising an isolated modified bacterial strain bacillus cuprevida according to the Budapest Treaty. The bacterial strain bacillus cobalos, which has been designated Accession number NRRL No. B-68291, and compositions comprising an isolated modified bacterial strain bacillus cobalos. The bacterial strain bacillus niccolum, which has been designated Accession number NRRL No. B-68292, and compositions comprising an isolated modified bacterial strain bacillus niccolum. The disclosed newly discovered bacterial strains are useful in copper, cobalt, and nickel metal extraction, production, and amplification. In particular, the present disclosure is directed to novel microorganisms useful to extract, produce and/or amplify these metals from substrates that they are cultured in.

Description

PATENT-PCT Atty. Docket No.3414.3100WO COMPOSITIONS AND METHODS FOR BIOLOGICAL PRODUCTION AND HARVEST OF COPPER, NICKEL, COBALT, AND MIXTURES THEREOF Cross Reference to Related Applications This application is entitled to and claims the benefit, under 35 U.S.C. §119(e) of earlier filed U.S. Provisional Application number 63611836, filed December 19, 2023, which earlier filed provisional application is incorporated by reference herein in its entirety. [0001] BACKGROUND INFORMATION [0002] Technical Field [0003] The present disclosure is directed to the field of copper, nickel, cobalt, and mixtures thereof extraction, production, and amplification. In particular, the present disclosure encompasses an isolated microorganism modified relative to wild-type and useful to extract, produce and/or amplify copper, nickel, and/or cobalt and/or mixtures thereof from a substrate such as an environmental substrate. [0004] Background Art [0005] Demand for battery metals and copper is being driven today by the switch to “green energy” and electric vehicles (“EVs”), and demand should increase over the coming decades. One projection for annual demand for cobalt predicts demand growing to more than 200 kilotons per year as soon as 2025 as the portable electronics and electric vehicle markets expand rapidly. (Mining.com) Cobalt is known to have high energy density, which promotes longer range of EVs, however, cobalt is sourced from countries or regions that are not palatable from various points of view and is expensive. Cobalt is increasingly being replaced in part by nickel. The move to nickel rich chemistries for EV batteries and a robust stainless steel industry – nickel’s number one source of demand – gives the metal a similar demand curve to cobalt. Cobalt is typically a byproduct of copper and nickel production. PATENT-PCT Atty. Docket No.3414.3100WO [0006] Copper-sulfide and nickel-sulfide mining is currently used as a primary source of copper and nickel today, and use of microbes is not unknown in the industry. For example, United States Patent App. No.20070042482 A1 discloses a sulfur-oxidizing bacterium and the use thereof in a bioleaching method at ambient temperatures for sulfured minerals. The bacterium (mesophilic sulfur-oxidizing bacteria) is used in acidic solution to deter the passivation phenomenon that acts as leaching inhibitor. [0007] The increase of demand for clean energy sources and growing popularity of electric vehicles and energy storage systems in the world may lead to an increased shortage of metals in the global market followed by a sharp increase in prices in years to come. According to recent estimates of the International Energy Agency (IEA), the demand for lithium will grow more than 40 times by 2040, while for cobalt and nickel by 20 times within the next two decades. A similar situation is expected to be observed in the case of copper. [0008] Therefore, a need in the art exists for compositions and improved methods to extract, produce and/or amplify copper and/or nickel and/or cobalt. [0009] SUMMARY [0010] One aspect of the present disclosure are compositions comprising an isolated modified bacterial strain bacillus cuprevida. In certain embodiments, the bacterial strain is ECO003, which has been designated Accession number NRRL No. B-68290. [0011] Another aspect of the present disclosure are compositions comprising an isolated modified bacterial strain bacillus cobalos. In certain embodiments, the bacterial strain is ECO004, which has been designated Accession number NRRL No. B-68291. [0012] Another aspect of the present disclosure are compositions comprising an isolated modified bacterial strain bacillus niccolum. In certain embodiments, the bacterial strain is ECO005, which has been designated Accession number NRRL No. B-68292. PATENT-PCT Atty. Docket No.3414.3100WO [0013] All of the above-mentioned bacilli have been deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023. [0014] In another aspect, the disclosure provides a method of extracting copper metal and/or nickel metal and/or cobalt metal comprising contacting a solid substrate with a composition comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these. In some embodiments, the method comprises extracting copper metal and the bacterial strain bacillus cuprevida is ECO003. In some embodiments, the method comprises extracting cobalt metal and the bacterial strain bacillus cobalos is ECO004. In some embodiments, the method comprises extracting nickel metal and the bacterial strain bacillus niccolum is ECO005. In some embodiments, the composition includes one or more microbes used in industrial mining and as described herein. [0015] In another aspect, the disclosure provides a method of amplifying copper metal and/or nickel and/or cobalt metal comprising contacting a solid substrate with a composition comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these. In some embodiments, the method comprises amplifying copper metal and the bacterial strain bacillus cuprevida is ECO003. In some embodiments, the method comprises amplifying cobalt metal and the bacterial strain bacillus cobalos is ECO004. In some embodiments, the method comprises amplifying nickel metal and the bacterial strain bacillus niccolum is ECO005. In some embodiments, the composition includes one or more microbes used in industrial mining and as described herein. [0016] In one aspect, the disclosure provides a method of recovering copper metal and/or nickel metal and/or cobalt metal contacting a solid substrate with a composition comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these. In some embodiments, the method comprises recovering PATENT-PCT Atty. Docket No.3414.3100WO copper metal and the bacterial strain bacillus cuprevida is ECO003. In some embodiments, the method comprises recovering cobalt metal and the bacterial strain bacillus cobalos is ECO004. In some embodiments, the method comprises recovering nickel metal and the bacterial strain bacillus niccolum is ECO005. In some embodiments, the composition includes one or more microbes used in industrial mining and as described herein. [0017] In each of the preceding embodiments, the solid substrate may be a geological substrate, such as one or more of sandstone, limestone, shale, coal, chalk deposit formations, refractory rock ore or a solid substrate obtained from one or more of a terrestrial, aquatic or marine source. In each of the preceding embodiments, the solid substrate may be one or more of soil, biofilm, sediment, native metal rock and sludge residue. [0018] In still another aspect, the disclosure provides a method of extracting copper metal and/or nickel metal and/or cobalt metal from a liquid substrate comprising contacting the liquid substrate with a composition comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these. In some embodiments, the method comprises extracting copper metal and the bacterial strain bacillus cuprevida is ECO003. In some embodiments, the method comprises extracting cobalt metal and the bacterial strain bacillus cobalos is ECO004. In some embodiments, the method comprises extracting nickel metal and the bacterial strain bacillus niccolum is ECO005. In some embodiments, the composition includes one or more microbes used in industrial mining and as described herein. [0019] In another aspect, the disclosure provides a method of amplifying copper metal and//or nickel metal and/or cobalt metal from a liquid substrate comprising contacting the liquid substrate with a composition comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these. In some embodiments, the method comprises amplifying copper metal and the bacterial strain bacillus cuprevida is ECO003. In some embodiments, the method comprises amplifying cobalt metal and the bacterial strain bacillus cobalos is ECO004. In some embodiments, the method comprises PATENT-PCT Atty. Docket No.3414.3100WO amplifying nickel metal and the bacterial strain bacillus niccolum is ECO005. In some embodiments, the composition includes one or more microbes used in industrial mining and as described herein. [0020] In another aspect, the disclosure provides a method of condensing copper metal and/or nickel metal and/or cobalt metal from a liquid substrate comprising contacting the liquid substrate with a composition comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these. In some embodiments, the method comprises condensing copper metal and the bacterial strain bacillus cuprevida is ECO003. In some embodiments, the method comprises condensing cobalt metal and the bacterial strain bacillus cobalos is ECO004. In some embodiments, the method comprises condensing nickel metal and the bacterial strain bacillus niccolum is ECO005. In some embodiments, the composition includes one or more microbes used in industrial mining and as described herein. [0021] In some embodiments, the bacterial strain may be inoculated at a concentration of about 1.0 x 10³ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁶ CFU/gm, about 1.0 x 10⁷ CFU/gm, about 1.0 x 10⁸ CFU/gm, about 1.0 x 10⁹ CFU/gm, about 1.0 x 10¹⁰ CFU/gm, about 1.0 x 10¹¹ CFU/gm, about 1.0 x 10¹² CFU/gm, about 1.0 x 10¹³ CFU/gm, about 1.0 x 10¹⁴ CFU/gm, about 1.0 x 10¹⁵ CFU/gm, about 1.0 x 10¹⁶ CFU/gm, or about 1.0 x 10¹⁷ CFU/gm (where “CFU” means colony forming units). [0022] In some embodiments, the liquid substrate may be obtained from one or more of a wastewater, sludge water, saltwater, freshwater, irrigation system, pond, lake, river, and estuary source. In each of the preceding embodiments, the substrate may be disinfected and/or sterilized prior to inoculation with the bacterial strain. [0023] In some embodiments, the methods of the present disclosure may further comprise adding a fertilizer, nutrient and/or by product composition one or more times to the substrate after inoculation with the bacterial strain. PATENT-PCT Atty. Docket No.3414.3100WO [0024] In some embodiments, the methods of the present disclosure may include allowing sufficient time for the bacterial strain to colonize and exponentially grow on or in the substrate. In some embodiments, the methods of the present disclosure may comprise using an anodic and cathodic LED having a wavelength generator set at a wavelength range of 2.0 – 22.0 KHz in the liquid substrate. [0025] In some embodiments, the methods of the present disclosure may comprise harvesting the copper metal and/or nickel metal and/or cobalt metal by separating the copper metal and/or nickel metal and/or cobalt metal from the substrate. [0026] In another aspect, the disclosure provides compositions comprising an isolated modified bacterial strain selected from bacillus cuprevida, bacillus cobalos, bacillus niccolum, and mixtures of two or more of these, about 0.01%/Wt. copper emulsion, about 0.01%/Wt. copper nanoparticles, about 0.01%/Wt. adenosine triphosphate, about 1%/Wt. seaweed extract, about 0.5%/Wt. humic acid, about 0.5%/Wt. mixture of nitrogen, phosphate, potassium and micronutrient mixture, about 0.1% light and mid chain hydrocarbon mixture, about 0.25%/Wt. green solvent, about 0.75%/Wt. sugar, about 1.0%/Wt. substrate selected from copper, nickel, and cobalt, and combinations thereof, and a carrier selected from water, agarose, or mixtures thereof. [0027] In some embodiments, the water carrier may be selected from deionized water, distilled water, filtered water, well water, tap water, fresh water, sea water, brackish water, mineralized water, carbonated water, saline water, ionically charged water, ionized water, hydrogen water and combinations thereof. [0028] In some embodiments, compositions may further comprise one or more components selected from biosolvents ethyl lactate, ATP, ADP, pyrophosphate, soy based solvents, chemical solvents, green solvents, range of organic acids, lactic acid, malic acid, ascorbic acid, alkanes, alkenes, alkynes, saturates, aromatics, resinoids, asphaltenes, light, mid chain and heavy chain hydrocarbons, sodium nitrate, sodium nitrite, ethanol, sulfur, sulfate, sulfite, nitrogen, chemical PATENT-PCT Atty. Docket No.3414.3100WO surfactants (ionic, anionic, cationic, zwitterionic surfactants), and combinations and mixtures thereof, polymers (low, mid, heavy chains), biosurfactants, glycolipids, rhamnolipids (J1 and J2), glycerin, propylene glycol, carbon sugars, dextrose, galactose, sucrose, fructose, complex carbohydrates, starch, cellulose, lignin, keratin, proteins and amino acids, manures, composts, green waste, sludge material, humic and fulvic acids, coal ash and coal derived waste, alumina cytokinins and seaweed extracts. [0029] These and other features of the compositions and methods of the present disclosure are set forth in the description below. Other features or advantages of the present invention will be apparent from the following drawings and detailed description, several examples, and from the appended claims. It should be understood that wherever the term “comprising” is used herein, other embodiments where the term “comprising” is substituted with “consisting essentially of” are explicitly disclosed herein, and vice versa. It should be further understood that wherever the term “comprising” is used herein, other embodiments where the term “comprising” is substituted with “consisting of” are explicitly disclosed herein, and vice versa. Moreover, the use of negative limitations is specifically contemplated; for example, certain compositions may include a surfactant or a certain microbe, while other compositions may be devoid of surfactant or that specific microbe. As another example, certain methods of the present disclosure may comprise a step of adding a fertilizer, nutrient and/or by product composition one or more times to the substrate after inoculation with the bacterial strain; however, certain other method embodiments may be devoid of a step of adding a fertilizer, nutrient and/or by product composition one or more times to the substrate after inoculation with the bacterial strain.    [0030] BRIEF DESCRIPTION OF THE DRAWINGS [0031] The manner in which the objectives of this disclosure and other desirable characteristics can be obtained is explained in the following description and attached drawings in which: [0032] FIGS.1 and 2 are schematic illustrations of an apparatus useful in discovering and isolating the microorganisms useful in the presently disclosed methods. PATENT-PCT Atty. Docket No.3414.3100WO [0033] DETAILED DESCRIPTION [0034] The present disclosure is based, at least in part, on the discovery of three bacterium isolated from the EcoBiome Innovation and Discovery apparatus, as illustrated schematically in FIGS.1 and 2. The Ecobiome apparatus and methods of use thereof are described in U.S. Patent Application number 16/258,112 (published U.S. Patent App. No.20220401947 A1), filed August 25, 2022, published December 22, 2022) and is herein incorporated by reference in its entirety. [0035] As illustrated schematically in FIG.1, the apparatus 1 generally comprises a body 2 (e.g., an elongated cylinder) having an interior cavity 3, an exterior 4, an upper end 5, an opening in the upper end configured to receive a sample 6, a closed lower end opposite of the upper end 7, a base attached to the lower end 8, at least one sidewall between the upper end and lower end 9, wherein the at least one sidewall forms the interior cavity configured to retain the sample 3; and at least one lateral port opening attached to the at least one sidewall of the cylinder between the upper end and lower end 10, allowing access into the interior cavity 3 through the internal aperture 13 of the lateral port opening. In preferred embodiments, a plurality of lateral port openings are attached to the at least one sidewall between the upper end and lower end, allowing access to the interior cavity of the apparatus in a variety of positions between the upper and lower ends. The lateral port openings are adapted to allow access to the interior of the cylinder and can be opened and closed, in non-limiting examples by placing a cap, plug, gasket, septum and the like, on the distal end of the lateral port opening. FIG. 2 shows in some embodiments, the distal end of the lateral port opening are threaded 11 as a means to close the distal end with a cap 12. The lateral port opening(s) comprise and internal aperture 13 which is continuous with hole in sidewall 15 at the point of connection with the lateral port, so as to allow access to the interior cavity of the body. FIG.2 also illustrates exemplary tablets 14 which comprise microorganisms isolated from the apparatus. [0036] In brief, copper oxide ore, copper sulfide ore, cobalt ore, and nickel ore mining samples were obtained and prepared for culturing in the Ecobiome apparatus. The copper oxide and the copper sulfide ores were obtained from pastureland in Texas; the cobalt ore was obtained from an agricultural field in Minnesota; and the nickel ore was obtained from a farm field in North Carolina. PATENT-PCT Atty. Docket No.3414.3100WO The mining samples were crushed and loaded into the Ecobiome apparatus for microbial gradation and speciation. The prepped mining sample was allowed to equilibrate, and microbial growth promoted. After some time, a population of microorganisms were isolated, including a newly discovered wild-type bacteria. After isolation, the wild-type bacteria were subjected to a number of extreme culture conditions, such as high and low pH, high and low temperature, and high and low salinity conditions which minimally forced enzymatic change (e.g., nitrate reductase, ligninase, cellulase, chitinase, and/or urease) thereby producing a modified bacterial strain relative to wild- type. Thus, as used herein, the term “modified” refers to a bacterial strain that has been forced to change, minimally, with respect to enzymatic gain of function. See, for example, the examples herein. [0037] Modification of the originally isolated wild-type bacteria resulted in the isolation and characterization of ECO003 (bacillus cuprevida), ECO004 (bacillus cobalos), and ECO005 (bacillus niccolum). Through various characterization methods it was found that ECO003 facilitated copper metal production, ECO004 facilitated cobalt metal production, and ECO005 facilitated nickel metal production from a variety of environmental solid and liquid substrata. The isolated ECO003, ECO004, and ECO005 demonstrated copper, nickel, and cobalt production, respectively, de novo, using eco-friendly and sustainable biochemical processes and methods. [0038] Altogether, the present disclosure provides multiple lines of evidence showing the presently disclosed bacterium and methods of using the same to extract, produce and/or amplify copper metal, cobalt metal, and nickel metal from a variety of environmental substrates. Other aspects and iterations of the invention are described more thoroughly below. [0039] The bacterial strains disclosed in this description have been deposited under conditions that assure that access to the cultures will be available during the pendency of this application. The bacterial strains disclosed in this description have been deposited in the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, Ill., 61064). The bacterial strains deposited were designated as bacillus cuprevida, bacillus cobalos, and bacillus niccolum. The deposits were received by the NRRL on July 13, 2023, and were given accession PATENT-PCT Atty. Docket No.3414.3100WO numbers by the International Depository Authority of B-68290, B-68291, and B-68292, respectively. The deposits have been made to and received by the International Depository Authority under the provisions of the Budapest Treaty, and all restrictions upon public access to the deposits will be irrevocably removed upon the grant of a patent on this application. The deposits will be available as required by foreign patent laws in countries wherein counterparts of the subject application, or its progeny, are filed. However, it should be understood that the availability of the deposits does not constitute a license to practice the subject invention. [0040] Further, the subject culture deposits will be stored and made available to the public in accord with the provisions of the Budapest Treaty for the Deposit of Microorganisms, i.e., they will be stored with all the care necessary to keep them viable and uncontaminated for a period of at least five years after the most recent request for the furnishing of a sample of a deposit, and in any case, for a period of at least thirty (30) years after the date of deposit or for the enforceable life of any patent which may issue disclosing the cultures. The depositor acknowledges the duty to replace the deposit(s) should the depository be unable to furnish a sample when requested due to the condition of the deposits. [0041] Accordingly, one aspect of the present disclosure encompasses an isolated bacteria strain bacillus cuprevida (ECO003), or bacillus cobalos (ECO004), or bacillus niccolum (ECO005), each of which are modified relative to wild-type. Another aspect of the disclosure provides a mutant or derivative of ECO003, ECO004, or ECO005 having the ability to extract, produce and/or amplify copper metal, cobalt metal, or nickel metal as described herein. The term “mutant or derivative” thereof includes naturally occurring and artificially induced mutants which retain their ability to extract, produce and/or amplify copper metal, cobalt metal, or nickel metal. Production of such mutants or derivatives will be well known by those skilled in the art including transgenic expression of heterologous nucleic acid sequences and/or genomic modifications. [0042] In another aspect, the present disclosure provides compositions comprising one or more of ECO003, ECO004, and/or ECO005. The concentration(s) of ECO003, ECO004, and/or ECO005 will vary depending on the type of composition. For example, but not being limited thereto, PATENT-PCT Atty. Docket No.3414.3100WO suitable ECO003 concentrations include but are not limited to at least about 0.5 x 10¹⁰ CFU/Gm, least about 1.0 x 10¹⁰ CFU/Gm, least about 1.5 x 10¹⁰ CFU/Gm, least about 2.0 x 10¹⁰ CFU/Gm, least about 2.5 x 10¹⁰ CFU/Gm, least about 3.0 x 10¹⁰ CFU/Gm, least about 3.5 x 10¹⁰ CFU/Gm, least about 4.0 x 10¹⁰ CFU/Gm, least about 4.5 x 10¹⁰ CFU/Gm, least about 5.0 x 10¹⁰ CFU/Gm or greater. Compositions where ECO004 or ECO005 is substituted for ECO003 at these aforementioned concentrations are also contemplated. [0043] A composition comprising ECO003, or ECO004, and/or ECO005 according to the present disclosure may comprise one or more additional components, including but not limited to, biosolvents ethyl lactate, ATP, ADP, pyrophosphate, soy based solvents, chemical solvents, green solvents, range of organic acids, lactic acid, malic acid, ascorbic acid, alkanes, alkenes, alkynes, saturates, aromatics, resinoids, asphaltenes, light, mid chain and heavy chain hydrocarbons, sodium nitrate, sodium nitrite, ethanol, sulfur, sulfate, sulfite, nitrogen, chemical surfactants (ionic, anionic, cationic, zwitterionic surfactants), polymers (low, mid, heavy chains), biosurfactants, glycolipids, rhamnolipids (J1 and J2), glycerin, propylene glycol, carbon sugars, dextrose, galactose, sucrose, fructose, complex carbohydrates, starch, cellulose, lignin, keratin, proteins and amino acids, fertilizer NPK (e.g., organic and inorganic fertilizers), manures, composts, green waste, sludge material, humic and fulvic acids, coal ash and coal derived waste, alumina cytokinins and seaweed extracts. [0044] A composition comprising ECO003, or ECO004, or ECO005 according to the present disclosure may comprise a water source for microbial culturing or final product carrier. Non- limiting examples include deionized water, distilled water, filtered water, well water, tap water, fresh water, sea water, brackish water, mineralized water, carbonated water, saline water, ionically charged water, ionized water, and hydrogen water. Thus, according to the present disclosure compositions comprising microorganisms of the disclosure for use within the methods of the disclosure may comprise a water source for microbial culturing or final product carrier. Non- limiting examples include deionized water, distilled water, filtered water, well water, tap water, fresh water, sea water, brackish water, mineralized water, carbonated water, saline water, ionically charged water, ionized water, and hydrogen water. The aqueous solution may contain sufficient PATENT-PCT Atty. Docket No.3414.3100WO nutrients to support microbial growth. The useful nutrients are both inorganic and organic compounds commonly used to grow and nourish microbes. Inorganic nutrients include nitric acid, ammonium nitrate, ammonium chloride, ammonium sulfate, sodium nitrate, sulfur, sodium sulfide, sodium chloride, sodium bicarbonate, sodium phosphate, potassium phosphate, sulfuric acid, nitric acid, cyanide, uranium, mercury, lead, lithium, sodium metabisulfite, ammonium nitrate, fertilizers, gluconic acid, phosphogypsum, ferric chloride, calcium chloride, and ammonium phosphate. Organic nutrients include microbial biomass, glucose, dextrose, sodium acetate, amino acids, and purines. Vitamins that can be included in the nutrient solution include pyridoxine, pyridoxamine- HCl, riboflavin, thiamine, niacin, pantothenic acid, p-aminobenzoic acid, folic acid, and biotin. Small amounts of trace elements such as iron, copper, molybdenum and zinc can also be provided in the nutrient solution. Useful nutrients can also be mineral ores used for recovery of metals. [0045] A composition comprising ECO003, or ECO004, or ECO005 according to the present disclosure may be formulated as a soil mixture, liquid, sludge or slurry substrate. [0046] In some embodiments, a composition comprising ECO003, or ECO004, or ECO005 according to the present disclosure may comprise sulfuric acid, nitric acid, cyanide, uranium, mercury, lead, lithium, sodium metabisulfite, ammonium nitrate, fertilizers, gluconic acid, or phosphogypsum. [0047] In one aspect, an ECO003 composition of the present disclosure may comprise bacillus cuprevida at a concentration of about 2.5 x 10¹⁰ CFU/Gm (5.0%/Wt.), copper emulsions at a concentration of about 0.01%/Wt., copper nanoparticles at a concentration of about 0.01%/Wt., adenosine Triphosphate (ATP) at a concentration of about 0.01%/Wt., seaweed at a concentration of about 1%/Wt., humic acid at a concentration of about 0.5%/Wt., NPK and micronutrients at a concentration of about 0.5%/Wt., a mixture of light and mid chain hydrocarbons at a concentration of about 0.1%/Wt., green solvents at a concentration of about 0.25%/Wt., a carbon sugar source at a concentration of about 0.75%/Wt., a representative substrate at a concentration of about 1.0%/Wt.; and an inert carrier, for example, a liquid or agarose which makes up the remainder of PATENT-PCT Atty. Docket No.3414.3100WO the mass to 100% final Weight (%/Wt.). Compositions where ECO004 or ECO005 is substituted for ECO003 at these aforementioned concentrations are also contemplated. [0048] Another aspect of the present disclosure is a method to extract, produce and/or amplify copper metal, cobalt metal, and/or nickel metal comprising culturing suitable microbe or plurality of suitable microbes. Non-limiting examples of suitable microbes include acidophilic archaea such as Sulfolobus metallicus and Metallosphaera sedula; mesophilic bacteria of the genera Acidithiobacillus or Leptospirillum ferrooxidans; Pyrococcus furiosus; thermoacidophilic archaeon Sulfolobus (Metallosphaera sedula); and Pyrobaculum islandicum. These microorganisms are basically 10, belonging to Bacteria: Acidiphilium sp., Leptospirillum sp., Sulfobacillus sp., Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans; and Archaea: Acidianus sp., Ferroplasma sp., Metallosphaera sp., Sulfolobus sp. and Thermoplasma sp. [0049] In a preferred embodiment, the methods include the bacterium strain ECO003 or a mutant or derivative thereof; the bacterium strain ECO004 or a mutant or derivative thereof; or the bacterium strain ECO005 or a mutant or derivative thereof. Without wishing to be bound by theory, the mode of action of producing copper, cobalt, and nickel metal is due to ECO003, ECO004, and ECO005’s innate ability to extract, produce and/or amplify copper metal, cobalt metal, and nickel metal, respectively from the environmental substrate that it is cultured in. Isolated ECO003, ECO004, and ECO005 are found to express various proteins and biochemicals which are modulated by the base concentrations of copper, cobalt, and nickel metals in their surrounding environments. Additionally, ECO003, ECO004, and ECO005 each generate a high concentration of biomass, or microbial colonies throughout the culturing process, that enable them to hold high rates of copper, cobalt, and nickel metals within their respective intracellular matrix. [0050] For purposes of this disclosure, the term “mineral” or “mineral ore” means a composition that comprises copper, cobalt, and/or nickel metal values. Thus, a mineral may be a mined mineral, ancient seabed deposit, ancient lakebed deposit, black sands, an ore concentrate, metal bearing sea water, and waste products, such as mining tails, industrial waste water, oil well brine, coal tars, oil shales, tar sands, and oil sands. Useful minerals contain trace amounts of copper, cobalt, and/or PATENT-PCT Atty. Docket No.3414.3100WO nickel metals. Trace amount means the detection limit or below detection limits of conventional assay procedures such as fire assay, AAS (atomic adsorption spectroscopy), ICP-MS (inductive coupled plasma-mass spectrometer), ICP-AES (atomic emission spectroscopy) and other spectroscopic instrumentation commonly used in analytical laboratories. Some spectroscopic methods can detect as little as 1 ppt (part per trillion) to 0.1 ppb (part per billion). As used herein “AOAC” refers to AOAC International, an international organization dedicated to standardizing analytical testing, formerly known as the Association of Official Analytical Chemists. [0051] In some embodiments, the methods of extracting, producing and/or amplifying copper, cobalt, and/or nickel metals generally comprise farming the copper, cobalt and/or nickel metals including the steps of inoculating the bacterial strains disclosed herein on solid substrates or geological substrates. A geologic substrate is a surface (or volume) of sediment or rock where physical, chemical, and biological processes occur, such as the movement and deposition of sediment, the formation of bedforms, and the attachment, burrowing, feeding, reproduction, and sheltering of organisms. Non limiting examples of a geological substrate useful for the present disclosure include sandstone, limestone, shale, coal, chalk deposit formations, refractory rock ore (e.g., single, double and triple refractory rock ore). Additional solid substrates include, but are not limited to an environmental sample collected from any terrestrial, aquatic or marine source such as soil, biofilms, sediments (e.g. coral or other marine sediments, aquifer sediments and the like), native metal rocks and sludge residue. In some embodiments, the solid substrate is disinfected prior to inoculation of the bacterial strains disclosed herein. Disinfection techniques include but are not limited to steam, autoclave, oven, microwave, biocide and fungicide solutions. Additional substrates include but are not limited to animal manures, bauxite, base metals, calcium phosphate, calcium silicate, clays and silicates, aluminum oxide, diatomaceous earth, diammonium phosphate, erionite and zeolites, feldspar, flint, food wastes, granite, graphite, gypsum, humic and fulvic acids, marble, mica, molten rock and lava, monoammonium phosphate, potash, pumice, silica, slate, seaweed, talc and recycled electronics and commercial devices. [0052] In some embodiments, one or more of ECO003, ECO004, and/or ECO005 may be applied to any solid substrate in a rock, powder, granulated or broken form for improved copper metal, PATENT-PCT Atty. Docket No.3414.3100WO cobalt metal and nickel metal leaching and extraction. In some embodiments, solid substrates are used in traditional farming, specialty farming, potted and greenhouse farming, hydroponics and aeroponics techniques. In some embodiments, the solid substrate includes old or recycled electronic components or batteries. [0053] In one embodiment, the biological process using microbes according to the disclosure is conducted in commercially available bioreactor consisting of a reactor having an agitation means. The agitation means can be mechanical stirring with a flat bladed impeller, percolation column, or air agitated pachuca reactor. The bioreactor can have air intake means, sterilization means, harvesting means, heating and/or cooling means, temperature controller means, pH controller means, filtration means and pressure controller means. All these features of bioreactors are known and commercially available in the biotechnology industry. [0054] The biological process using microbes according to the disclosure can also be done by heap leaching techniques. In heap bio leaching techniques, a large body of mineral ore is treated with mutant microbes in nutrient solution in large contaminant ponds with no agitation and/or only occasional agitation. Generally, the contact time for heap type bio treatment is substantially longer than the agitated bioreactors and range from 10 days to 100 days. [0055] As used herein, the term “inoculating” refers to the act of introducing a microorganism or a plurality of microorganisms (e.g. ECO003, ECO004, and/or ECO005) into a substrate where it will be metabolically active and/or propagate. In preferred embodiments, the step of inoculating is performed using aseptic technique. In some embodiments, the bacterial strain is inoculated at a concentration of about 1.0 x 10³ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁶ CFU/gm, about 1.0 x 10⁷ CFU/gm, about 1.0 x 10⁸ CFU/gm, about 1.0 x 10⁹ CFU/gm, about 1.0 x 10¹⁰ CFU/gm, about 1.0 x 10¹¹ CFU/gm, about 1.0 x 10¹² CFU/gm, about 1.0 x 10¹³ CFU/gm, about 1.0 x 10¹⁴ CFU/gm, about 1.0 x 10¹⁵ CFU/gm, about 1.0 x 10¹⁶ CFU/gm, or about 1.0 x 10¹⁷ CFU/gm. In a preferred embodiment, the bacterial strain is inoculated at a concentration from about 1.0 x 10⁶ CFU/gm to about 1.0 x 10¹² CFU/gm. The inoculating step can PATENT-PCT Atty. Docket No.3414.3100WO occur one or more times during the duration of extracting, producing and/or amplifying copper, cobalt, and/or nickel metal from the solid substrate. [0056] Inoculation of the solid substrate can occur by any means known to the skilled artisan which provides the microbe to the substrate in a sufficient amount. In some embodiments, after inoculation additional solid substrate is added to increase the surface area of the solid substrate which is in contact with the bacterial strain. In one aspect, additional solid substrate is added to create a 4-6 inch depth over the initial inoculation depth. [0057] After inoculation the solid substrate is optionally irrigated and/or fertilized one or more times to stimulate colonization and exponential growth throughout of the bacterial strain throughout the solid substrate. Exemplary fertilizers include a low NPK plus micronutrient fertilizer, solutions comprising a complex or simple sugar, a seaweed or cytokine and a vitamin blend. In addition, specialty nutrients and by-products can be added to the inoculated solid substrate one or more times to establish new, increased and rigorous colonization by the bacterial strain. [0058] In addition, the solid substrate may be covered to maintain a stable temperature or allow for an increase in the solid substrate temperature, for example using a poly covering for consistent temperature control and to control microbial contaminants from colonizing. In some embodiments, the inoculated solid substrate is maintained at a temperature between about 20°C to about 60°C including any range therein. In a preferred embodiment, the inoculated solid substrate is maintained at a temperature between about 29°C to about 50°C. [0059] After the bacterial strain has had sufficient time to colonize and biochemically process the solid substrate (non-limiting example 2-10 weeks) the solid substrate can be tested and processed for copper, cobalt, and/or nickel metals production. The testing and/or processing steps include harvesting the solid substrate which has been colonized by the bacterial strain, generating a slurry by adding a solution to the solid substrate, and centrifugation at a minimum of 8,000 RPM to concentrate the precipitate which contains the de novo copper, cobalt, and/or nickel metals. These PATENT-PCT Atty. Docket No.3414.3100WO steps may optionally include a bacterial lysis step to release any metals within the bacterial strains intracellular matrix. [0060] In a still another aspect, the methods of extracting, producing and/or amplifying copper, cobalt, and/or nickel metals generally comprise inoculating the bacterial strains disclosed herein in liquid substrates. Suitable liquid substrates include but are not limited to balanced salt and nutrient solutions, broths, environmental samples collected from any aquatic or marine source, waste waters, sludge waters, saltwater, freshwater, irrigation systems, ponds, lakes, rivers, and estuaries. In some embodiments, the liquid substrate is disinfected prior to inoculation of the bacterial strains disclosed herein. Disinfection techniques include but are not limited to steam, autoclave, oven, microwave, biocide and fungicide solutions. In a preferred embodiment, the disinfection step will reduce microbial colony and propagule concentrations to below or at about 5.0 x 10⁵ CFU/ml. [0061] Inoculation of the liquid substrate can occur by any means known to the skilled artisan at concentration described above for the solid substrate. The inoculating step can occur one or more times during the duration of extracting, producing and/or amplifying copper, cobalt, and/or nickel metals from the liquid substrate. After inoculation the liquid substrate is preferably agitated during the extraction, production and/or amplification of the copper, cobalt, and/or nickel metals. In an exemplary embodiment, agitation of the liquid substrate occurs using an air pump for aerobic respiration. [0062] After inoculation of the liquid substrate, optionally specialty nutrients and by-products can be added to the inoculated liquid substrate one or more times to establish new, increased and rigorous colonization by the bacterial strain, for example by adding solutions comprising a complex or simple sugar, a seaweed or cytokinin and a vitamin blend. In addition, for accelerated reactions establish an anodic and cathodic LED using a wavelength generator set at a range of 2.0 – 22.0 KHz. PATENT-PCT Atty. Docket No.3414.3100WO [0063] After the bacterial strain has had sufficient time to colonize and biochemically process the liquid substrate (non-limiting example 12-72 hours) the liquid substrate can be tested and processed for copper, cobalt, and/or nickel metals production. The testing and/or processing steps include collecting the liquid substrate which has been colonized by the bacterial strain, generating a slurry by adding a solution to the solid substrate, and centrifugation of the liquid solution through an in line and continuous centrifuge at a minimum of 8,000 RPM to concentrate the precipitation. These steps may optionally include a bacterial lysis step to release any metals within the bacterial strains intracellular matrix. [0064] In each of the above embodiments, a bioreactor, fermenter, reaction vessel can be used in the disclosed methods. Moreover, the present disclosure contemplates the use of the disclosed microbes for bioleaching and heap leaching and therefore the use of leach pits are contemplated within the methods as well. [0065] Bio treatment temperature ranges from 15 degrees centigrade to 50 degrees centigrade, preferably from 20 degrees to 30 degrees centigrade. pH can be acidic (pH 1 to 3) or basic (pH 9 to 12), although slightly acidic (pH 4) to slightly basic (pH 8) pH ranges are preferred. The most preferred pH ranges are the neutral range of from pH 6.5 to pH 7.5. [0066] In accordance with the methods of the present disclosure, pressure is not critical and can be at atmospheric, below atmospheric, and/or above atmospheric. The biological transmutation process can be conducted in aerobic or anaerobic conditions. The biological transmutation process can be conducted in the presence of nitrogen, carbon dioxide, and oxygen in the atmosphere. Oxygen can be provided chemically, for example, with hydrogen peroxide, or as a gas from pressurized vessels. [0067] Microbe concentration is not critical. At low microbe concentration, the contact duration is generally longer to allow the microbe to grow and multiply. However, microbe concentration should not exceed the maximum microbe concentration that the nutrient solution can sustain. Contact time can vary from a few hours to several weeks and depends in part on the type and mesh PATENT-PCT Atty. Docket No.3414.3100WO size of the mineral ore digested. Contact time ranges can be from 1 day to 30 days, more preferably from 1 day to 10 days. [0068] The biological process using microbes according to the disclosure can be conducted in aerobic or anaerobic conditions. However, preferably conducted in the presence of oxygen, nitrogen and carbon dioxide in the atmosphere. Oxygen can also be provided chemically, for example, with hydrogen peroxide, or as a gas from pressurized vessels. [0069] Nutrients can also be provided during the biological transmutation process to support growth of the mutant microbes. Nutrients can be inorganic, including nitric acid, sulfur, ammonium nitrate, ammonium chloride, ammonium sulfate, sodium nitrate, sodium chloride, sodium bicarbonate, sodium phosphate, potassium nitrate, potassium phosphate, ferric chloride, calcium chloride, and ammonium phosphate, and organic, including glucose, dextrose, sodium acetate, amino acids, and purines. Vitamins that can be included in the nutrient solution include pyridoxine, pyridoxamine-HCl, riboflavin, thiamine, niacin, pantothenic acid, p-aminobenzoic acid, folic acid, and biotin. Small amounts of traces elements such as iron, copper, molybdenum and zinc can also be provided in the nutrient solution. [0070] After the biological transmutation process, the recovery of metal produced from the starting material and microbial solution can be performed by conventional metallurgical methods such as smelting, leaching, electrolysis, resins and other methods known to those skilled in art of metallurgy. In another embodiment, the precious metals in the microbes or biomass of dead microbes can be recovered by methods described for recovery of precious metals from mineral ore. [0071] Fire assaying and cupellation are described by C. W. Ammen, Recovery and Refining of Precious Metals, second edition 1993, Chapter 12, pp 302-329. [0072] Also provided are kits. Such kits can include an agent or composition described herein and, in certain embodiments, instructions for use. Such kits can facilitate performance of the methods described herein. When supplied as a kit, the different components of the composition can be PATENT-PCT Atty. Docket No.3414.3100WO packaged in separate containers and admixed immediately before use. Components include but are not limited to ECO003, ECO004, and ECO005 compositions and formulations for use or stability, as described herein. Such packaging of the components separately can, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the composition. The pack may, for example, comprise metal or plastic foil such as a blister pack. Such packaging of the components separately can also, in certain instances, permit long-term storage without losing activity of the components. [0073] Kits may also include reagents in separate containers such as, for example, sterile water or saline to be added to a lyophilized active component packaged separately. For example, sealed glass ampules may contain a lyophilized component and in a separate ampule, sterile water, sterile saline or sterile each of which has been packaged under a neutral non-reacting gas, such as nitrogen. Ampules may consist of any suitable material, such as glass, organic polymers, such as polycarbonate, polystyrene, ceramic, metal or any other material typically employed to hold reagents. Other examples of suitable containers include bottles that may be fabricated from similar substances as ampules, and envelopes that may consist of foil-lined interiors, such as aluminum or an alloy. Other containers include test tubes, vials, flasks, bottles, syringes, and the like. Containers may have a sterile access port, such as a bottle having a stopper that can be pierced by a hypodermic injection needle. Other containers may have two compartments that are separated by a readily removable membrane that upon removal permits the components to mix. Removable membranes may be glass, plastic, rubber, and the like. [0074] In certain embodiments, kits can be supplied with instructional materials. Instructions may be printed on paper or other substrate, and/or may be supplied as an electronic-readable medium, such as a floppy disc, mini-CD-ROM, CD-ROM, DVD-ROM, Zip disc, videotape, audio tape, and the like. Detailed instructions may not be physically associated with the kit; instead, a user may be directed to an Internet web site specified by the manufacturer or distributor of the kit. [0075] Compositions and methods described herein utilizing molecular biology protocols can be according to a variety of standard techniques known to the art (see, e.g., Sambrook and Russel PATENT-PCT Atty. Docket No.3414.3100WO (2006) Condensed Protocols from Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, ISBN-10: 0879697717; Ausubel et al. (2002) Short Protocols in Molecular Biology, 5th ed., Current Protocols, ISBN-10: 0471250929; Sambrook and Russel (2001) Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor Laboratory Press, ISBN- 10: 0879695773; Elhai, J. and Wolk, C. P.1988. Methods in Enzymology 167, 747-754; Studier (2005) Protein Expr Purif. 41(1), 207–234; Gellissen, ed. (2005) Production of Recombinant Proteins: Novel Microbial and Eukaryotic Expression Systems, Wiley-VCH, ISBN-10: 3527310363; Baneyx (2004) Protein Expression Technologies, Taylor & Francis, ISBN-10: 0954523253). [0076] General Techniques [0077] The practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature, such as Molecular Cloning: A Laboratory Manual, second edition (Sambrook, et al., 1989) Cold Spring Harbor Press; Oligonucleotide Synthesis (M. J. Gait, ed.1984); Methods in Molecular Biology, Humana Press; Cell Biology: A Laboratory Notebook (J. E. Cellis, ed., 1989) Academic Press; Animal Cell Culture (R. I. Freshney, ed.1987); Introduction to Cell and Tissue Culture (J. P. Mather and P. E. Roberts, 1998) Plenum Press; Cell and Tissue Culture: Laboratory Procedures (A. Doyle, J. B. Griffiths, and D. G. Newell, eds. 1993-8) J. Wiley and Sons; Methods in Enzymology (Academic Press, Inc.); Handbook of Experimental Immunology (D. M. Weir and C. C. Blackwell, eds.): Gene Transfer Vectors for Mammalian Cells (J. M. Miller and M. P. Calos, eds., 1987); Current Protocols in Molecular Biology (F. M. Ausubel, et al. eds. 1987); PCR: The Polymerase Chain Reaction, (Mullis, et al., eds. 1994); Current Protocols in Immunology (J. E. Coligan et al., eds., 1991); Short Protocols in Molecular Biology (Wiley and Sons, 1999); Immunobiology (C. A. Janeway and P. Travers, 1997); Antibodies (P. Finch, 1997); Antibodies: a practice approach (D. Catty., ed., IRL Press, 1988-1989); Monoclonal antibodies: a practical approach (P. Shepherd and C. Dean, eds., Oxford University Press, 2000); Using antibodies: a laboratory manual (E. Harlow and D. Lane (Cold Spring Harbor Laboratory Press, PATENT-PCT Atty. Docket No.3414.3100WO 1999); The Antibodies (M. Zanetti and J. D. Capra, eds. Harwood Academic Publishers, 1995); DNA Cloning: A practical Approach, Volumes I and II (D.N. Glover ed. 1985); Nucleic Acid Hybridization (B.D. Hames & S.J. Higgins eds.(1985»; Transcription and Translation (B.D. Hames & S.J. Higgins, eds. (1984»; Animal Cell Culture (R.I. Freshney, ed. (1986»; Immobilized Cells and Enzymes (lRL Press, (1986»; and B. Perbal, A practical Guide To Molecular Cloning (1984); F.M. Ausubel et al. (eds.). [0078] So that the present disclosure may be more readily understood, certain terms are first defined. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which embodiments of the invention pertain. Many methods and materials similar, modified, or equivalent to those described herein can be used in the practice of the embodiments of the present invention without undue experimentation, the preferred materials and methods are described herein. In describing and claiming the embodiments of the present invention, the following terminology will be used in accordance with the definitions set out below. [0079] Concentrations, amounts, and other numerical data may be expressed or presented herein in a range format. It is to be understood that such a range format is used merely for convenience and brevity and should be interpreted flexibly to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub- ranges encompassed within that range as if each numerical value and sub-range is explicitly recited. As an illustration, a numerical range of “about 2 to about 50” should be interpreted to include not only the explicitly recited values of 2 to 50, but also include all individual values and sub-ranges within the indicated range. Thus, included in this numerical range are individual values such as 2, 2.4, 3, 3.7, 4, 5.5, 10, 10.1, 14, 15, 15.98, 20, 20.13, 23, 25.06, 30, 35.1, 38.0, 40, 44, 44.6, 45, 48, and sub-ranges such as from 1-3, from 2-4, from 5-10, from 5-20, from 5-25, from 5-30, from 5- 35, from 5-40, from 5-50, from 2-10, from 2-20, from 2-30, from 2-40, from 2-50, etc. This same principle applies to ranges reciting only one numerical value as a minimum or a maximum. Furthermore, such an interpretation should apply regardless of the breadth of the range or the characteristics being described. PATENT-PCT Atty. Docket No.3414.3100WO [0080] The term “about,” as used herein, refers to variation of in the numerical quantity that can occur, for example, through typical measuring techniques and equipment, with respect to any quantifiable variable, including, but not limited to, mass, volume, time, distance, and amount. Further, given solid and liquid handling procedures used in the real world, there is certain inadvertent error and variation that is likely through differences in the manufacture, source, or purity of the ingredients used to make the compositions or carry out the methods and the like. The term “about” also encompasses these variations, which can be up to ± 5%, but can also be ± 4%, 3%, 2%,1%, etc. Whether or not modified by the term “about,” the claims include equivalents to the quantities. [0081] When introducing elements of the present disclosure or the preferred aspects(s) thereof, the articles “a,” “an,” “the,” and “said” are intended to mean that there are one or more of the elements unless the contrary is explicitly mentioned. The terms “comprising,” “including,” and “having” are intended to be inclusive and mean that there may be additional elements other than the listed elements. [0082] In this disclosure, “comprises,” “comprising,” “containing,” and “having” and the like can have the meaning ascribed to them in U.S. Patent Law and can mean “includes,” “including,” and the like, and are generally interpreted to be open ended terms. The terms “consisting of” or “consists of” are closed terms, and include only the components, structures, steps, or the like specifically listed in conjunction with such terms, as well as that which is in accordance with U.S. Patent law. “Consisting essentially of” or “consists essentially of” have the meaning generally ascribed to them by U.S. Patent law. In particular, such terms are generally closed terms, with the exception of allowing inclusion of additional items, materials, components, steps, or elements, that do not materially affect the basic and novel characteristics or function of the item(s) used in connection therewith. For example, trace elements present in a composition, but not affecting the composition’s nature or characteristics would be permissible if present under the “consisting essentially of” language, even though not expressly recited in a list of items following such terminology. In this specification when using an open-ended term, like “comprising” or “including,” PATENT-PCT Atty. Docket No.3414.3100WO it is understood that direct support should be afforded also to “consisting essentially of” language as well as “consisting of” language as if stated explicitly and vice versa. [0083] Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present invention to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. All publications cited herein are incorporated by reference for the purposes or subject matter referenced herein. [0084] As various changes could be made in the above-described materials and methods without departing from the scope of the invention, it is intended that all matter contained in the above description and in the examples given below, shall be interpreted as illustrative and not in a limiting sense. [0085] EXAMPLES [0086] The following examples are included to demonstrate various embodiments of the present disclosure. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the scope of the invention. [0087] Example 1: Novel Microorganism Isolation and Classification [0088] It has been estimated that only 2% of all microbial isolates can be cultured in a lab. Therefore, the microbes that can be grown in the laboratory represent only a small fraction of the total diversity that exists in nature. At all levels of microbial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other PATENT-PCT Atty. Docket No.3414.3100WO elements, synthesizing novel by-products, and impacting the surrounding organisms and environment. The ability to culture difficult to culture or previously uncultured microbial strains provides a wealth of information about their role in the environment, ecology, and nutrient cycling. But perhaps even more importantly, screening of novel isolates will reveal novel products that can have profound effects for the discovery of novel drugs, improve agricultural techniques and products, and in the production of copper, cobalt, nickel, and other metals. To solve this problem the Applicant developed a novel apparatus (Ecobiome Discovery apparatus) allowing for the controlled growth, isolation and characterization of microorganisms including those that are difficult to culture or are uncultivable at the present time. [0089] In an effort to isolate and characterize novel microbes, an experiment utilizing the Ecobiome Discovery apparatus was used. Ores were obtained and prepared for culturing in the Ecobiome apparatus. The copper oxide and the copper sulfide ores were obtained from pastureland in Texas; the cobalt ore was obtained from an agricultural field in Minnesota; and the nickel ore was obtained from a farm field in North Carolina. In short, in each case the sample was crushed and loaded into the Ecobiome for microbial gradiation and speciation. The prepped samples were allowed to equilibrate, and microbial growth promoted. After some time, a population of microorganisms, including the newly discovered organisms (ECO003, ECO004, and ECO005) were isolated. [0090] After isolation of the individual microbe populations comprising ECO003, ECO004, and ECO005, challenge tests were performed on each, which included tests specific for copper, cobalt, and nickel remediation microbes. These tests resulted in the isolation and characterization of ECO003 (bacillus cuprevida), ECO004 (bacillus cobalos), and ECO005 (bacillus niccolum). [0091] ECO003, ECO004, and ECO005 are each gram-negative bacteria, non-spore formers that are capable of metabolizing simple and complex polymers as well as metals through heterotrophic and chemoheterotrophic biochemical pathways. ECO003, ECO004, and ECO005 are facultative anaerobes and are tolerant of low and high temperatures, e.g., ranging between about 5^oC to about 46^oC. In addition, each is tolerant of a pH range from about 2 to about 9. Each microorganism PATENT-PCT Atty. Docket No.3414.3100WO reaches exponential growth with high agitation (>360 rpm) and oxygenation (DO > 90%) within 6-8 hours. [0092] Example 2: Manufacturing Copper, Cobalt, and Nickel Elements  [0093] Five pounds of each of the samples was used as the processing soil for each trial. The five pounds were weighed out and placed in a bucket container fashioned specifically for holding soil and dry material during processing in a bioreactor. The bucket of soil was inserted into the bioreactor and the reactor was filled to 40 gallons of filtered water. Once the water level exceeded the height of the bucket the circulating water pump was turned on in addition to a continuous air pump into the bioreactor. Prior to inoculation with the microorganism, a disinfection process was initiated using Calcium Hypochlorite followed by Ascorbic Acid neutralization. This allowed for the disinfection of any contaminant microorganisms that may have been present in water, soil or air contaminants to be removed. After ascorbic acid neutralization of the bioreactor contents, the EcoBiome ECO003 microorganism was transferred and inoculated into the bioreactor at a rate of 1.0 x 10¹⁰ CFU/ml. Nutrient contents were then added which consisted of a blend of NPK fertilizer, seaweed extract, zinc citrate, zinc sulfate, Vitamin blend, Dextrose and 3 liters of Nutrient Broth (autoclaved and sterilized). The reaction was closed and sealed and allowed to react for 48 hours with an internal liquid temperature of approximately 40^oC using continuous aeration and recirculation. Once the reaction was completed, all liquid contents were run through centrifugation, harvested, dried in an oven and then analyzed via an X-Ray Fluorescence Analyzer for precious metals and rare earth elements. % Copper production is reported in Tables 1 and 2 for Heap Leach Column Tests using X-ray Fluorescence testing (XRF). The tests were repeated, using ECO004, and Tables 3-6 report % cobalt production using inductively-coupled plasma – mass spectroscopy (ICP-MS) testing. The test were repeated again using ECO005, and Table 7 reports % nickel production, using XRF testing.

PATENT-PCT Atty. Docket No.3414.3100WO Table 1: Copper Oxide (Heap Leach Column Tests) Sample Copper %/Wt. (+/- 0.001) Microbiology CFU/Gm ore XRF Total Copper Cycling

nutrients DRIVE: Programmed to target Copper

PATENT-PCT Atty. Docket No.3414.3100WO Table 2: Copper Sulfide (Heap Leach Column Tests) Sample Copper %/Wt. (+/- 0.001) Microbiology CFU/Gm ore XRF Total Copper Cycling

nutrients DRIVE: Programmed to target Copper     PATENT-PCT Atty. Docket No.3414.3100WO Table 3: EcoBiome Cobalt Cycling Microbes (% by wt.) Sample Cobalt %/wt. Cobalt %/wt. Untreated (as is) EcoBiome Treated

Table 4: EcoBiome Cobalt Cycling Microbes (%/wt.) Sample Cobalt %/wt. Cobalt %/wt. Untreated (as is) EcoBiome Treated

Table 5: EcoBiome Cobalt Cycling Microbes Sample Cobalt cycling microbes Cobalt cycling Minimum Untreated (s is) microbes Recommendation

Table 6: EcoBiome Cobalt Cycling Microbes Sample Cobalt cycling microbes Cobalt cycling Minimum Untreated (s is) microbes Recommendation

96 Hour residence time (Bio leaching) Neutral pH Temperature Range between 90^F – 105^F (32^C – 41^C)   PATENT-PCT Atty. Docket No.3414.3100WO Table 7: Nickel Ore Test Nickel heap leach column testing EcoBiome Nickel Microbe Treated versus Untreated Sample Untreated As is (Water only) EcoBiome Treated (Nickel Microbe XRF Analyzer %/Wt. Cycler)

[0094] As can be seen from Tables 1-7, the untreated control (soil without ECO003, ECO004, or ECO005 inoculation) lacked copper, cobalt, and nickel concentration, respectively, within the limit of detection by the analyzer, while the Ecobiome treated samples all showed greater concentrations of copper, cobalt, and nickel, respectively. [0095] Comparative Assays and Enzymatic Activity Tests – Wild types vs. inventive microorganisms [0096] Description of Tests [0097] Microbial Urease Enzyme Activity Assay [0098] This assay measures the activity of the Urease enzyme. Urease is a protein enzyme that catalyzes the hydrolysis of urea into NH₃ and CO₂ according to the following reaction: NH₂-CO-NH₂ + H₂O → NH₃ + NH₂-COOH → NH₃ + CO₂ PATENT-PCT Atty. Docket No.3414.3100WO [0099] Microbial Respiration Assay [0100] This assay measures the ability of a microorganism to utilize oxygen or an alternative final electron acceptor in its metabolic pathway. [0101] Microbial Phosphorus Solubilization Assay [0102] This assay measures the ability of a microorganism to cleave phosphorus from a compound and then metabolize that compound. [0103] Microbial Hydrogen Sulfide Assay [0104] This assay measures the ability of a microorganism to metabolize sulfur compounds and produce H2S and gas. [0105] Microbial Chitinase Enzyme Assay [0106] This assay measures the ability of a microorganism to produce an extracellular Chitinase enzyme that catabolizes chitin compounds in the soil. [0107] Microbial Cellulase Enzyme Activity [0108] This assay measures the ability of a microorganism to produce an extracellular Cellulase enzyme that catabolizes cellulose and hemi-cellulose compounds in the soil. [0109] Microbial Ligninase Enzyme Activity [0110] This assay measures the ability of a microorganism to produce an extracellular Ligninase enzyme that catabolizes lignin compounds in the soil. [0111] Each of microorganisms ECO003, ECO004, and ECO005 were tested and compared to their wild types according to these seven tests. Results of these seven comparative tests are listed in Tables 8-14. PATENT-PCT Atty. Docket No.3414.3100WO Table 8. Urease Enzyme Activity Microorganism Urease Enzyme Activity wild type 1 - [011

sed fertilizers for enhanced nitrogen uptake.

PATENT-PCT Atty. Docket No.3414.3100WO Table 9. Bacterial Final Electron Acceptor Metabolic Activity Microorganism Metabolic Oxygen Activity wild type 1 Aerobic [011

at the roots of the plants with minimal oxygen for enhanced plant growth promotion.

PATENT-PCT Atty. Docket No.3414.3100WO Table 10. Phosphorus Solubilization Activity Microorganism Phosphorus Solubilization wild type 1 - [011

lease phosphorus from the soil for enhanced phosphorus plant root uptake.

PATENT-PCT Atty. Docket No.3414.3100WO Table 11. Hydrogen Sulfide Activity (post 2-weeks) Microorganism Hydrogen Sulfide Activity wild type 1 ++ [011

a low oxygen environment, this were able to effectively metabolize nutrients with substitute electron acceptors besides oxygen for efficient plant growth promotion.

PATENT-PCT Atty. Docket No.3414.3100WO Table 12. Chitinase Enzyme Activity Microorganism Chitinase Enzyme Activity wild type 1 - [011

itin, the second most abundant complex polymer in the soil and the primary component of fungal walls and nematode eggs, for improved soil mineralization.

PATENT-PCT Atty. Docket No.3414.3100WO Table 13. Cellulase Enzyme Activity Microorganism Cellulase Enzyme Activity wild type 1 - [011

decompose cellulose, the most abundant complex polymer in the soil for increased mineralization and nutrient cycling. Cellulose is the building block of all stalk, stover and crop residue.

PATENT-PCT Atty. Docket No.3414.3100WO Table 14. Ligninase Enzyme Activity Microorganism Ligninase Enzyme Activity wild type 1 - [011

PATENT-PCT Atty. Docket No.3414.3100WO Table 15. Sugar Activity (most abundant sugars found in nature) M_icroorganism ^{glucose xylose sucrose fructose lactose galactose} wild type 1 - - - - ++ ++

PATENT-PCT Atty. Docket No.3414.3100WO Table 16. Complex Organic Activity (most abundant complex organic polymers found in nature) Microorganism Cellulose Lignin Starch Pectin Chitin Keratin* (hemi-

PATENT-PCT Atty. Docket No.3414.3100WO Table 17. Nitrate Reductase Assay (NH3 ^ NO3- ^ NO2- ) Microorganism Nitrate Reductase

wild type 1 -

PATENT-PCT Atty. Docket No.3414.3100WO Table 18. Diverse Nitrogen Sources in Nature Microorganism Urea Uric Nitrate Ammonia Putrescine Xanthine Acid

PATENT-PCT Atty. Docket No.3414.3100WO Table 19. Diverse Phosphorus and Sulfur Sources in Nature Microorganism A B C D E F

PATENT-PCT Atty. Docket No.3414.3100WO Table 20. Diverse Saline and Osmotic Environments Microorganism A B C D E F

PATENT-PCT Atty. Docket No.3414.3100WO Table 21. Diverse pH Environments Microorganism pH 4 pH 4.5 + pH 7 pH 9 pH 9.5 pH 9.5 Urea + Urea

PATENT-PCT Atty. Docket No.3414.3100WO [0119] While several inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the inventive embodiments described herein. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the inventive teachings is/are used. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present disclosure are directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the inventive scope of the present disclosure. [0120] All references, patents and patent applications disclosed herein are incorporated by reference with respect to the subject matter for which each is cited, which in some cases may encompass the entirety of the document. [0121] The phrase “and/or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and/or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and/or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and/or B”, when used in conjunction PATENT-PCT Atty. Docket No.3414.3100WO with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc. [0122] As used herein in the specification and in the claims, “or” should be understood to have the same meaning as “and/or” as defined above. For example, when separating items in a list, “or” or “and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of” or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law. [0123] As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “at least one of A and B” (or, equivalently, “at least one of A or B,” or, equivalently “at least one of A and/or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc. PATENT-PCT Atty. Docket No.3414.3100WO [0124] As used herein, the term “isolated” in the context of an isolated bacterial strain, is one which is altered or removed from the natural state through human intervention.

Claims

PATENT-PCT Atty. Docket No.3414.3100WO What is claimed is: 1. An isolated bacterial strain bacillus cuprevida (ECO003), which has been designated Accession number NRRL No. B-68290, deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023. 2. A method of extracting, amplifying, or producing copper metal comprising inoculating a substrate selected from solid substrates, geological substrates, and liquid substrates with the isolated bacterial strain of claim 1. 3. The method of claim 2, wherein the bacterial strain is inoculated at a concentration of about 1.0 x 10³ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁶ CFU/gm, about 1.0 x 10⁷ CFU/gm, about 1.0 x 10⁸ CFU/gm, about 1.0 x 10⁹ CFU/gm, about 1.0 x 10¹⁰ CFU/gm, about 1.0 x 10¹¹ CFU/gm, about 1.0 x 10¹² CFU/gm, about 1.0 x 10¹³ CFU/gm, about 1.0 x 10¹⁴ CFU/gm, about 1.0 x 10¹⁵ CFU/gm, about 1.0 x 10¹⁶ CFU/gm, or about 1.0 x 10¹⁷ CFU/gm. 4. The method of claim 2, wherein the solid substrate is obtained from one or more of a terrestrial, aquatic or marine source. 5. The method of claim 4, wherein, the solid substrate is one or more of soil, biofilm, sediment, native metal rock and sludge residue. 6. The method of claim 2, wherein the geological substrate is one or more of sandstone, limestone, shale, coal, chalk deposit formations, refractory rock ore. 7. The method of claim 2, wherein the liquid substrate is obtained from one or more of a waste waters, sludge waters, saltwater, freshwater, irrigation systems, ponds, lakes, rivers, and estuaries source. PATENT-PCT Atty. Docket No.3414.3100WO 8. The method of claim 2, wherein the solid substrate is disinfected and/or sterilized prior to inoculation with the bacterial strain. 9. The method of claim 2, further comprising adding a fertilizer, nutrient and/or by product composition one or more times to the substrate after inoculation with the bacterial strain. 10. A composition comprising an isolated bacterial strain bacillus cuprevida (ECO003), which has been designated Accession number NRRL No. B-68290, deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023, about 0.01%/Wt. copper emulsion, about 0.01%/Wt. copper nanoparticles, about 0.01%/Wt. adenosine triphosphate, about 1%/Wt. seaweed extract, about 0.5%/Wt. humic acid, about 0.5%/Wt. mixture of nitrogen, phosphate, potassium and micronutrient mixture, about 0.1% light and mid chain hydrocarbon mixture, about 0.25%/Wt. green solvent, about 0.75%/Wt. sugar, about 1.0%/Wt. substrate comprising copper, and a carrier selected from water or agarose. 11. An isolated bacterial strain bacillus cobalos (ECO004), which has been designated Accession number NRRL No. B-68291, deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023. 12. A method of extracting, amplifying, or producing cobalt metal comprising inoculating a substrate selected from solid substrates, geological substrates, and liquid substrates with the isolated bacterial strain of claim 11. 13. The method of claim 12, wherein the solid substrate is obtained from one or more of a terrestrial, aquatic or marine source. PATENT-PCT Atty. Docket No.3414.3100WO 14. The method of claim 13, wherein, the solid substrate is one or more of soil, biofilm, sediment, native metal rock and sludge residue. 15. The method of claim 12, wherein the geological substrate is one or more of sandstone, limestone, shale, coal, chalk deposit formations, refractory rock ore. 19. The method of claim 12, wherein the liquid substrate is obtained from one or more of a waste waters, sludge waters, saltwater, freshwater, irrigation systems, ponds, lakes, rivers, and estuaries source. 20. The method of claim 12, wherein the solid substrate is disinfected and/or sterilized prior to inoculation with the bacterial strain. 21. The method of claim 12, further comprising adding a fertilizer, nutrient and/or by product composition one or more times to the substrate after inoculation with the bacterial strain. 22. A composition comprising an isolated bacterial strain bacillus cobalos (ECO004), which has been designated Accession number NRRL No. B-68291, deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023, about 0.01%/Wt. copper emulsion, about 0.01%/Wt. copper nanoparticles, about 0.01%/Wt. adenosine triphosphate, about 1%/Wt. seaweed extract, about 0.5%/Wt. humic acid, about 0.5%/Wt. mixture of nitrogen, phosphate, potassium and micronutrient mixture, about 0.1% light and mid chain hydrocarbon mixture, about 0.25%/Wt. green solvent, about 0.75%/Wt. sugar, about 1.0%/Wt. substrate comprising cobalt, and a carrier selected from water or agarose. PATENT-PCT Atty. Docket No.3414.3100WO 23. An isolated bacterial strain bacillus niccolum (ECO005), which has been designated Accession number NRRL No. B-68292, deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023. 24. A method of extracting, amplifying, or producing nickel metal comprising inoculating a substrate selected from solid substrates, geological substrates, and liquid substrates with the isolated bacterial strain of claim 23. 25. The method of claim 23, wherein the bacterial strain is inoculated at a concentration of about 1.0 x 10³ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁴ CFU/gm, about 1.0 x 10⁶ CFU/gm, about 1.0 x 10⁷ CFU/gm, about 1.0 x 10⁸ CFU/gm, about 1.0 x 10⁹ CFU/gm, about 1.0 x 10¹⁰ CFU/gm, about 1.0 x 10¹¹ CFU/gm, about 1.0 x 10¹² CFU/gm, about 1.0 x 10¹³ CFU/gm, about 1.0 x 10¹⁴ CFU/gm, about 1.0 x 10¹⁵ CFU/gm, about 1.0 x 10¹⁶ CFU/gm, or about 1.0 x 10¹⁷ CFU/gm. 26. The method of claim 23, wherein the solid substrate is obtained from one or more of a terrestrial, aquatic or marine source. 27. The method of claim 26, wherein, the solid substrate is one or more of soil, biofilm, sediment, native metal rock and sludge residue. 28. The method of claim 23, wherein the geological substrate is one or more of sandstone, limestone, shale, coal, chalk deposit formations, refractory rock ore. 29. The method of claim 23, wherein the liquid substrate is obtained from one or more of a waste waters, sludge waters, saltwater, freshwater, irrigation systems, ponds, lakes, rivers, and estuaries source. PATENT-PCT Atty. Docket No.3414.3100WO 30. The method of claim 23, wherein the solid substrate is disinfected and/or sterilized prior to inoculation with the bacterial strain. 31. The method of claim 23, further comprising adding a fertilizer, nutrient and/or by product composition one or more times to the substrate after inoculation with the bacterial strain. 32. A composition comprising an isolated bacterial strain bacillus niccolum (ECO005), which has been designated Accession number NRRL No. B-68292, deposited in accordance with the Budapest Treaty at the Agricultural Research Service Culture Collection (USDA, ARS, 1815 North University Street, Peoria, IL, 61064) on July 13, 2023, about 0.01%/Wt. nickel emulsion, about 0.01%/Wt. nickel nanoparticles, about 0.01%/Wt. adenosine triphosphate, about 1%/Wt. seaweed extract, about 0.5%/Wt. humic acid, about 0.5%/Wt. mixture of nitrogen, phosphate, potassium and micronutrient mixture, about 0.1% light and mid chain hydrocarbon mixture, about 0.25%/Wt. green solvent, about 0.75%/Wt. sugar, about 1.0%/Wt. substrate comprising nickel, and a carrier selected from water or agarose.