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Lane BR, Anderson HM, Dicko AH, Fulcher MR, Kinkel LL. Temporal variability in nutrient use among Streptomyces suggests dynamic niche partitioning. Environ Microbiol 2023; 25:3527-3535. [PMID: 37669222 DOI: 10.1111/1462-2920.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023]
Abstract
Soil bacteria spend significant periods in dormant or semi-dormant states that are interrupted by resource pulses which can lead to periods of rapid growth and intense nutrient competition. Microbial populations have evolved diverse strategies to circumvent competitive interactions and facilitate coexistence. Here, we show that nutrient use of soilborne Streptomyces is temporally partitioned during experimental resource pulses, leading to reduced niche overlap, and potential coexistence. Streptomyces grew rapidly on the majority of distinct 95 carbon sources but varied in which individual resources were utilized in the first 24 h. Only a handful of carbon sources (19 out of 95) were consistently utilized (>95% of isolates) most rapidly in the first 24 h. These consistently utilized carbon sources also generated the majority of biomass accumulated by isolates. Our results shed new light on a novel mechanism microbes may employ to alleviate competitive interactions by temporally partitioning the consumption of carbon resources. As competitive interactions have been proposed to drive the suppression of disease-causing microbes in agronomic soils, our findings may hold widespread implications for soil management for plant health.
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Affiliation(s)
- Brett R Lane
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Hannah M Anderson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Amadou H Dicko
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Faculty of Agronomy and Animal Sciences, University of Segou, Ségou, Mali
| | - Michael R Fulcher
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research, Frederick, Maryland, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
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2
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Kopecky J, Kamenik Z, Omelka M, Novotna J, Stefani T, Sagova-Mareckova M. Phylogenetically related soil actinomycetes distinguish isolation sites by their metabolic activities. FEMS Microbiol Ecol 2023; 99:fiad139. [PMID: 37935470 DOI: 10.1093/femsec/fiad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/24/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Soil environments are inhabited by microorganisms adapted to its diversified microhabitats. The metabolic activity of individual strains/populations reflects resources available at a particular spot, quality of which may not comply with broad soil characteristics. To explore the potential of individual strains to adapt to particular micro-niches of carbon sources, a set of 331 Actinomycetia strains were collected at ten sites differing in vegetation, soil pH, organic matter content and quality. The strains were isolated on the same complex medium with neutral pH and their metabolites analyzed by UHPLC and LC-MS/MS in spent cultivation medium (metabolic profiles). For all strains, their metabolic profiles correlated with soil pH and organic matter content of the original sites. In comparison, strains phylogeny based on either 16S rRNA or the beta-subunit of DNA-dependent RNA polymerase (rpoB) genes was partially correlated with soil organic matter content but not soil pH at the sites. Antimicrobial activities of strains against Kocuria rhizophila, Escherichia coli, and Saccharomyces cerevisiae were both site- and phylogeny-dependent. The precise adaptation of metabolic profiles to overall sites characteristics was further supported by the production of locally specific bioactive metabolites and suggested that carbon resources represent a significant selection pressure connected to specific antibiotic activities.
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Affiliation(s)
- Jan Kopecky
- Epidemiology and Ecology of Microorganisms, Crop Research Institute, 161 06 Prague, Czechia
| | - Zdenek Kamenik
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology, Czech Acad Sci, 142 20 Prague, Czechia
| | - Marek Omelka
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, 186 75 Prague, Czechia
| | - Jitka Novotna
- Epidemiology and Ecology of Microorganisms, Crop Research Institute, 161 06 Prague, Czechia
| | - Tommaso Stefani
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology, Czech Acad Sci, 142 20 Prague, Czechia
| | - Marketa Sagova-Mareckova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 21 Prague, Czechia
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3
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Ndinga-Muniania C, Wornson N, Fulcher MR, Borer ET, Seabloom EW, Kinkel L, May G. Cryptic functional diversity within a grass mycobiome. PLoS One 2023; 18:e0287990. [PMID: 37471328 PMCID: PMC10358963 DOI: 10.1371/journal.pone.0287990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 07/22/2023] Open
Abstract
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nicholas Wornson
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael R Fulcher
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Linda Kinkel
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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4
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Chen S, Wang L, Zhang S, Li N, Wei X, Wei Y, Wei L, Li J, Huang S, Chen Q, Zhang T, Bolan NS. Soil organic carbon stability mediate soil phosphorus in greenhouse vegetable soil by shifting phoD-harboring bacterial communities and keystone taxa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162400. [PMID: 36842585 DOI: 10.1016/j.scitotenv.2023.162400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Addition of organic amendments, such as manure and straw, to arable fields as a partial substitute for mineral phosphorus (P), are a sustainable practice in high-efficiency agricultural production. Different organic inputs may induce varied soil organic carbon (OC) stability and phoD harboring microbes, subsequently regulate P behavior, but the underlying mechanisms are poorly understood. A 11-year field experiment examined P forms by 31P-nuclear magnetic resonance (NMR), OC chemical composition by 13C NMR, and biologically-based P availability methods, phoD bacterial communities, and their co-occurrence in soils amended with chemical P fertilizer (CF), chemical P partly substituted by organic amendments including pig manure (CM), a mixture of pig manure and corn straw (CMS), and corn straw (CS), with equal P input in all treatments. Organic amendments significantly increased soil labile Pi (CaCl2-P, citrate-P, 2.91-3.26 and 1.16-1.32 times higher than CF) and Po (enzyme-P, diesters, 4.08-7.47 and 1.71-2.14 times higher than CF) contents and phosphatase activities, while significantly decreased aromaticity (AI) and recalcitrance indexes (RI) of soil C, compared with CF. The keystone genera in manured soils (Alienimomas and Streptomyces) and straw-applied soils (Janthinobacterium and Caulobacter) were significantly correlated with soil enzyme-P, microbial biomass P (MBP), diesters, and citrate-P. Soil AI and RI were significantly correlated with the phoD keystone and soil P species. It suggested that the keystone was impacted by soil OC stability and play a role in regulating P redistribution in amended soils. This study highlights how manure and straw incorporation altered soil OC stability, shaped the phoD harboring community, and enhanced soil P biological processes promoted by the keystone taxa. The partial substitution of mineral P by mixture of manure and straw is effectively promote soil P availability and beneficial for environmental sustainability.
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Affiliation(s)
- Shuo Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
| | - Liying Wang
- Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China
| | - Shuai Zhang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
| | - Naihui Li
- Department of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Xiaomeng Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yuquan Wei
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, PR China
| | - Lulu Wei
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
| | - Ji Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, PR China
| | - Shaowen Huang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
| | - Qing Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China.
| | - Tao Zhang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
| | - Nanthi S Bolan
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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5
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Wang Y, Wilhelm RC, Swenson TL, Silver A, Andeer PF, Golini A, Kosina SM, Bowen BP, Buckley DH, Northen TR. Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies. Front Microbiol 2022; 13:914472. [PMID: 35756023 PMCID: PMC9225577 DOI: 10.3389/fmicb.2022.914472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.
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Affiliation(s)
- Ying Wang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anita Silver
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amber Golini
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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6
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Wadler CS, Wolters JF, Fortney NW, Throckmorton KO, Zhang Y, Miller CR, Schneider RM, Wendt-Pienkowski E, Currie CR, Donohue TJ, Noguera DR, Hittinger CT, Thomas MG. Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:70. [PMID: 35751080 PMCID: PMC9233362 DOI: 10.1186/s13068-022-02168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. RESULTS We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. CONCLUSIONS We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.
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Affiliation(s)
- Caryn S Wadler
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - John F Wolters
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Nathaniel W Fortney
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Kurt O Throckmorton
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Yaoping Zhang
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Caroline R Miller
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Rachel M Schneider
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Evelyn Wendt-Pienkowski
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Daniel R Noguera
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Chris Todd Hittinger
- Wisconsin Energy Institute, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 425-g Henry Mall, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI, 53706, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA.
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7
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Michalska-Smith M, Song Z, Spawn-Lee SA, Hansen ZA, Johnson M, May G, Borer ET, Seabloom EW, Kinkel LL. Network structure of resource use and niche overlap within the endophytic microbiome. THE ISME JOURNAL 2022; 16:435-446. [PMID: 34413476 PMCID: PMC8776778 DOI: 10.1038/s41396-021-01080-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function.
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Affiliation(s)
- Matthew Michalska-Smith
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA.
- Department of Plant Pathology, University of Minnesota, St Paul, MN, USA.
| | - Zewei Song
- Department of Plant Pathology, University of Minnesota, St Paul, MN, USA
| | - Seth A Spawn-Lee
- Department of Geography, University of Wisconsin, Madison, WI, USA
- Center for Sustainability and the Global Environment (SAGE), University of Wisconsin, Madison, WI, USA
| | - Zoe A Hansen
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Mitch Johnson
- Department of Horticultural Science, University of Minnesota, St Paul, MN, USA
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, USA
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, St Paul, MN, USA
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8
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Easterday CA, Kendig AE, Lacroix C, Seabloom EW, Borer ET. Long-term nitrogen enrichment mediates the effects of nitrogen supply and co-inoculation on a viral pathogen. Ecol Evol 2022; 12:e8450. [PMID: 35136545 PMCID: PMC8809429 DOI: 10.1002/ece3.8450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 11/12/2022] Open
Abstract
Host nutrient supply can mediate host-pathogen and pathogen-pathogen interactions. In terrestrial systems, plant nutrient supply is mediated by soil microbes, suggesting a potential role of soil microbes in plant diseases beyond soil-borne pathogens and induced plant defenses. Long-term nitrogen (N) enrichment can shift pathogenic and nonpathogenic soil microbial community composition and function, but it is unclear if these shifts affect plant-pathogen and pathogen-pathogen interactions. In a growth chamber experiment, we tested the effect of long-term N enrichment on infection by Barley Yellow Dwarf Virus (BYDV-PAV) and Cereal Yellow Dwarf Virus (CYDV-RPV), aphid-vectored RNA viruses, in a grass host. We inoculated sterilized growing medium with soil collected from a long-term N enrichment experiment (ambient, low, and high N soil treatments) to isolate effects mediated by the soil microbial community. We crossed soil treatments with a N supply treatment (low, high) and virus inoculation treatment (mock-, singly-, and co-inoculated) to evaluate the effects of long-term N enrichment on plant-pathogen and pathogen-pathogen interactions, as mediated by N availability. We measured the proportion of plants infected (i.e., incidence), plant biomass, and leaf chlorophyll content. BYDV-PAV incidence (0.96) declined with low N soil (to 0.46), high N supply (to 0.61), and co-inoculation (to 0.32). Low N soil mediated the effect of N supply on BYDV-PAV: instead of N supply reducing BYDV-PAV incidence, the incidence increased. Additionally, ambient and low N soil ameliorated the negative effect of co-inoculation on BYDV-PAV incidence. BYDV-PAV infection only reduced chlorophyll when plants were grown with low N supply and ambient N soil. There were no significant effects of long-term N soil on CYDV-RPV incidence. Soil inoculant with different levels of long-term N enrichment had different effects on host-pathogen and pathogen-pathogen interactions, suggesting that shifts in soil microbial communities with long-term N enrichment may mediate disease dynamics.
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Affiliation(s)
- Casey A. Easterday
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
- Present address:
Carlson School of ManagementUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Amy E. Kendig
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Christelle Lacroix
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
- Present address:
Pathologie VégétaleINRAEMontfavetFrance
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSt. PaulMinnesotaUSA
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9
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Higgins SA, Panke-Buisse K, Buckley DH. The biogeography of Streptomyces in New Zealand enabled by high-throughput sequencing of genus-specific rpoB amplicons. Environ Microbiol 2020; 23:1452-1468. [PMID: 33283920 DOI: 10.1111/1462-2920.15350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/02/2020] [Indexed: 01/10/2023]
Abstract
We evaluated Streptomyces biogeography in soils along a 1200 km latitudinal transect across New Zealand (NZ). Streptomyces diversity was examined using high-throughput sequencing of rpoB amplicons generated with a Streptomyces specific primer set. We detected 1287 Streptomyces rpoB operational taxonomic units (OTUs) with 159 ± 92 (average ± SD) rpoB OTUs per site. Only 12% (n = 149) of these OTUs matched rpoB sequences from cultured specimens (99% nucleotide identity cutoff). Streptomyces phylogenetic diversity (Faith's PD) was correlated with soil pH, mean annual temperature and plant community richness (Spearman's r: 0.77, 0.64 and -0.79, respectively; P < 0.05), but not with latitude. In addition, soil pH and plant community richness both explained significant variation in Streptomyces beta diversity. Streptomyces communities exhibited both high dissimilarity and strong dominance of one or a few species at each site. Taken together, these results suggest that dispersal limitation due to competitive interactions limits the colonization success of spores that relocate to new sites. Cultivated Streptomyces isolates represent a major source of clinically useful antibiotics, but only a small fraction of extant diversity within the genus have been identified and most species of Streptomyces have yet to be described.
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Affiliation(s)
- S A Higgins
- School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA.,Boyce Thompson Institute, Ithaca, NY, USA
| | - K Panke-Buisse
- School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA.,USDA Agricultural Research Service, Madison, WI, USA
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10
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Dundore-Arias JP, Felice L, Dill-Macky R, Kinkel LL. Carbon Amendments Induce Shifts in Nutrient Use, Inhibitory, and Resistance Phenotypes Among Soilborne Streptomyces. Front Microbiol 2019; 10:498. [PMID: 30972036 PMCID: PMC6445949 DOI: 10.3389/fmicb.2019.00498] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 02/26/2019] [Indexed: 11/13/2022] Open
Abstract
Carbon amendments are used in agriculture for increasing microbial activity and biomass in the soil. Changes in microbial community composition and function in response to carbon additions to soil have been associated with biological suppression of soilborne diseases. However, the specific selective impacts of carbon amendments on microbial antagonistic populations are not well understood. We investigated the effects of soil carbon amendments on nutrient use profiles, and antibiotic inhibitory and resistance phenotypes of Streptomyces populations from agricultural soils. Soil mesocosms were amended at intervals over 9 months with low or high dose solutions of glucose, fructose, a complex amendment, or water only (non-amendment control). Over 130 Streptomyces isolates were collected from amended and non-amended mesocosm soils, and nutrient utilization profiles on 95 different carbon substrates were determined. A subset of isolates (n = 40) was characterized for their ability to inhibit or resist one another. Carbon amendments resulted in Streptomyces populations with greater niche widths, and increased growth efficiencies as compared with Streptomyces in non-amended soils. Shifts in microbial nutrient use and growth capacities coincided with positive selection for Streptomyces antibiotic inhibitory phenotypes in carbon-amended soils, resulting in populations dominated by phenotypes that combine both antagonistic capacities and a generalist lifestyle. Carbon inputs resulted in populations that on average were more resistant to one another than populations in non-amended soils. Shifts in metabolic capacities and antagonistic activity indicate that carbon additions to soil may selectively enrich Streptomyces antagonistic phenotypes, that are rare under non-nutrient selection, but can inhibit more intensively nutrient competitors, and resist phenotypes with similar functional traits. These results shed light on the potential for using carbon amendments to strategically mediate soil microbial community assembly, and contribute to the establishment of pathogen-suppressive soils in agricultural systems.
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Affiliation(s)
| | - Laura Felice
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
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11
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Hayden HL, Rochfort SJ, Ezernieks V, Savin KW, Mele PM. Metabolomics approaches for the discrimination of disease suppressive soils for Rhizoctonia solani AG8 in cereal crops using 1H NMR and LC-MS. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1627-1638. [PMID: 30360288 DOI: 10.1016/j.scitotenv.2018.09.249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies.
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Affiliation(s)
- Helen L Hayden
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia.
| | - Simone J Rochfort
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Vilnis Ezernieks
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Keith W Savin
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Pauline M Mele
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
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12
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Antony-Babu S, Stien D, Eparvier V, Parrot D, Tomasi S, Suzuki MT. Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences. Sci Rep 2017; 7:11089. [PMID: 28894255 PMCID: PMC5593946 DOI: 10.1038/s41598-017-11363-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 08/23/2017] [Indexed: 11/19/2022] Open
Abstract
Microbial diversity studies using small subunit (SSU) rRNA gene sequences continue to advance our understanding of biological and ecological systems. Although a good predictor of overall diversity, using this gene to infer the presence of a species in a sample is more controversial. Here, we present a detailed polyphasic analysis of 10 bacterial strains isolated from three coastal lichens Lichina confinis, Lichina pygmaea and Roccella fuciformis with SSU rRNA gene sequences identical to the type strain of Streptomyces cyaneofuscatus. This analysis included phenotypic, microscopic, genetic and genomic comparisons and showed that despite their identical SSU rRNA sequences the strains had markedly different properties, and could be distinguished as 5 different species. Significantly, secondary metabolites profiles from these strains were also found to be different. It is thus clear that SSU rRNA based operational taxonomy units, even at the most stringent cut-off can represent multiple bacterial species, and that at least for the case of Streptomyces, strain de-replication based on SSU gene sequences prior to screening for bioactive molecules can miss potentially interesting novel molecules produced by this group that is notorious for the production of drug-leads.
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Affiliation(s)
- Sanjay Antony-Babu
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Didier Stien
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Véronique Eparvier
- CNRS, Institut de Chimie des Substances Naturelles, 91198, Gif-sur-Yvette cedex, France
| | - Delphine Parrot
- UMR CNRS 6226, Institut des Sciences Chimiques de Rennes, Equipe CORINT "Chimie Organique et Interface", UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire, 2 Avenue du Pr. Léon Bernard, F-35043, Rennes, France
| | - Sophie Tomasi
- UMR CNRS 6226, Institut des Sciences Chimiques de Rennes, Equipe CORINT "Chimie Organique et Interface", UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire, 2 Avenue du Pr. Léon Bernard, F-35043, Rennes, France
| | - Marcelino T Suzuki
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650, Banyuls-sur-Mer, France.
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13
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Tomihama T, Nishi Y, Mori K, Shirao T, Iida T, Uzuhashi S, Ohkuma M, Ikeda S. Rice Bran Amendment Suppresses Potato Common Scab by Increasing Antagonistic Bacterial Community Levels in the Rhizosphere. PHYTOPATHOLOGY 2016; 106:719-728. [PMID: 27050572 DOI: 10.1094/phyto-12-15-0322-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Potato common scab (PCS), caused by pathogenic Streptomyces spp., is a serious disease in potato production worldwide. Cultural practices, such as optimizing the soil pH and irrigation, are recommended but it is often difficult to establish stable disease reductions using these methods. Traditionally, local farmers in southwest Japan have amended soils with rice bran (RB) to suppress PCS. However, the scientific mechanism underlying disease suppression by RB has not been elucidated. The present study showed that RB amendment reduced PCS by repressing the pathogenic Streptomyces population in young tubers. Amplicon sequencing analyses of 16S ribosomal RNA genes from the rhizosphere microbiome revealed that RB amendment dramatically changed bacterial composition and led to an increase in the relative abundance of gram-positive bacteria such as Streptomyces spp., and this was negatively correlated with PCS disease severity. Most actinomycete isolates derived from the RB-amended soil showed antagonistic activity against pathogenic Streptomyces scabiei and S. turgidiscabies on R2A medium. Some of the Streptomyces isolates suppressed PCS when they were inoculated onto potato plants in a field experiment. These results suggest that RB amendment increases the levels of antagonistic bacteria against PCS pathogens in the potato rhizosphere.
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Affiliation(s)
- Tsuyoshi Tomihama
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Yatsuka Nishi
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Kiyofumi Mori
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Tsukasa Shirao
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Toshiya Iida
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Shihomi Uzuhashi
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Moriya Ohkuma
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Seishi Ikeda
- First, second, third, and fourth authors: Plant Pathology and Entomology Laboratory, Kagoshima Prefectural Institute for Agricultural Development, 2200 Oono, Kinpo-cho, Minamikyushu-shi, Kagoshima, 899-3401, Japan; fifth, sixth, and seventh authors: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, 3-1-1 Kounodai, Tsukuba, Ibaragi, 305-0074, Japan; and eighth author: Agricultural Research Center for Hokkaido, National Agricultural and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
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14
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Schlatter DC, Kinkel LL. Do tradeoffs structure antibiotic inhibition, resistance, and resource use among soil-borne Streptomyces? BMC Evol Biol 2015; 15:186. [PMID: 26370703 PMCID: PMC4570699 DOI: 10.1186/s12862-015-0470-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/27/2015] [Indexed: 01/01/2023] Open
Abstract
Background Tradeoffs among competing traits are believed to be crucial to the maintenance of diversity in complex communities. The production of antibiotics to inhibit competitors and resistance to antibiotic inhibition are two traits hypothesized to be critical to microbial fitness in natural habitats, yet data on costs or tradeoffs associated with these traits are limited. In this work we characterized tradeoffs between antibiotic inhibition or resistance capacities and growth efficiencies or niche widths for a broad collection of Streptomyces from soil. Results Streptomyces isolates tended to have either very little or very high inhibitory capacity. In contrast, Streptomyces isolates were most commonly resistant to antibiotic inhibition by an intermediate number of other isolates. Streptomyces with either very high antibiotic inhibitory or resistance capacities had less efficient growth and utilized a smaller number of resources for growth (smaller niche width) than those with low inhibition or resistance capacities, suggesting tradeoffs between antibiotic inhibitory or resistance and resource use phenotypes. Conclusions This work suggests that life-history tradeoffs may be crucial to the maintenance of the vast diversity of antibiotic inhibitory and resistance phenotypes found among Streptomyces in natural communities. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0470-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel C Schlatter
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA.
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15
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Sun P, Zhao X, Shangguan N, Chang D, Ma Q. The roles of inoculants’ carbon source use in the biocontrol of potato scab disease. Can J Microbiol 2015; 61:257-62. [DOI: 10.1139/cjm-2014-0655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the application of multiple strains in the biocontrol of plant diseases, multistrain inoculation is still constrained by its inconsistency in the field. Nutrients, especially carbons, play an important role in the biocontrol processes. However, little work has been done on the systematic estimation of inoculants’ carbon source use on biocontrol efficacies in vivo. In the present study, 7 nonpathogenic Streptomyces strains alone and in different combinations were inoculated as biocontrol agents against the potato scab disease, under field conditions and greenhouse treatments. The influence of the inoculants’ carbon source use properties on biocontrol efficacies was investigated. The results showed that increasing the number of inoculated strains did not necessarily result in greater biocontrol efficacy in vivo. However, single strains with higher growth rates or multiple strains with less carbon source competition had positive effects on the biocontrol efficacies. These findings may shed light on optimizing the consistent biocontrol of plant disease with the consideration of inoculants’ carbon source use properties.
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Affiliation(s)
- Pingping Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Xinbei Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Nini Shangguan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Dongwei Chang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Qing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
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16
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Sagova-Mareckova M, Daniel O, Omelka M, Kristufek V, Divis J, Kopecky J. Determination of factors associated with natural soil suppressivity to potato common scab. PLoS One 2015; 10:e0116291. [PMID: 25612311 PMCID: PMC4303419 DOI: 10.1371/journal.pone.0116291] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/06/2014] [Indexed: 11/19/2022] Open
Abstract
Common scab of potatoes is a disease, which is difficult to manage due to complex interactions of the pathogenic bacteria (Streptomyces spp.) with soil, microbial community and potato plants. In Bohemian-Moravian Highlands in the Czech Republic two sites (Vyklantice and Zdirec) were selected for a study of common scab disease suppressivity. At both sites, a field with low disease severity occurs next to one with high severity and the situation was regularly observed over four decades although all four fields undergo a crop rotation. In the four fields, quantities of bacteria, actinobacteria and the gene txtB from the biosynthetic gene cluster of thaxtomin, the main pathogenicity factor of common scab, were analyzed by real-time PCR. Microbial community structure was compared by terminal fragment length polymorphism analysis. Soil and potato periderm were characterized by contents of carbon, nitrogen, phosphorus, sulphur, calcium, magnesium, and iron. Quality of organic matter was assessed by high performance liquid chromatography of soil extracts. The study demonstrated that the suppressive character of the fields is locally specific. At Zdirec, the suppressivity was associated with low txtB gene copies in bulk soil, while at Vyklantice site it was associated with low txtB gene copies in the tuberosphere. The differences were discussed with respect to the effect of abiotic conditions at Zdirec and interaction between potato plant and soil microbial community at Vyklantice. Soil pH, Ca soil content or cation concentrations, although different were not in the range to predict the disease severity. Low severity of common scab was associated with low content of soil C, N, C/N, Ca and Fe suggesting that oligotrophic conditions may be favorable to common scab suppression.
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Affiliation(s)
- Marketa Sagova-Mareckova
- Crop Research Institute, Dept. Epidemiology and Ecology of Microorganisms, Prague, Czech Republic
- * E-mail:
| | - Ondrej Daniel
- Crop Research Institute, Dept. Epidemiology and Ecology of Microorganisms, Prague, Czech Republic
| | - Marek Omelka
- Faculty of Mathematics and Physics, Dept. Probability and Mathematical Statistics, Charles University, Prague, Czech Republic
| | - Vaclav Kristufek
- Biology Centre of the Academy of Sciences of the Czech Republic, v. v. i., Institute of Soil Biology, Ceske Budejovice, Czech Republic
| | - Jiri Divis
- Faculty of Agriculture, Dept. Plant Production, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Jan Kopecky
- Crop Research Institute, Dept. Epidemiology and Ecology of Microorganisms, Prague, Czech Republic
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17
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Becklund KK, Kinkel LL, Powers JS. Landscape-scale Variation in Pathogen-suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica. Biotropica 2014. [DOI: 10.1111/btp.12155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Kristen K. Becklund
- Department of Ecology, Evolution and Behavior; University of Minnesota; 100 Ecology Building 1987 Upper Buford Circle St. Paul MN 55108 U.S.A
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; St. Paul MN 55108 U.S.A
| | - Jennifer S. Powers
- Department of Ecology, Evolution and Behavior; University of Minnesota; 100 Ecology Building 1987 Upper Buford Circle St. Paul MN 55108 U.S.A
- Department of Plant Biology; University of Minnesota; St. Paul MN 55108 U.S.A
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18
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Vaz Jauri P, Kinkel LL. Nutrient overlap, genetic relatedness and spatial origin influence interaction-mediated shifts in inhibitory phenotype amongStreptomycesspp. FEMS Microbiol Ecol 2014; 90:264-75. [DOI: 10.1111/1574-6941.12389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/18/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Patricia Vaz Jauri
- Department of Plant Pathology; University of Minnesota; Twin Cities MN USA
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; Twin Cities MN USA
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19
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Schlatter DC, Kinkel LL. Global biogeography ofStreptomycesantibiotic inhibition, resistance, and resource use. FEMS Microbiol Ecol 2014; 88:386-97. [DOI: 10.1111/1574-6941.12307] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/10/2014] [Accepted: 02/13/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; Saint Paul MN USA
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20
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Bakker MG, Schlatter DC, Otto-Hanson L, Kinkel LL. Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome. Mol Ecol 2013; 23:1571-1583. [DOI: 10.1111/mec.12571] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/20/2013] [Accepted: 09/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew G. Bakker
- Center for Rhizosphere Biology; Colorado State University; Fort Collins CO 80523-1173 USA
| | - Daniel C. Schlatter
- Department of Plant Pathology; University of Minnesota; Saint Paul MN 55108 USA
| | - Lindsey Otto-Hanson
- Department of Plant Pathology; University of Minnesota; Saint Paul MN 55108 USA
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; Saint Paul MN 55108 USA
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