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Michalska-Smith M, Schlatter DC, Pombubpa N, Castle SC, Grandy AS, Borer ET, Seabloom EW, Kinkel LL. Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes. Front Microbiol 2024; 15:1452534. [PMID: 39435438 PMCID: PMC11491370 DOI: 10.3389/fmicb.2024.1452534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/27/2024] [Indexed: 10/23/2024] Open
Abstract
Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.
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Affiliation(s)
- Matthew Michalska-Smith
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
| | - Daniel C. Schlatter
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Plant Science Research Unit, St. Paul, MN, United States
| | - Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Sarah C. Castle
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - A. Stuart Grandy
- Center for Biogeochemistry and Microbial Ecology (Soil BioME), University of New Hampshire, Durham, NC, United States
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NC, United States
| | - Elizabeth T. Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
| | - Eric W. Seabloom
- Department of Ecology, Evolution and Behavior, 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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2
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Shi F, Yang D, Meng X, Li J, Zhu Y, Liu J. Effects of Paecilomyces lilacinus and Bacillus pumilus on stem nematode and rhizosphere bacterial communities of sweet potato. Sci Rep 2024; 14:23290. [PMID: 39375441 PMCID: PMC11458784 DOI: 10.1038/s41598-024-74268-w] [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: 03/12/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024] Open
Abstract
Stem nematode (Ditylenchus destructor Thorne) is considered one of the most economically devastating species affecting sweet potato production. Biocontrol offers a sustainable strategy for nematode control. This study conducted a pot experiment to evaluate the biocontrol efficacy of Paecilomyces lilacinus CS-Z and Bacillus pumilus Y-26 against the stem nematode, as well as to examine their influence on the bacterial communities in the sweet potato rhizosphere. The findings indicated that B.pumilus Y-26 and P.lilacinus CS-Z exhibited respective suppression rates of 82.9% and 85.1% against the stem nematode, while also stimulating sweet potato plant growth. Both high-throughput sequencing and Biolog analysis revealed distinct impacts of the treatments on the bacterial communities. At the phylum level, B.pumilus Y-26 enhanced the abundance of Actinobacteria but reduced the abundance of Cyanobacteria, with P.lilacinus CS-Z exhibiting similar effects. Additionally, the treatment with B.pumilus Y-26 resulted in increased abundances of Crossiella, Gaiella, Bacillus, and Streptomyces at the genus level, while the treatment with P.lilacinus CS-Z showed increased abundances of Crossiella and Streptomyces. In contrast, the abundance of Pseudarthrobacter was reduced in the treatment with B.pumilus Y-26. Conversely, the application of the nematicide fosthiazate exhibited minor influence on the bacterial community. The findings indicated that the application of P.lilacinus CS-Z and B.pumilus Y-26 led to an increase in the relative abundances of beneficial microorganisms, including Gaiella, Bacillus, and Streptomyces, in the rhizosphere soil. In conclusion, P.lilacinus CS-Z and B.pumilus Y-26 demonstrated their potential as environmentally friendly biocontrol agents for managing stem nematode disease of sweet potato.
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Affiliation(s)
- Fengyu Shi
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei, China
| | - Dan Yang
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei, China
| | - Xinpeng Meng
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei, China
| | - Jiaxin Li
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei, China
| | - Yingbo Zhu
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei, China.
| | - Jianbin Liu
- Institute of Plant Nutrition, Resources and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
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3
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Hoskisson PA, Barona-Gómez F, Rozen DE. Phenotypic heterogeneity in Streptomyces colonies. Curr Opin Microbiol 2024; 78:102448. [PMID: 38447313 DOI: 10.1016/j.mib.2024.102448] [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: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.
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Affiliation(s)
- Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | | | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, The Netherlands.
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4
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Hansen ZA, Fulcher MR, Wornson N, Spawn-Lee SA, Johnson M, Song Z, Michalska-Smith M, May G, Seabloom EW, Borer ET, Kinkel LL. Soil nutrient amendment increases the potential for inter-kingdom resource competition among foliar endophytes. ISME COMMUNICATIONS 2024; 4:ycae130. [PMID: 39583585 PMCID: PMC11586052 DOI: 10.1093/ismeco/ycae130] [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: 07/11/2024] [Revised: 09/03/2024] [Accepted: 10/24/2024] [Indexed: 11/26/2024]
Abstract
Foliar endophytes play crucial roles in large-scale ecosystem functions such as plant productivity, decomposition, and nutrient cycling. While the possible effects of environmental nutrient supply on the growth and carbon use of endophytic microbes have critical implications for these processes, these impacts are not fully understood. Here, we examined the effects of long-term elevated nitrogen, phosphorus, potassium, and micronutrient (NPKμ) supply on culturable bacterial and fungal foliar endophytes inhabiting the prairie grass Andropogon gerardii. We hypothesized that elevated soil nutrients alter the taxonomic composition and carbon use phenotypes of foliar endophytes and significantly shift the potential for resource competition among microbes within leaves. We observed changes in taxonomic composition and carbon use patterns of fungal, but not bacterial, endophytes of A. gerardii growing in NPKμ-amended versus ambient conditions. Fungal endophytes from NPKμ-amended plants had distinct carbon use profiles and demonstrated greater specialization across carbon sources compared to control plots. Resource niche overlap between bacterial and fungal endophytes also increased with plot nutrient supply, suggesting enhanced potential for inter-kingdom competition. Collectively, this work suggests that soil nutrient enrichment alters how fungal endophyte communities exist in the foliar environment, with potentially significant implications for broad-scale ecosystem function.
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Affiliation(s)
- Zoe A Hansen
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Michael R Fulcher
- United States Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702, United States
| | - Nicholas Wornson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Seth A Spawn-Lee
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Mitch Johnson
- Department of Horticulture, University of Minnesota, Saint Paul, MN 55108, United States
| | - Zewei Song
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
| | - Matthew Michalska-Smith
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, United States
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, United States
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, United States
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, United States
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, United States
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5
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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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6
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Yang M, Qi Y, Liu J, Gao P, Huang F, Yu L, Chen H. Different Response Mechanisms of Rhizosphere Microbial Communities in Two Species of Amorphophallus to Pectobacterium carotovorum subsp. carotovorum Infection. THE PLANT PATHOLOGY JOURNAL 2023; 39:207-219. [PMID: 37019830 PMCID: PMC10102568 DOI: 10.5423/ppj.oa.12.2022.0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 06/19/2023]
Abstract
Soft rot is a widespread, catastrophic disease caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) that severely damages the production of Amorphophallus spp. This study evaluated the rhizosphere bacterial and fungal communities in Pcc-infected and uninfected plants of two species of Amorphophallus, A. muelleri and A. konjac. Principal component analysis showed that the samples formed different clusters according to the Pcc infection status, indicating that Pcc infection can cause a large number of changes in the bacterial and fungal communities in the Amorphophallus spp. rhizosphere soil. However, the response mechanisms of A. muelleri and A. konjac are different. There was little difference in the overall microbial species composition among the four treatments, but the relative abundances of core microbiome members were significantly different. The relative abundances of Actinobacteria, Chloroflexi, Acidobacteria, Firmicutes, Bacillus, and Lysobacter were lower in infected A. konjac plants than in healthy plants; in contrast, those of infected A. muelleri plants were higher than those in healthy plants. For fungi, the relative abundances of Ascomycota and Fusarium in the rhizosphere of infected A. konjac plants were significantly higher than those of healthy plants, but those of infected A. muelleri plants were lower than those of healthy plants. The relative abundance of beneficial Penicillium fungi was lower in infected A. konjac plants than in healthy plants, and that of infected A. muelleri plants was higher than that of healthy plants. These findings can provide theoretical references for further functional research and utilization of Amorphophallus spp. rhizosphere microbial communities in the future.
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Affiliation(s)
- Min Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201,
China
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214,
China
| | - Ying Qi
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214,
China
| | - Jiani Liu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214,
China
| | - Penghua Gao
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214,
China
| | - Feiyan Huang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214,
China
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214,
China
| | - Hairu Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201,
China
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7
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Bai L, Wang Y, Li Y, Zhang X, Lu Z, Zhang D, Sun F, Zhao X. Changes in the Microbial Community in Maize ( Zea mays L.) Root Spatial Structure Following Short-Term Nitrogen Application. ACS OMEGA 2023; 8:208-218. [PMID: 36643453 PMCID: PMC9835084 DOI: 10.1021/acsomega.2c01711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
The beneficial interactions between crop roots and microbiomes play a key role in crop nutrient availability, growth promotion, and disease suppression. Recent research, however, rarely reported the effects of nitrogen (N) application rate on microbial community composition at different spatial structures in the maize root zone. Therefore, one experiment was conducted to examine the influence of three N-application levels (0, 180, and 360 kg N ha-1) on microbial community composition in three root-associated compartments of maize (bulk soil, rhizoplane, and endosphere). The microbial diversity and community composition differed significantly among the various compartments. The effects of N application on fungal composition decreased in the order bulk soil > rhizosphere > endosphere at different sampling positions. Also, the fungal composition was more sensitive to the N-fertilizer rate in the bulk soil and the rhizosphere than the bacterial community. A total of 14.42, 9.46, and 3.55% of all taxonomic groups were sensitive to N fertilizer, respectively. The keystone species fungal groups were Humicola (bulk soil), Gibberella (rhizosphere soil), and Humicola (endosphere). Together, our results demonstrate that compared with that of the bacterial community, the fungal community composition was more susceptible to different N-application rates. N fertilization affected the distribution of microflora by changing soil physicochemical properties and enzyme activities. There were strong correlations between microbial communities in maize under the N180 treatment. Moreover, the N180 treatment had the maximum fresh yield and biomass at 64.5 and 24.3 kg·ha-1, respectively.
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Affiliation(s)
- Lanfang Bai
- Faculty
of Agronomy College, Inner Mongolia Agricultural
University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Yufen Wang
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Yahua Li
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Xiangqian Zhang
- Faculty
of Agronomy College, Inner Mongolia Agricultural
University, Hohhot, Inner Mongolia 010070, P. R. China
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
| | - Zhanyuan Lu
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
| | - Dejian Zhang
- Key
Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of
Education, School of Life Science, Inner
Mongolia University, Hohhot, Inner Mongolia 010070, P. R. China
| | - Fengcheng Sun
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
| | - Xiaoqing Zhao
- Inner
Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia 010031, P. R. China
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8
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Tong W, Li J, Cong W, Zhang C, Xu Z, Chen X, Yang M, Liu J, Yu L, Deng X. Bacterial Community Structure and Function Shift in Rhizosphere Soil of Tobacco Plants Infected by Meloidogyne incognita. THE PLANT PATHOLOGY JOURNAL 2022; 38:583-592. [PMID: 36503187 PMCID: PMC9742794 DOI: 10.5423/ppj.oa.08.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 06/17/2023]
Abstract
Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.
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Affiliation(s)
- Wenjie Tong
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
| | - Junying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
| | - Wenfeng Cong
- National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193,
China
| | - Cuiping Zhang
- Yuxi Branch of Yunnan Provincial Tobacco Company, Yuxi 653100, Yunnan,
China
| | - Zhaoli Xu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
| | - Xiaolong Chen
- Tobacco Leaf Purchase Center, China Tobacco Henan Industrial Co., Ltd., Zhengzhou 450000,
China
| | - Min Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, Yunnan,
China
| | - Jiani Liu
- College of Agronomy, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, Yunnan,
China
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, Yunnan,
China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
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9
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Mhuireach GÁ, Dietz L, Gillett T. One or many? Multi-species livestock grazing influences soil microbiome community structure and antibiotic resistance potential. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.926824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil health has been highlighted as a key dimension of regenerative agriculture, given its critical importance for food production, carbon sequestration, water filtration, and nutrient cycling. Microorganisms are critical components of soil health, as they are responsible for mediating 90% of soil functions. Multi-species rotational grazing (MSRG) is a promising strategy for maintaining and improving soil health, yet the potential effects of MSRG on soil microbiomes are poorly understood. To address this knowledge gap, we collected soil microbial samples at three timepoints during the 2020 grazing season for 12 total paddocks, which were equally split into four different grazing treatments—cattle only, sheep only, swine only, or multi-species. Shallow shotgun metagenomic sequencing was used to characterize soil microbial community taxonomy and antibiotic resistome. Results demonstrated broad microbial diversity in all paddock soil microbiomes. Samples collected early in the season tended to have greater archaeal and bacterial alpha diversity than samples collected later for all grazing treatments, while no effect was observed for fungi or viruses. Beta diversity, however, was strongly influenced by both grazing treatment and month for all microbial kingdoms, suggesting a pronounced effect of different livestock on microbial composition. Cattle-only and swine-only paddocks were more dissimilar from multi-species paddocks than those grazed by sheep. We identified a large number of differentially abundant taxa driving community dissimilarities, including Methanosarcina spp., Candidatus Nitrocosmicus oleophilus, Streptomyces spp., Pyricularia spp., Fusarium spp., and Tunggulvirus Pseudomonas virus ϕ-2. In addition, a wide variety of antibiotic resistance genes (ARGs) were present in all samples, regardless of grazing treatment; the majority of these encoded efflux pumps and antibiotic modification enzymes (e.g., transferases). This novel study demonstrates that grazing different species of livestock, either separately or together, can impact soil microbial community structure and antibiotic resistance capacity, though further research is needed to fully characterize these impacts. Increasing the knowledge base about soil microbial community structure and function under real-world grazing conditions will help to construct metrics that can be incorporated into traditional soil health tests and allow producers to manage livestock operations for optimal soil microbiomes.
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10
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Wang Y, Liu L, Zhang J, Li D, Yu J, Gao H, Li H, Zhao Z. Soil phytoremediation reveals alteration in soil microbial metabolic activities along time gradient of cover crop mulching. ENVIRONMENTAL RESEARCH 2022; 209:112884. [PMID: 35131319 DOI: 10.1016/j.envres.2022.112884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
The vitality and diversity of soil microbial metabolism are the core of soil function expression, cover crop is an environmentally friendly agricultural production practice; however, shifts in soil microbial metabolic activities along time gradient of cover crop remain unclear. Here, we used metagenomic and biological techniques to investigate soil microbial potential function and carbon (C) source utilization capacity in the time series of white clover (WC, Trifolium repens L.) for 6, 10, and 15 years in a typical semiarid apple orchard. Conventional tillage (CT) was taken as the control. This study demonstrated that living mulch 6 years of WC had little effect on soil microbial functions. However, after 10 and 15 years of crop cover, an enrichment of genes related to amino acid metabolism, carbon cycle, and nitrogen metabolism was observed in soil microorganisms. Furthermore, average well color development (AWCD) was increased in 10 and 15 years of cover crop, soil microbiome exhibited a stronger preference for carbohydrates, amino acids, and polymers as C sources. The results mainly provided insight into the variation character of microbial metabolic function under increasing duration of cover crop.
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Affiliation(s)
- Yuanji Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Li Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Jiatao Zhang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Dongmei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Jing Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Hua Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China.
| | - Huike Li
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, China.
| | - Zhengyang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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11
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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: 7.3] [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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12
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Schaedel M, Hidrobo G, Grossman J. From Microns to Meters: Exploring Advances in Legume Microbiome Diversity for Agroecosystem Benefits. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.668195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Legumes are of primary importance for agroecosystems because they provide protein-rich foods and enhance soil fertility through fixed atmospheric nitrogen. The legume-rhizobia symbiosis that makes this possible has been extensively studied, from basic research on biochemical signaling to practical applications in cropping systems. While rhizobia are the most-studied group of associated microorganisms, the functional benefit they confer to their legume hosts by fixing nitrogen is not performed in isolation. Indeed, non-rhizobia members of the rhizosphere and nodule microbiome are now understood to contribute in multiple ways to nodule formation, legume fitness, and other agroecosystem services. In this review, we summarize advances contributing to our understanding of the diversity and composition of bacterial members of the belowground legume microbiome. We also highlight applied work in legume food and forage crops that link microbial community composition with plant functional benefits. Ultimately, further research will assist in the development of multi-species microbial inoculants and cropping systems that maximize plant nutrient benefits, while reducing sources of agricultural pollution.
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13
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Abstract
Bacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. One of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require “elicitors” to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors, and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing strains of streptomycetes, we show that strains commonly inhibit each other’s growth and that this occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreases in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competition. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.
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14
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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: 1.0] [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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15
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Gonzalo M, Deveau A, Aigle B. Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil. MICROBIAL ECOLOGY 2020; 80:872-884. [PMID: 32879989 DOI: 10.1007/s00248-020-01579-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.
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Affiliation(s)
- Milena Gonzalo
- Université de Lorraine, INRAE, IAM, F-54000, Nancy, France
- Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France
| | - Aurélie Deveau
- Université de Lorraine, INRAE, IAM, F-54000, Nancy, France.
| | - Bertrand Aigle
- Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France.
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16
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Wang Y, Liu L, Yang J, Duan Y, Luo Y, Taherzadeh MJ, Li Y, Li H, Awasthi MK, Zhao Z. The diversity of microbial community and function varied in response to different agricultural residues composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136983. [PMID: 32041001 DOI: 10.1016/j.scitotenv.2020.136983] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Microbial activities are the dynamic core in the soil nutrient cycle. To improve the knowledges about the responses of soil microbial community structure and potential function to long-term cover crops practice. The co-occurrence patterns of soil microbial community structure and functional genes were evaluated using 16SrRNA, ITS and metagenomic technique in 13 years cover crops of orchard grass (OG, Dactylis glomerata L.) with high C/N and white clover (WC, Trifolium repens L.) with low C/N. Conventional tillage (CT) was control. The experiment was implemented in an apple orchard located on the Loess Plateau, China, from 2006 to 2018. We also measured soil physicochemical properties and enzyme activities related to carbon and nitrogen cycling. The conclusions showed that the dominant bacterial phyla were Actinobacteria 27.68% in OG treatment and Proteobacteria 25.89% in WC treatment. Organic matter inputs stimulated growth of the phyla of Actinobacteria, Firmicutes, Chloroflexi, Ascomycota and genera of Bacillus, Blastococcus, Streptomyces and Penicillium. Interestingly, the OG and WC treatments promoted the fungal and bacterial alpha-diversity compared to CT treatment, respectively. In addition, compared to CT treatment, OG treatment was beneficial to the increase of C-cycle enzyme activity, while WC treatment tended to increase the N-cycle enzyme activity. Notably, compared to CT treatment, they both enriched carbon fixation and cycle pathways genes, while WC treatment increased the nitrogen metabolism pathway genes. Moreover, OG treatment was more conducive to the enrichment of carbohydrate enzymes genes involved in the hydrolysis of cellulose and hemicellulose compared to WC treatment. Overall, different quality of plant residues stimulated the specific expressions of soil microbial community structure and function. Long-term planted white clover was effective strategy to improve soil quality.
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Affiliation(s)
- Yuanji Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Liu
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jianfeng Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | | | - Yongfu Li
- Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, Zhejiang A & F University, Hangzhou 311300, China
| | - Huike Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhengyang Zhao
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
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17
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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: 0.8] [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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18
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Malik A, Kim YR, Jang IH, Hwang S, Oh DC, Kim SB. Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium. BMC Genomics 2020; 21:118. [PMID: 32013859 PMCID: PMC6998099 DOI: 10.1186/s12864-020-6468-5] [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: 07/31/2018] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. RESULTS A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. CONCLUSIONS This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.
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Affiliation(s)
- Adeel Malik
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - In Hee Jang
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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19
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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: 0.8] [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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20
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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: 10] [Impact Index Per Article: 1.7] [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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21
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Chouvenc T, Elliott ML, Šobotník J, Efstathion CA, Su NY. The Termite Fecal Nest: A Framework for the Opportunistic Acquisition of Beneficial Soil Streptomyces (Actinomycetales: Streptomycetaceae). ENVIRONMENTAL ENTOMOLOGY 2018; 47:1431-1439. [PMID: 30321327 DOI: 10.1093/ee/nvy152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Mutualistic associations between insects and microorganisms must imply gains for both partners, and the emphasis has mostly focused on coevolved host-symbiont systems. However, some insect hosts may have evolved traits that allow for various means of association with opportunistic microbial communities, especially when the microbes are omnipresent in their environment. It was previously shown that colonies of the subterranean termite Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) build nests out of fecal material that host a community of Streptomyces Waksman and Henrici (Actinomycetales: Streptomycetaceae). These Actinobacteria produce an array of bioactive metabolites that provides a level of protection for termites against certain entomopathogenic fungi. How C. formosanus acquires and maintains this association remains unknown. This study shows that the majority of Streptomyces isolates found in field termite fecal nest materials are identical to Streptomyces isolates from soils surrounding the nests and are not vertically inherited. A survey of Streptomyces communities from C. formosanus fecal nest materials sampled at 20 locations around the world revealed that all nests are reliably associated with a diverse Streptomyces community. The C. formosanus fecal nest material therefore provides a nutritional framework that can recruit beneficial Streptomyces from the soil environment, in the absence of long-term coevolutionary processes. A diverse Streptomyces community is reliably present in soils, and subterranean termite colonies can acquire such facultative symbionts each social cycle into their fecal nest. This association probably emerged as an exaptation from the existing termite nest structure and benefits both the termite and the opportunistic colonizing bacteria.
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Affiliation(s)
- Thomas Chouvenc
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, College Avenue, Fort Lauderdale, FL
| | - Monica L Elliott
- Department of Plant Pathology, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, College Avenue, Fort Lauderdale, FL
| | - Jan Šobotník
- Termite Research Team, Faculty of Forestry and Wood Sciences CULS, Kamýcká, Prague Suchdol, Czechia, EU
| | - Caroline A Efstathion
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, College Avenue, Fort Lauderdale, FL
| | - Nan-Yao Su
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, College Avenue, Fort Lauderdale, FL
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22
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Sarwar A, Latif Z, Zhang S, Zhu J, Zechel DL, Bechthold A. Biological Control of Potato Common Scab With Rare Isatropolone C Compound Produced by Plant Growth Promoting Streptomyces A1RT. Front Microbiol 2018; 9:1126. [PMID: 29899736 PMCID: PMC5989138 DOI: 10.3389/fmicb.2018.01126] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/14/2018] [Indexed: 12/01/2022] Open
Abstract
Potato is prone to many drastic diseases like potato common scab (CS). As no highly effective methods exist for managing CS, this study explored the possibility of using biological control. Ten bacterial strains were isolated from CS-infected potato tubers from four different locations of Punjab, Pakistan, and identified based on biochemical and molecular analysis. Analysis of 16s rDNA sequences amplified by PCR revealed the isolated bacterial strains to be Streptomyces scabies, S. turgidiscabies and S. stelliscabiei. Pathogenic islands were also confirmed among the isolates after identification of txtAB, nec1, and tomA genes with PCR amplification. One strain isolated from soil was antagonistic to the pathogenic Streptomyces spp., and determined to be Streptomyces A1RT on the basis of 16s rRNA sequencing. A methanolic extract of Streptomyces A1RT contained Isatropolone C, which was purified and structurally determined by 1H- and 13C-NMR, 1H/1H-COSY, HMQC, and HMBC techniques. Streptomyces A1RT also produced the plant growth hormone indole-3-acetic acid (IAA) with a titer of 26 μg ml-1 as confirmed by spectrophotometry and HPLC. In a greenhouse assay, disease severity index was established from 0 to 500. Average disease severity indexes were recorded as 63, 130.5, and 78 for Streptomyces scabies, S. turgidiscabies and S. stelliscabiei, respectively. When Streptomyces A1RT was applied in soil that contained one of these pathogenic isolates, the average disease severity indexes were significantly (P < 0.05) reduced to 11.1, 5.6 and 8.4, respectively. A significant increase in tuber weight and shoot development was also observed with the tubers treated with Streptomyces A1RT. The use of the plant growth-promoting Streptomyces A1RT against potato CS thus provides an alternative strategy to control the disease without affecting environmental, plants, animals and human health.
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Affiliation(s)
- Arslan Sarwar
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Zakia Latif
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jing Zhu
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
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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: 6.6] [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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Essarioui A, LeBlanc N, Kistler HC, Kinkel LL. Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere. MICROBIAL ECOLOGY 2017; 74:157-167. [PMID: 28058470 DOI: 10.1007/s00248-016-0907-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this work, we characterized antagonistic activities and nutrient use among Streptomyces and Fusarium from the rhizosphere of Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants growing in communities of 1 (monoculture) or 16 (polyculture) plant species. Streptomyces from monoculture were more antagonistic against Fusarium than those from polyculture. In contrast, Fusarium isolates from polyculture had greater inhibitory capacities against Streptomyces than isolates from monoculture. Although Fusarium isolates had on average greater niche widths, the collection of Streptomyces isolates in total used a greater diversity of nutrients for growth. Plant richness, but not plant host, influenced the potential for resource competition between the two taxa. Fusarium isolates had greater niche overlap with Streptomyces in monoculture than polyculture, suggesting greater potential for Fusarium to competitively challenge Streptomyces in monoculture plant communities. In contrast, Streptomyces had greater niche overlap with Fusarium in polyculture than monoculture, suggesting that Fusarium experiences greater resource competition with Streptomyces in polyculture than monoculture. These patterns of competitive and inhibitory phenotypes among Streptomyces and Fusarium populations are consistent with selection for Fusarium-antagonistic Streptomyces populations in the presence of strong Fusarium resource competition in plant monocultures. Similarly, these results suggest selection for Streptomyces-inhibitory Fusarium populations in the presence of strong Streptomyces resource competition in more diverse plant communities. Thus, landscape-scale variation in plant species richness may be critical to mediating the coevolutionary dynamics and selective trajectories for inhibitory and nutrient use phenotypes among Streptomyces and Fusarium populations in soil, with significant implications for microbial community functional characteristics.
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Affiliation(s)
- Adil Essarioui
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, USA.
- National Institute of Agronomic Research, Regional Center of Errachidia, Errachidia, Morocco.
| | - Nicholas LeBlanc
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Harold C Kistler
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, USA
- Cereal Disease Lab, USDA-ARS, 1551 Lindig Street, St Paul, MN, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, USA
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25
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Sarikhani E, Sagova-Mareckova M, Omelka M, Kopecky J. The effect of peat and iron supplements on the severity of potato common scab and bacterial community in tuberosphere soil. FEMS Microbiol Ecol 2016; 93:fiw206. [PMID: 27794015 DOI: 10.1093/femsec/fiw206] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 02/03/2023] Open
Abstract
The control of common scab (CS) of potatoes includes resistant cultivars, specific fertilization, increase of soil moisture and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. In order to determine the effects of soil organic matter, iron and pH on CS development, peat and DTPA-chelated iron were supplemented to pots filled with soil conducive for CS. All results were compared with the same data obtained for a suppressive soil, which has naturally low severity of CS and occurs nearby. Bacteria, Actinobacteria and the txtB genes from the biosynthetic cluster of thaxtomin, which is responsible for the disease development, were quantified by qPCR in tuberosphere soil and potato periderm. Illumina amplicon sequencing of bacterial 16S rRNA genes was performed for tuberosphere soils. Both peat and iron supplements controlled potato scab, and the combination of the two supplements reduced CS most effectively. The bacterial community was modified by all treatments but the highest number of operational taxonomic units (OTUs) changed towards the suppressive soil after the combined peat and iron treatment. It seemed that iron supplement supported plant defense while both iron and peat additions changed the bacterial community in favor of CS suppression.
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Affiliation(s)
- Ensyeh Sarikhani
- Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic
| | - Marketa Sagova-Mareckova
- Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic
| | - Marek Omelka
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, 186 75 Prague, Czech Republic
| | - Jan Kopecky
- Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic
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26
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Pinheiro GL, de Azevedo-Martins AC, Albano RM, de Souza W, Frases S. Comprehensive analysis of the cellulolytic system reveals its potential for deconstruction of lignocellulosic biomass in a novel Streptomyces sp. Appl Microbiol Biotechnol 2016; 101:301-319. [DOI: 10.1007/s00253-016-7851-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/21/2016] [Accepted: 09/07/2016] [Indexed: 12/30/2022]
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27
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Tree species effects on pathogen-suppressive capacities of soil bacteria across two tropical dry forests in Costa Rica. Oecologia 2016; 182:789-802. [PMID: 27573616 DOI: 10.1007/s00442-016-3702-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
Abstract
Antibiotic-producing bacteria in the genus Streptomyces can inhibit soil-borne plant pathogens, and have the potential to mediate the impacts of disease on plant communities. Little is known about how antibiotic production varies among soil communities in tropical forests, despite a long history of interest in the role of soil-borne pathogens in these ecosystems. Our objective was to determine how tree species and soils influence variation in antibiotic-mediated pathogen suppression among Streptomyces communities in two tropical dry forest sites (Santa Rosa and Palo Verde). We targeted tree species that co-occur in both sites and used a culture-based functional assay to quantify pathogen-suppressive capacities of Streptomyces communities beneath 50 focal trees. We also measured host-associated litter and soil element concentrations as potential mechanisms by which trees may influence soil microbes. Pathogen-suppressive capacities of Streptomyces communities varied within and among tree species, and inhibitory phenotypes were significantly related to soil and litter element concentrations. Average proportions of inhibitory Streptomyces in soils from the same tree species varied between 1.6 and 3.3-fold between sites. Densities and proportions of pathogen-suppressive bacteria were always higher in Santa Rosa than Palo Verde. Our results suggest that spatial heterogeneity in the potential for antibiotic-mediated disease suppression is shaped by tree species, site, and soil characteristics, which could have significant implications for understanding plant community composition and diversity in tropical dry forests.
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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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29
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Sagova-Mareckova M, Ulanova D, Sanderova P, Omelka M, Kamenik Z, Olsovska J, Kopecky J. Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria. BMC Microbiol 2015; 15:81. [PMID: 25887892 PMCID: PMC4391685 DOI: 10.1186/s12866-015-0416-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 03/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. RESULTS Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. CONCLUSIONS The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.
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Affiliation(s)
| | - Dana Ulanova
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the AS CR, v.v.i., Prague, Czech Republic.
- Oceanography Section, Science Research Center, Kochi University, IMT-MEXT, Kochi, Japan.
| | - Petra Sanderova
- Epidemiology and Ecology of Microorganisms, Crop Research Institute, Prague, Czech Republic.
- Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic.
| | - Marek Omelka
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
| | - Zdenek Kamenik
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the AS CR, v.v.i., Prague, Czech Republic.
| | - Jana Olsovska
- Analytical and Testing Laboratory, Research Institute of Brewing and Malting, PLC, Prague, Czech Republic.
| | - Jan Kopecky
- Epidemiology and Ecology of Microorganisms, Crop Research Institute, Prague, Czech Republic.
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30
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Schlatter DC, Bakker MG, Bradeen JM, Kinkel LL. Plant community richness and microbial interactions structure bacterial communities in soil. Ecology 2015; 96:134-42. [DOI: 10.1890/13-1648.1] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Daniel C. Schlatter
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
| | - Matthew G. Bakker
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
| | - Linda L. Kinkel
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
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31
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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: 0.5] [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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32
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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: 2.0] [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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33
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Diversity of two-domain laccase-like multicopper oxidase genes in Streptomyces spp.: identification of genes potentially involved in extracellular activities and lignocellulose degradation during composting of agricultural waste. Appl Environ Microbiol 2014; 80:3305-14. [PMID: 24657870 DOI: 10.1128/aem.00223-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Traditional three-domain fungal and bacterial laccases have been extensively studied for their significance in various biotechnological applications. Growing molecular evidence points to a wide occurrence of more recently recognized two-domain laccase-like multicopper oxidase (LMCO) genes in Streptomyces spp. However, the current knowledge about their ecological role and distribution in natural or artificial ecosystems is insufficient. The aim of this study was to investigate the diversity and composition of Streptomyces two-domain LMCO genes in agricultural waste composting, which will contribute to the understanding of the ecological function of Streptomyces two-domain LMCOs with potential extracellular activity and ligninolytic capacity. A new specific PCR primer pair was designed to target the two conserved copper binding regions of Streptomyces two-domain LMCO genes. The obtained sequences mainly clustered with Streptomyces coelicolor, Streptomyces violaceusniger, and Streptomyces griseus. Gene libraries retrieved from six composting samples revealed high diversity and a rapid succession of Streptomyces two-domain LMCO genes during composting. The obtained sequence types cluster in 8 distinct clades, most of which are homologous with Streptomyces two-domain LMCO genes, but the sequences of clades III and VIII do not match with any reference sequence of known streptomycetes. Both lignocellulose degradation rates and phenol oxidase activity at pH 8.0 in the composting process were found to be positively associated with the abundance of Streptomyces two-domain LMCO genes. These observations provide important clues that Streptomyces two-domain LMCOs are potentially involved in bacterial extracellular phenol oxidase activities and lignocellulose breakdown during agricultural waste composting.
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34
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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: 3.0] [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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35
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Short-term dynamics of culturable bacteria in a soil amended with biotransformed dry olive residue. Syst Appl Microbiol 2014; 37:113-20. [DOI: 10.1016/j.syapm.2013.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 01/18/2023]
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36
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Vaz Jauri P, Bakker MG, Salomon CE, Kinkel LL. Subinhibitory antibiotic concentrations mediate nutrient use and competition among soil streptomyces. PLoS One 2013; 8:e81064. [PMID: 24339897 PMCID: PMC3855208 DOI: 10.1371/journal.pone.0081064] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/08/2013] [Indexed: 11/23/2022] Open
Abstract
Though traditionally perceived as weapons, antibiotics are also hypothesized to act as microbial signals in natural habitats. However, while subinhibitory concentrations of antibiotics (SICA) are known to shift bacterial gene expression, specific hypotheses as to how SICA influence the ecology of natural populations are scarce. We explored whether antibiotic ‘signals’, or SICA, have the potential to alter nutrient utilization, niche overlap, and competitive species interactions among Streptomyces populations in soil. For nine diverse Streptomyces isolates, we evaluated nutrient utilization patterns on 95 different nutrient sources in the presence and absence of subinhibitory concentrations of five antibiotics. There were significant changes in nutrient use among Streptomyces isolates, including both increases and decreases in the capacity to use individual nutrients in the presence vs. in the absence of SICA. Isolates varied in their responses to SICA and antibiotics varied in their effects on isolates. Furthermore, for some isolate-isolate-antibiotic combinations, competition-free growth (growth for an isolate on all nutrients that were not utilized by a competing isolate), was increased in the presence of SICA, reducing the potential fitness cost of nutrient competition among those competitors. This suggests that antibiotics may provide a mechanism for bacteria to actively minimize niche overlap among competitors in soil. Thus, in contrast to antagonistic coevolutionary dynamics, antibiotics as signals may mediate coevolutionary displacement among coexisting Streptomyces, thereby hindering the emergence of antibiotic resistant phenotypes. These results contribute to our broad understanding of the ecology and evolutionary biology of antibiotics and microbial signals in nature.
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Affiliation(s)
- Patricia Vaz Jauri
- Department of Plant Pathology, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Matthew G. Bakker
- Department of Plant Pathology, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Christine E. Salomon
- Center for Drug Design, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Linda L. Kinkel
- Department of Plant Pathology, University of Minnesota, Twin Cities, Minnesota, United States of America
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37
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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: 1.1] [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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38
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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: 5.7] [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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39
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Chouvenc T, Efstathion CA, Elliott ML, Su NY. Extended disease resistance emerging from the faecal nest of a subterranean termite. Proc Biol Sci 2013; 280:20131885. [PMID: 24048157 PMCID: PMC3779336 DOI: 10.1098/rspb.2013.1885] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Social insects nesting in soil environments are in constant contact with entomopathogens but have evolved a range of defence mechanisms, resulting in both individual and social immunity that reduce the chance for epizootics in the colony, as in the case of subterranean termites. Coptotermes formosanus uses its faeces as building material for its nest structure that result into a ‘carton material’, and here, we report that the faecal nest supports the growth of Actinobacteria which provide another level of protection to the social group against entomopathogens. A Streptomyces species with in vivo antimicrobial activity against fungal entomopathogens was isolated from the nest material of multiple termite colonies. Termite groups were exposed to Metarhizium anisopliae, a fungal entomopathogen, during their foraging activity and the presence of Streptomyces within the nest structure provided a significant survival benefit to the termites. Therefore, this report describes a non-nutritional exosymbiosis in a termite, in the form of a defensive mutualism which has emerged from the use of faecal material in the nesting structure of Coptotermes. The association with an Actinobacteria community in the termite faecal material provides an extended disease resistance to the termite group as another level of defence, in addition to their individual and social immunity.
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Affiliation(s)
- Thomas Chouvenc
- Department of Entomology and Nematology, University of Florida, Institute of Food and Agricultural Sciences, , 3205 College Avenue, Fort Lauderdale, FL 33314, USA, Department of Plant Pathology, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, , 3205 College Avenue, Fort Lauderdale, FL 33314, USA
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40
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Bontemps C, Toussaint M, Revol PV, Hotel L, Jeanbille M, Uroz S, Turpault MP, Blaudez D, Leblond P. Taxonomic and functional diversity of Streptomyces in a forest soil. FEMS Microbiol Lett 2013; 342:157-67. [PMID: 23489323 DOI: 10.1111/1574-6968.12126] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 03/07/2013] [Indexed: 12/26/2022] Open
Abstract
In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities.
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Affiliation(s)
- Cyril Bontemps
- Dynamique des Génomes et Adaptation Microbienne, UMR1128, Université de Lorraine, Vandoeuvre-lès-Nancy F-54506, France.
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41
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Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces. Sci Rep 2013; 3:1030. [PMID: 23301151 PMCID: PMC3538285 DOI: 10.1038/srep01030] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/01/2012] [Indexed: 12/16/2022] Open
Abstract
Streptomyces are best known for producing antimicrobial secondary metabolites, but they are also recognized for their contributions to biomass utilization. Despite their importance to carbon cycling in terrestrial ecosystems, our understanding of the cellulolytic ability of Streptomyces is currently limited to a few soil-isolates. Here, we demonstrate the biomass-deconstructing capability of Streptomyces sp. SirexAA-E (ActE), an aerobic bacterium associated with the invasive pine-boring woodwasp Sirex noctilio. When grown on plant biomass, ActE secretes a suite of enzymes including endo- and exo-cellulases, CBM33 polysaccharide-monooxygenases, and hemicellulases. Genome-wide transcriptomic and proteomic analyses, and biochemical assays have revealed the key enzymes used to deconstruct crystalline cellulose, other pure polysaccharides, and biomass. The mixture of enzymes obtained from growth on biomass has biomass-degrading activity comparable to a cellulolytic enzyme cocktail from the fungus Trichoderma reesei, and thus provides a compelling example of high cellulolytic capacity in an aerobic bacterium.
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42
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Otto-Hanson LK, Grabau Z, Rosen C, Salomon CE, Kinkel LL. Pathogen variation and urea influence selection and success of Streptomyces mixtures in biological control. PHYTOPATHOLOGY 2013; 103:34-42. [PMID: 23035630 DOI: 10.1094/phyto-06-12-0129-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Success in biological control of plant diseases remains inconsistent in the field. A collection of well-characterized Streptomyces antagonists (n = 19 isolates) was tested for their capacities to inhibit pathogenic Streptomyces scabies (n = 15 isolates). There was significant variation among antagonists in ability to inhibit pathogen isolates and among pathogens in their susceptibility to inhibition. Only one antagonist could inhibit all pathogens, and antagonist-pathogen interactions were highly specific, highlighting the limitations of single-strain inoculum in biological control. However, the collection of pathogens could be inhibited by several combinations of antagonists, suggesting the potential for successful antagonist mixtures. Urea generally increased effectiveness of antagonists at inhibiting pathogens in vitro (increased mean inhibition zones) but its specific effects varied among antagonist-pathogen combinations. In greenhouse trials, urea enhanced the effectiveness of antagonist mixtures relative to individual antagonists in controlling potato scab. Although antagonist mixtures were frequently antagonistic in the absence of urea, all n= 2 and n = 3 antagonist-isolate combinations were synergistic in the presence of urea. This work provides insights into the efficacy of single- versus multiple-strain inocula in biological control and on the potential for nutrients to influence mixture success.
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Affiliation(s)
- L K Otto-Hanson
- Department of Plant Pathology, University of Minnesota, St. Paul 55108, USA.
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43
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Kinkel LL, Schlatter DC, Bakker MG, Arenz BE. Streptomyces competition and co-evolution in relation to plant disease suppression. Res Microbiol 2012; 163:490-9. [PMID: 22922402 DOI: 10.1016/j.resmic.2012.07.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/04/2012] [Indexed: 01/01/2023]
Abstract
High densities of antagonistic Streptomyces are associated with plant disease suppression in many soils. Here we review use of inoculation and organic matter amendments for enriching antagonistic Streptomyces populations to reduce plant disease and note that effective and consistent disease suppression in response to management has been elusive. We argue that shifting the focus of research from short-term disease suppression to the population ecology and evolutionary biology of antagonistic Streptomyces in soil will enhance prospects for effective management. A framework is presented for considering the impacts of short- and long-term management on competitive and coevolutionary dynamics among Streptomyces populations in relation to disease suppression.
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Affiliation(s)
- Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
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Rosenzweig N, Tiedje JM, Quensen JF, Meng Q, Hao JJ. Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses. PLANT DISEASE 2012; 96:718-725. [PMID: 30727523 DOI: 10.1094/pdis-07-11-0571] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.
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Affiliation(s)
| | - James M Tiedje
- Department of Crop and Soil Science and Center for Microbial Ecology
| | - John F Quensen
- Department of Crop and Soil Science and Center for Microbial Ecology
| | | | - Jianjun J Hao
- Department of Plant Pathology, Michigan State University, East Lansing 48824
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45
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Pseudomonas and other Microbes in Disease-Suppressive Soils. SUSTAINABLE AGRICULTURE REVIEWS 2012. [DOI: 10.1007/978-94-007-4113-3_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Sagova-Mareckova M, Omelka M, Cermak L, Kamenik Z, Olsovska J, Hackl E, Kopecky J, Hadacek F. Microbial communities show parallels at sites with distinct litter and soil characteristics. Appl Environ Microbiol 2011; 77:7560-7. [PMID: 21926225 PMCID: PMC3209186 DOI: 10.1128/aem.00527-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 09/02/2011] [Indexed: 11/20/2022] Open
Abstract
Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.
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Affiliation(s)
- Marketa Sagova-Mareckova
- Laboratory for Diagnostics and Epidemiology of Microorganisms, Crop Research Institute, Prague, Czech Republic
| | - Marek Omelka
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Ladislav Cermak
- Laboratory for Diagnostics and Epidemiology of Microorganisms, Crop Research Institute, Prague, Czech Republic
| | | | - Jana Olsovska
- Research Institute of Brewing and Malting, Prague, Czech Republic
| | - Evelyn Hackl
- Bioresources Unit, AIT Austrian Institute of Technology GmbH, Seibersdorf, Austria
| | - Jan Kopecky
- Laboratory for Diagnostics and Epidemiology of Microorganisms, Crop Research Institute, Prague, Czech Republic
| | - Franz Hadacek
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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Kinkel LL, Bakker MG, Schlatter DC. A coevolutionary framework for managing disease-suppressive soils. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:47-67. [PMID: 21639781 DOI: 10.1146/annurev-phyto-072910-095232] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
This review explores a coevolutionary framework for the study and management of disease-suppressive soil microbial communities. Because antagonistic microbial interactions are especially important to disease suppression, conceptual, theoretical, and empirical work on antagonistic coevolution and its relevance to disease suppression is reviewed. In addition, principles of coevolution are used to develop specific predictions regarding the drivers of disease-suppressive potential in soil microbial communities and to highlight important areas for future research. This approach brings an evolutionary perspective to microbial community management and emphasizes the role of species interactions among indigenous nonpathogenic microbes in developing and maintaining disease-suppressive activities in soil.
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Affiliation(s)
- Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108, USA.
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48
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Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H. The complex extracellular biology ofStreptomyces. FEMS Microbiol Rev 2010; 34:171-98. [DOI: 10.1111/j.1574-6976.2009.00206.x] [Citation(s) in RCA: 336] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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