Microbial compositions and methods

Abstract

Microbial compositions for application to plants, plant parts and plant seeds are provided for improvement of plant disease resistance and/or other beneficial plant traits, particularly resistance or tolerance to soybean sudden death syndrome (SDS) caused by a Fusarium species and/or disease caused by a Pythium species. Methods of making and applying microbial compositions or p formulations to plants, plant parts or plant seeds or to growth media are further provided to increase or improve plant disease resistance N and/or other beneficial plant traits.

1 . An isolated  Pseudomonas chlororaphis  strain deposited as ATCC accession number PTA-123716. 
     
     
         2 . An isolated  Pseudomonas  strain, wherein the  Pseudomonas  strain has a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1, and wherein the  Pseudomonas  strain confers a positive agricultural trait or benefit to a crop plant when the crop plant is treated or associated with the  Pseudomonas  strain. 
     
     
         3 . An isolated  Pseudomonas  strain, wherein the  Pseudomonas  strain has a whole (or partial) genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding genome sequence of the  Pseudomonas chlororaphis  strain deposited as ATCC accession number PTA-123716, and wherein the  Pseudomonas  strain confers a positive agricultural trait or benefit to a crop plant treated or associated with the  Pseudomonas  strain. 
     
     
         4 . The isolated  Pseudomonas  strain of  claim 2  or  3 , wherein the positive agricultural trait or benefit is decreased disease severity or symptoms relative to a control plant. 
     
     
         5 . The isolated  Pseudomonas  strain of  claim 2  or  3 , wherein the  Pseudomonas  strain is a progeny of the  Pseudomonas chlororaphis  strain of  claim 1 . 
     
     
         6 . A functional variant of the  Pseudomonas chlororaphis  strain of  claim 1 . 
     
     
         7 . A pure or substantially pure culture or population of the  Pseudomonas chlororaphis  or  Pseudomonas  strain or isolate in any one of  claims 1 - 5 . 
     
     
         8 . A composition comprising a microbial strain or isolate and an agriculturally acceptable carrier, wherein the microbial strain or isolate has a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, or at least 99.95% identical to SEQ ID NO: 1. 
     
     
         9 . A composition comprising a microbial strain or isolate and an agriculturally acceptable carrier, wherein the microbial strain or isolate has a 16S rDNA sequence that is at least 99.9%, or at least 99.95% identical to SEQ ID NO: 1. 
     
     
         10 . The composition of  claim 8  or  9 , wherein the microbial strain or isolate has a 16S rDNA sequence that is 100% identical to SEQ ID NO: 1. 
     
     
         11 . The composition of any one of  claims 8 - 10 , wherein the microbial strain or isolate has a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716. 
     
     
         12 . A composition comprising a microbial strain or isolate and an agriculturally acceptable carrier, wherein the microbial strain or isolate has a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716. 
     
     
         13 . The composition of any one of  claims 8 - 12 , wherein the microbial strain or isolate is  Pseudomonas chlororaphis.    
     
     
         14 . The composition of any one of  claims 8 - 13 , wherein the microbial strain or isolate is the bacterial strain or isolate deposited as ATCC accession number PTA-123716. 
     
     
         15 . The composition of any one of  claims 8 - 14 , wherein the agriculturally acceptable carrier confers at least one beneficial characteristic to the composition. 
     
     
         16 . The composition of  claim 15 , wherein the improved characteristic is improved efficacy, stability, wetting, flowability or coating onto a plant, plant part or seed relative to a control composition lacking the agriculturally acceptable carrier. 
     
     
         17 . The composition of any one of  claims 8 - 16 , wherein the agriculturally acceptable carrier comprises a wetting agent or dispersant. 
     
     
         18 . The composition of any one of  claims 8 - 16 , wherein the agriculturally acceptable carrier comprises a binder or adherent. 
     
     
         19 . The composition of any one of  claims 8 - 18 , wherein the agriculturally acceptable carrier comprises an aqueous solvent and a non-aqueous co-solvent. 
     
     
         20 . The composition of any one of  claims 8 - 19 , further comprising a pesticidal agent. 
     
     
         21 . The composition of  claim 20 , wherein the pesticidal agent is one or more of a fungicide, herbicide, insecticide, miticide, acaricide, nematicide, or gastropodicide. 
     
     
         22 . The composition of  claim 21 , where the pesticidal agent is selected from the group consisting of ipconozole, metalaxyl, azoxystrobin, prothioconazole, metalaxyl, fluoxastrobin, clothianidin,  Bacillus firmus, Penicillium bilaiae, Trichoderma virens , and  Bacillius amyloliquefaciens.    
     
     
         23 . The composition of any one of  claims 9 - 22 , further comprising a plant nutrient or fertilizer. 
     
     
         24 . The composition of any one of  claims 9 - 23 , wherein the composition is formulated as a solid. 
     
     
         25 . The composition of  claim 24 , wherein the composition is formulated as a powder, lyophilisate, pellet or granules. 
     
     
         26 . The composition of any one of  claims 9 - 23 , wherein the composition is formulated as a liquid or gel. 
     
     
         27 . The composition of  claim 26 , wherein the composition is formulated as an emulsion, colloid, suspension or solution. 
     
     
         28 . The composition of any one of  claims 9 - 27 , further comprising one or more of a lipo-chitooligosaccharide (LCO), a chitooligosaccharide (CO), a LCO-producing bacteria or fungus, and a chitinous compound. 
     
     
         29 . The composition of any one of  claims 9 - 28 , further comprising one or more of a flavonoid, humic acid, fulvic acid, jasmonic acid or derivatives thereof, linoleic acid or derivatives thereof, linolenic acid or derivatives thereof, karrikin, and gluconolactone. 
     
     
         30 . The composition of any one of  claims 9 - 29 , wherein the microbial strain or isolate is present in the composition at a concentration of at least 10 3  cfu per milliliter or gram. 
     
     
         31 . The composition of any one of  claims 9 - 30 , comprising a pure or substantially pure population of the microbial strain or isolate. 
     
     
         32 . The composition of any one of  claims 9 - 31 , wherein the composition confers a positive agricultural trait or benefit to a crop plant treated or associated with the composition, wherein the positive agricultural trait or benefit is decreased disease severity or symptoms relative to a control plant. 
     
     
         33 . A kit or container comprising or containing the composition of any one of  claims 9 - 32 . 
     
     
         34 . A plant, plant part or plant seed associated with the composition of any one of  claims 9 - 32 . 
     
     
         35 . A plant, plant part or plant seed having applied or coated on at least a portion of the plant, plant part or plant seed a composition comprising a microbial strain or isolate, wherein the microbial strain or isolate is heterologous with respect to the plant, plant part or plant seed and has a 16S rDNA sequence that is at least 99.9% identical to SEQ ID NO: 1. 
     
     
         36 . The plant, plant part or plant seed of  claim 35 , wherein the composition is applied or coated on at least a portion of the outer surface of the plant, plant part or plant seed. 
     
     
         37 . The plant, plant part or plant seed of  claim 35  or  36 , wherein the plant, plant part or plant seed is transgenic. 
     
     
         38 . A plant, plant part or plant seed having applied or coated on at least a portion of the plant, plant part or plant seed a composition comprising a microbial strain or isolate, wherein the microbial strain or isolate is heterologous with respect to the plant, plant part or plant seed and has a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716. 
     
     
         39 . The plant, plant part or plant seed of  claim 38 , wherein the composition is applied or coated on at least a portion of the outer surface of the plant, plant part or plant seed. 
     
     
         40 . The plant, plant part or plant seed of  claim 38 , wherein the plant, plant part or plant seed is transgenic. 
     
     
         41 . A plant seed having on at least a portion of its outer surface a composition comprising a microbial strain or isolate, wherein the microbial strain or isolate is heterologous with respect to the plant seed, and wherein the microbial strain or isolate has either or both of:
 (i) a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, and   (ii) a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1.   
     
     
         42 . The plant seed of  claim 41 , wherein the plant seed is a dicotyledonous plant seed. 
     
     
         43 . A soybean plant seed of  claim 42 . 
     
     
         44 . A bag or container comprising or containing the plant seed of any one of  claims 38 - 43 . 
     
     
         45 . A plant grown or developed from the plant seed of any one of  claims 38 - 43 . 
     
     
         46 . The plant of  claim 45 , wherein the plant has decreased disease severity or symptoms relative to a control plant grown or developed from a plant seed that was not treated with the microbial strain or isolate. 
     
     
         47 . The plant of  claim 46 , wherein the plant has decreased severity or symptoms of sudden death syndrome (SDS) caused by a  Fusarium  species relative to a control plant grown or developed from a plant seed that was not treated with the microbial strain or isolate. 
     
     
         48 . A method comprising:
 applying a composition to a plant, plant part or plant seed, the composition comprising a microbial strain or isolate and an agriculturally acceptable carrier,   wherein the microbial strain or isolate is heterologous with respect to the plant, plant part or plant seed, and wherein the microbial strain or isolate has either or both of:   (i) a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, and   (ii) a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1.   
     
     
         49 . The method of  claim 48 , wherein the microbial strain or isolate has a 16S rDNA sequence that is 100% identical to SEQ ID NO: 1. 
     
     
         50 . The method of  claim 49 , wherein the microbial strain or isolate is the bacterial strain or isolate deposited as ATCC accession number PTA-123716. 
     
     
         51 . The method of any one of  claims 48 - 50 , wherein the applying step comprises coating the composition onto at least a portion of the outer surface of the plant, plant part or plant seed. 
     
     
         52 . The method of any one of  claims 48 - 51 , wherein the applying step comprises coating the composition onto at least a portion of the outer surface of a plant seed. 
     
     
         53 . The method of  claim 52 , wherein the plant seed is a soybean seed. 
     
     
         54 . The method of any one of  claims 48 - 53 , wherein the applying step comprises solid matrix priming, imbibing, coating, spraying, tumbling, agitating, dripping, soaking, immersing, dusting or encapsulating with the composition. 
     
     
         55 . The method of any one of  claims 48 - 54 , wherein the composition is applied to a crop plant, and wherein the composition comprises an effective amount of the microbial strain or isolate to decrease the severity or symptoms of disease by the crop plant relative to a control plant not treated with the composition. 
     
     
         56 . The method of  claim 55 , wherein the composition comprises an effective amount of the microbial strain or isolate to decrease the severity or symptoms of sudden death syndrome (SDS) by the crop plant caused by a  Fusarium  species, relative to a control plant not treated with the composition. 
     
     
         57 . The method of any one of  claims 48 - 55 , wherein the composition is applied to a plant part or plant seed, and wherein the composition comprises an effective amount of the microbial strain or isolate to decrease the severity or symptoms of disease by a crop plant grown, developed or regenerated from the plant part or plant seed after planting. 
     
     
         58 . The method of  claim 57 , wherein the composition comprises an effective amount of the microbial strain or isolate to decrease the severity or symptoms of the crop plant grown, developed or regenerated from the plant part or plant seed due to sudden death syndrome (SDS) caused by a  Fusarium  species, relative to a control plant grown, developed or regenerated from a plant part or plant seed not treated with the composition. 
     
     
         59 . A method of increasing the disease resistance of a crop plant comprising:
 (a) planting a plant part or seed, wherein the plant part or seed is at least partially coated with a composition comprising a microbial strain or isolate and an agriculturally acceptable carrier, wherein the microbial strain or isolate is heterologous with respect to the plant, plant part or plant seed, and   wherein the microbial strain or isolate has either or both of:
 (i) a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, and 
 (ii) a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1, and 
   (b) growing or regenerating the crop plant from the plant part or seed.   
     
     
         60 . The method of  claim 59 , further comprising:
 (c) harvesting seed from the crop plant.   
     
     
         61 . The method of  claim 59  or  60 , wherein the crop plant has one or more of the following improved traits under SDS disease pressure: increased yield, increased biomass, increased leaf area, increased bushels per acre, increased seed weight per plant, increased seed number, increased pod length, increased number of filled pods, increased number of pods, improved nutritional content, greater resistance to lodging, increased root length, improved plant growth or vigor, increased stress tolerance, increased harvest index, and increased bushels per acre. 
     
     
         62 . A method of increasing the disease resistance of a crop plant comprising:
 (a) applying to the crop plant a composition comprising a microbial strain or isolate and an agriculturally acceptable carrier,   wherein the microbial strain or isolate is heterologous with respect to the crop plant, and wherein the microbial strain or isolate has either or both of:
 (i) a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, and 
 (ii) a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1, and 
   (b) growing or developing the crop plant.   
     
     
         63 . The method of  claim 62 , further comprising:
 (c) harvesting seed from the crop plant.   
     
     
         64 . The method of  claim 62  or  63 , wherein the composition is applied as a foliar treatment. 
     
     
         65 . The method of any one of  claims 62 - 64 , wherein the crop plant has one or more of the following traits under SDS disease pressure: increased yield, increased biomass, increased leaf area, increased bushels per acre, increased seed weight per plant, increased seed number, increased pod length, increased number of filled pods, increased number of pods, improved nutritional content, greater resistance to lodging, increased root length, improved plant growth or vigor, increased stress tolerance, increased harvest index, and increased bushels per acre. 
     
     
         66 . A method of decreasing the severity or symptoms of disease of a crop plant comprising:
 (a) applying to a growth medium associated with the crop plant a composition comprising a microbial strain or isolate and an agriculturally acceptable carrier,   wherein the microbial strain or isolate is heterologous with respect to the crop plant, and wherein the microbial strain or isolate has either or both of:
 (i) a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, and 
 (ii) a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1, and 
   (b) growing or developing the crop plant.   
     
     
         67 . The method of  claim 66 , further comprising:
 (c) harvesting seed from the crop plant.   
     
     
         68 . The method of  claim 66  or  67 , wherein the composition is applied to the growth medium as a drip, spray, irrigation or soil drench. 
     
     
         69 . The method of any one of  claims 66 - 68 , wherein the growth medium is soil. 
     
     
         70 . The method of any one of  claims 66 - 69 , wherein the crop plant has one or more of the following traits under SDS disease pressure: increased yield, increased biomass, increased leaf area, increased bushels per acre, increased seed weight per plant, increased seed number, increased pod length, increased number of filled pods, increased number of pods, improved nutritional content, greater resistance to lodging, increased root length, improved plant growth or vigor, increased stress tolerance, increased harvest index, and increased bushels per acre. 
     
     
         71 . A method of increasing the disease resistance of a crop plant comprising:
 (a) applying to a growth medium associated with a plant part or plant seed a composition comprising a microbial strain or isolate and an agriculturally acceptable carrier, wherein the microbial strain or isolate is heterologous with respect to the crop plant, and wherein the microbial strain or isolate has either or both of:
 (i) a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, and 
 (ii) a 16S rDNA sequence that is at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1, and 
   (b) growing or regenerating the crop plant from the plant part or plant seed.   
     
     
         72 . The method of  claim 71 , further comprising:
 (c) harvesting seed from the crop plant.   
     
     
         73 . The method of  claim 71  or  72 , wherein the composition is applied to the growth medium as a drip, spray, irrigation or soil drench. 
     
     
         74 . The method of any one of  claims 71 - 73 , wherein the growth medium is soil. 
     
     
         75 . The method of any one of  claims 71 - 74 , wherein the composition is applied to the growth medium before, simultaneously with, or after the plant part or plant seed being planted in the growth medium. 
     
     
         76 . The method of claim any one of  claims 71 - 75 , wherein the crop plant has one or more of the following traits under SDS disease pressure: increased yield, increased biomass, increased leaf area, increased bushels per acre, increased seed weight per plant, increased seed number, increased pod length, increased number of filled pods, increased number of pods, improved nutritional content, greater resistance to lodging, increased root length, improved plant growth or vigor, increased stress tolerance, increased harvest index, and increased bushels per acre. 
     
     
         77 . A modified microbial strain having a 16S rDNA sequence that is at least 99.9%, at least 99.95%, or 100% identical to SEQ ID NO: 1, wherein the modified microbial strain confers a positive agricultural trait or benefit to a crop plant when the crop plant is treated or associated with the modified microbial strain. 
     
     
         78 . A modified microbial strain having a partial or whole genome sequence that is at least 99%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.55%, at least 99.6%, at least 99.65%, at least 99.7%, at least 99.75%, at least 99.8%, at least 99.85%, at least 99.9%, or at least 99.95% identical to the corresponding partial or whole genome sequence of the bacterial strain or isolate deposited as ATCC accession number PTA-123716, wherein the modified microbial strain confers a positive agricultural trait or benefit to a crop plant when the crop plant is treated or associated with the modified microbial strain.