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Streptomyces species from the rhizosphere of the medicinal plant Artemisia herba-alba Asso: screening for biological activities. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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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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3
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Lozano-Huntelman NA, Zhou A, Tekin E, Cruz-Loya M, Østman B, Boyd S, Savage VM, Yeh P. Hidden suppressive interactions are common in higher-order drug combinations. iScience 2021; 24:102355. [PMID: 33870144 PMCID: PMC8044428 DOI: 10.1016/j.isci.2021.102355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/26/2021] [Accepted: 03/22/2021] [Indexed: 11/25/2022] Open
Abstract
The rapid increase of multi-drug resistant bacteria has led to a greater emphasis on multi-drug combination treatments. However, some combinations can be suppressive—that is, bacteria grow faster in some drug combinations than when treated with a single drug. Typically, when studying interactions, the overall effect of the combination is only compared with the single-drug effects. However, doing so could miss “hidden” cases of suppression, which occur when the highest order is suppressive compared with a lower-order combination but not to a single drug. We examined an extensive dataset of 5-drug combinations and all lower-order—single, 2-, 3-, and 4-drug—combinations. We found that a majority of all combinations—54%—contain hidden suppression. Examining hidden interactions is critical to understanding the architecture of higher-order interactions and can substantially affect our understanding and predictions of the evolution of antibiotic resistance under multi-drug treatments. Most instances of suppressive interactions are missed by standard methods A majority (54%) of all antibiotic combinations tested contain hidden suppression Identifying hidden suppression can affect what combinations should be used
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Affiliation(s)
| | - April Zhou
- Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USA.,Computational and Systems Biology, University of California, Los Angeles, 90095, USA
| | - Elif Tekin
- Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USA
| | - Mauricio Cruz-Loya
- Computational and Systems Biology, University of California, Los Angeles, 90095, USA
| | - Bjørn Østman
- Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USA
| | - Sada Boyd
- Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USA
| | - Van M Savage
- Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USA.,Computational and Systems Biology, University of California, Los Angeles, 90095, USA.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pamela Yeh
- Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USA.,Santa Fe Institute, Santa Fe, NM 87501, USA
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4
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Otto-Hanson LK, Kinkel LL. Densities and inhibitory phenotypes among indigenous Streptomyces spp. vary across native and agricultural habitats. MICROBIAL ECOLOGY 2020; 79:694-705. [PMID: 31656973 DOI: 10.1007/s00248-019-01443-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Streptomyces spp. perform vital roles in natural and agricultural soil ecosystems including in decomposition and nutrient cycling, promotion of plant growth and fitness, and plant disease suppression. Streptomyces densities can vary across the landscape, and inhibitory phenotypes are often a result of selection mediated by microbial competitive interactions in soil communities. Diverse environmental factors, including those specific to habitat, are likely to determine microbial densities in the soil and the outcomes of microbial species interactions. Here, we characterized indigenous Streptomyces densities and inhibitory phenotypes from soil samples (n = 82) collected in 6 distinct habitats across the Cedar Creek Ecosystem Science Reserve (CCESR; agricultural, prairie, savanna, wetland, wet-woodland, and forest). Significant variation in Streptomyces density and the frequency of antagonistic Streptomyces were observed among habitats. There was also significant variation in soil chemical properties among habitats, including percent carbon, percent nitrogen, available phosphorus, extractable potassium, and pH. Density and frequency of antagonists were significantly correlated with one or more environmental parameters across all habitats, though relationships with some parameters differed among habitats. In addition, we found that habitat rather than spatial proximity was a better predictor of variation in Streptomyces density and inhibitory phenotypes. Moreover, habitats least conducive for Streptomyces growth and proliferation, as determined by population density, had increased frequencies of inhibitory phenotypes. Identifying environmental parameters that structure variation in density and frequency of antagonistic Streptomyces can provide insight for determining factors that mediate selection for inhibitory phenotypes across the landscape.
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Affiliation(s)
- L K Otto-Hanson
- University of Minnesota-Twin Cities, 1991 Upper Buford Circle, 495 Borlaug Hall, Saint Paul, MN, 55108, USA.
| | - L L Kinkel
- University of Minnesota-Twin Cities, 1991 Upper Buford Circle, 495 Borlaug Hall, Saint Paul, MN, 55108, USA
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5
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Dundore-Arias JP, Castle SC, Felice L, Dill-Macky R, Kinkel LL. Carbon Amendments Influence Composition and Functional Capacities of Indigenous Soil Microbiomes. Front Mol Biosci 2020; 6:151. [PMID: 31993439 PMCID: PMC6964746 DOI: 10.3389/fmolb.2019.00151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/10/2019] [Indexed: 02/01/2023] Open
Abstract
Soil nutrient amendments are recognized for their potential to improve microbial activity and biomass in the soil. However, the specific selective impacts of carbon amendments on indigenous microbiomes and their metabolic functions in agricultural soils remain poorly understood. We investigated the changes in soil chemical characteristics and phenotypes of Streptomyces communities following carbon amendments to soil. Mesocosms were established with soil from two field sites varying in soil organic matter content (low organic matter, LOM; high organic matter, HOM), that were amended at intervals over nine months with low or high dose solutions of glucose, fructose, malic acid, a mixture of these compounds, or water only (non-amended control). Significant shifts in soil chemical characteristics and antibiotic inhibitory capacities of indigenous Streptomyces were observed in response to carbon additions. All high dose carbon amendments consistently increased soil total carbon, while amendments with malic acid decreased soil pH. In LOM soils, higher frequencies of Streptomyces inhibitory phenotypes of the two plant pathogens, Streptomyces scabies and Fusarium oxysporum, were observed in response to soil carbon additions. Additionally, to determine if shifts in Streptomyces functional characteristics correlated with microbiome composition, we investigated whether shifts in functional characteristics of soil Streptomyces correlated with composition of soil bacterial communities, analyzed using 16S rRNA gene sequencing. Regardless of dose, community composition differed significantly among carbon-amended and non-amended soils from both sites. Carbon type and dose had significant effects on bacterial community composition in both LOM and HOM soils. Relationships among microbial community richness (observed species number), diversity, and soil characteristics varied among soils from different sites. These results suggest that manipulation of soil resource availability has the potential to selectively modify the functional capacities of soil microbiomes, and specifically to enhance pathogen inhibitory populations of high value to agricultural systems.
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Affiliation(s)
- José Pablo Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA, United States.,Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Sarah C Castle
- Plant Science Research Unit, USDA-ARS, Saint Paul, MN, United States
| | - Laura Felice
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
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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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7
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Tekin E, White C, Kang TM, Singh N, Cruz-Loya M, Damoiseaux R, Savage VM, Yeh PJ. Prevalence and patterns of higher-order drug interactions in Escherichia coli. NPJ Syst Biol Appl 2018; 4:31. [PMID: 30181902 PMCID: PMC6119685 DOI: 10.1038/s41540-018-0069-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 01/23/2023] Open
Abstract
Interactions and emergent processes are essential for research on complex systems involving many components. Most studies focus solely on pairwise interactions and ignore higher-order interactions among three or more components. To gain deeper insights into higher-order interactions and complex environments, we study antibiotic combinations applied to pathogenic Escherichia coli and obtain unprecedented amounts of detailed data (251 two-drug combinations, 1512 three-drug combinations, 5670 four-drug combinations, and 13608 five-drug combinations). Directly opposite to previous assumptions and reports, we find higher-order interactions increase in frequency with the number of drugs in the bacteria’s environment. Specifically, as more drugs are added, we observe an elevated frequency of net synergy (effect greater than expected based on independent individual effects) and also increased instances of emergent antagonism (effect less than expected based on lower-order interaction effects). These findings have implications for the potential efficacy of drug combinations and are crucial for better navigating problems associated with the combinatorial complexity of multi-component systems. Interactions play an important role in determining the dynamics of complex systems yet higher-order interactions that involve more than two components are poorly understood. A research team from University of California, Los Angeles led by Pamela Yeh, use a bacteria system to show that higher-order interactions among antibiotics are prevalent and also that there are systematic patterns in how they occur: the frequency of higher-order interactions increases with the number of components, net interactions tend to be more synergistic, and emergent interactions—arising at specific higher-order levels—tend toward antagonism. By detecting patterns in interactions as the number of drugs increases, they provide a method to handle the combinatorial complexity that results from higher-order interactions, yielding a solid foundation for exploring the patterns and consequences of emergent phenomena in other research areas.
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Affiliation(s)
- Elif Tekin
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA.,2Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA 90095 USA
| | - Cynthia White
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| | - Tina Manzhu Kang
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| | - Nina Singh
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
| | - Mauricio Cruz-Loya
- 2Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA 90095 USA
| | - Robert Damoiseaux
- 3California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, CA 90095 USA
| | - Van M Savage
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA.,2Department of Biomathematics, University of California, David Geffen School of Medicine, Los Angeles, CA 90095 USA.,4Santa Fe Institute, Santa Fe, NM 87501 USA
| | - Pamela J Yeh
- 1Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA.,4Santa Fe Institute, Santa Fe, NM 87501 USA
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8
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Staley C, Breuillin-Sessoms F, Wang P, Kaiser T, Venterea RT, Sadowsky MJ. Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils. Front Microbiol 2018; 9:634. [PMID: 29670600 PMCID: PMC5893814 DOI: 10.3389/fmicb.2018.00634] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs.
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Affiliation(s)
- Christopher Staley
- The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | | | - Ping Wang
- The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Thomas Kaiser
- The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Rodney T Venterea
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, United States.,Soil and Water Management Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, United States.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
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9
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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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10
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Bardin M, Ajouz S, Comby M, Lopez-Ferber M, Graillot B, Siegwart M, Nicot PC. Is the efficacy of biological control against plant diseases likely to be more durable than that of chemical pesticides? FRONTIERS IN PLANT SCIENCE 2015; 6:566. [PMID: 26284088 PMCID: PMC4515547 DOI: 10.3389/fpls.2015.00566] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/09/2015] [Indexed: 05/18/2023]
Abstract
The durability of a control method for plant protection is defined as the persistence of its efficacy in space and time. It depends on (i) the selection pressure exerted by it on populations of plant pathogens and (ii) on the capacity of these pathogens to adapt to the control method. Erosion of effectiveness of conventional plant protection methods has been widely studied in the past. For example, apparition of resistance to chemical pesticides in plant pathogens or pests has been extensively documented. The durability of biological control has often been assumed to be higher than that of chemical control. Results concerning pest management in agricultural systems have shown that this assumption may not always be justified. Resistance of various pests to one or several toxins of Bacillus thuringiensis and apparition of resistance of the codling moth Cydia pomonella to the C. pomonella granulovirus have, for example, been described. In contrast with the situation for pests, the durability of biological control of plant diseases has hardly been studied and no scientific reports proving the loss of efficiency of biological control agents against plant pathogens in practice has been published so far. Knowledge concerning the possible erosion of effectiveness of biological control is essential to ensure a durable efficacy of biological control agents on target plant pathogens. This knowledge will result in identifying risk factors that can foster the selection of strains of plant pathogens resistant to biological control agents. It will also result in identifying types of biological control agents with lower risk of efficacy loss, i.e., modes of action of biological control agents that does not favor the selection of resistant isolates in natural populations of plant pathogens. An analysis of the scientific literature was then conducted to assess the potential for plant pathogens to become resistant to biological control agents.
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Affiliation(s)
- Marc Bardin
- Plant Pathology Unit, Institut National de la Recherche Agronomique, UR407, Montfavet, France
| | - Sakhr Ajouz
- Plant Pathology Unit, Institut National de la Recherche Agronomique, UR407, Montfavet, France
| | - Morgane Comby
- Plant Pathology Unit, Institut National de la Recherche Agronomique, UR407, Montfavet, France
| | - Miguel Lopez-Ferber
- Laboratoire de Génie de l’Environnement Industriel, Ecole des Mines d’Alès, Institut Mines-Telecom, Alès, France
| | - Benoît Graillot
- Laboratoire de Génie de l’Environnement Industriel, Ecole des Mines d’Alès, Institut Mines-Telecom, Alès, France
- Natural Plant Protection,Arysta LifeScience Group, Pau, France
| | - Myriam Siegwart
- Plantes et Systèmes de Culture Horticoles Unit, Institut National de la Recherche Agronomique, UR1115, Avignon, France
| | - Philippe C. Nicot
- Plant Pathology Unit, Institut National de la Recherche Agronomique, UR407, Montfavet, France
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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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12
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Weiland JE. Pythium Species and Isolate Diversity Influence Inhibition by the Biological Control Agent Streptomyces lydicus. PLANT DISEASE 2014; 98:653-659. [PMID: 30708563 DOI: 10.1094/pdis-05-13-0482-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Disease control of soilborne pathogens by biological control agents (BCAs) is often inconsistent under field conditions. This inconsistency may be partly influenced by pathogen diversity if there is a differential response among pathogen species and isolates to selected BCAs. The responses of 148 Pythium isolates obtained from soil at three forest nurseries and representative of 16 Pythium spp. were evaluated in the presence of Streptomyces lydicus strain WYEC108 in an in vitro assay. Percent growth inhibition, inhibition zone distance, mortality, and growth rate were recorded for each isolate, and data were analyzed for effects of species and isolate. Responses of three Pythium spp. (Pythium irregulare, P. sylvaticum, and P. ultimum) were further analyzed for a location (nursery) effect. Although S. lydicus inhibited all Pythium isolates, differences in percent growth inhibition, inhibition zone distance, and mortality were observed among Pythium spp. and isolates. Small but significant location effects were also noted. Growth rate also varied among Pythium spp. and isolates and was found to strongly bias percent growth inhibition and, to a lesser degree, inhibition zone distance; depending on which measure was used, slower-growing isolates appeared less sensitive (growth inhibition) or more sensitive (inhibition zone) to S. lydicus than faster-growing isolates. Results illustrate the importance of using multiple, representative pathogen isolates in preliminary BCA inhibition assays as well as accounting for the effect of pathogen growth rate on pathogen inhibition by BCAs. Future studies should take pathogen diversity into account when evaluating biological control efficacy.
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Affiliation(s)
- Jerry E Weiland
- United States Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Oregon State University, Department of Botany and Plant Pathology, Corvallis 97331
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13
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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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Schlatter DC, DavelosBaines AL, Xiao K, Kinkel LL. Resource use of soilborne Streptomyces varies with location, phylogeny, and nitrogen amendment. MICROBIAL ECOLOGY 2013; 66:961-971. [PMID: 23959115 DOI: 10.1007/s00248-013-0280-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/06/2013] [Indexed: 06/02/2023]
Abstract
In this study, we explore variation in resource use among Streptomyces in prairie soils. Resource use patterns were highly variable among Streptomyces isolates and were significantly related to location, phylogeny, and nitrogen (N) amendment history. Streptomyces populations from soils less than 1 m apart differed significantly in their ability to use resources, indicating that drivers of resource use phenotypes in soil are highly localized. Variation in resource use within Streptomyces genetic groups was significantly associated with the location from which Streptomyces were isolated, suggesting that resource use is adapted to local environments. Streptomyces from soils under long-term N amendment used fewer resources and grew less efficiently than those from non-amended soils, demonstrating that N amendment selects for Streptomyces with more limited catabolic capacities. Finally, resource use among Streptomyces populations was correlated with soil carbon content and Streptomyces population densities. We hypothesize that variation in resource use among Streptomyces reflects adaptation to local resource availability and competitive species interactions in soil and that N amendments alter selection for resource use phenotypes.
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Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. ISME JOURNAL 2013; 8:249-56. [PMID: 24152720 DOI: 10.1038/ismej.2013.175] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 11/08/2022]
Abstract
Soil bacteria produce a diverse array of antibiotics, yet our understanding of the specific roles of antibiotics in the ecological and evolutionary dynamics of microbial interactions in natural habitats remains limited. Here, we show a significant role for antibiotics in mediating antagonistic interactions and nutrient competition among locally coexisting Streptomycete populations from soil. We found that antibiotic inhibition is significantly more intense among sympatric than allopatric Streptomycete populations, indicating local selection for inhibitory phenotypes. For sympatric but not allopatric populations, antibiotic inhibition is significantly positively correlated with niche overlap, indicating that inhibition is targeted toward bacteria that pose the greatest competitive threat. Our results support the hypothesis that antibiotics serve as weapons in mediating local microbial interactions in soil and suggest that coevolutionary niche displacement may reduce the likelihood of an antibiotic arms race. Further insight into the diverse roles of antibiotics in microbial ecology and evolution has significant implications for understanding the persistence of antibiotic inhibitory and resistance phenotypes in environmental microbes, optimizing antibiotic drug discovery and developing strategies for managing microbial coevolutionary dynamics to enhance inhibitory phenotypes.
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