1
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Yang QE, Ma X, Li M, Zhao M, Zeng L, He M, Deng H, Liao H, Rensing C, Friman VP, Zhou S, Walsh TR. Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages. Nat Commun 2024; 15:3654. [PMID: 38688912 PMCID: PMC11061290 DOI: 10.1038/s41467-024-48006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodan Ma
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengshi Zhao
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingshuang Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minzhen He
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui Deng
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3RE, UK.
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2
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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3
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Wang J, Wang X, Yang K, Lu C, Fields B, Xu Y, Shen Q, Wei Z, Friman VP. Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant-pathogenic bacterium irrespective of the growth temperature. Evol Lett 2024; 8:253-266. [PMID: 38525025 PMCID: PMC10959482 DOI: 10.1093/evlett/qrad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 03/26/2024] Open
Abstract
While temperature has been shown to affect the survival and growth of bacteria and their phage parasites, it is unclear if trade-offs between phage resistance and other bacterial traits depend on the temperature. Here, we experimentally compared the evolution of phage resistance-virulence trade-offs and underlying molecular mechanisms in phytopathogenic Ralstonia solanacearum bacterium at 25 °C and 35 °C temperature environments. We found that while phages reduced R. solanacearum densities relatively more at 25 °C, no difference in the final level of phage resistance was observed between temperature treatments. Instead, small colony variants (SCVs) with increased growth rate and mutations in the quorum-sensing (QS) signaling receptor gene, phcS, evolved in both temperature treatments. Interestingly, SCVs were also phage-resistant and reached higher frequencies in the presence of phages. Evolving phage resistance was costly, resulting in reduced carrying capacity, biofilm formation, and virulence in planta, possibly due to loss of QS-mediated expression of key virulence genes. We also observed mucoid phage-resistant colonies that showed loss of virulence and reduced twitching motility likely due to parallel mutations in prepilin peptidase gene, pilD. Moreover, phage-resistant SCVs from 35 °C-phage treatment had parallel mutations in type II secretion system (T2SS) genes (gspE and gspF). Adsorption assays confirmed the role of pilD as a phage receptor, while no loss of adsorption was found with phcS or T2SS mutants, indicative of other downstream phage resistance mechanisms. Additional transcriptomic analysis revealed upregulation of CBASS and type I restriction-modification phage defense systems in response to phage exposure, which coincided with reduced expression of motility and virulence-associated genes, including pilD and type II and III secretion systems. Together, these results suggest that while phage resistance-virulence trade-offs are not affected by the growth temperature, they could be mediated through both pre- and postinfection phage resistance mechanisms.
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Affiliation(s)
- Jianing Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Xiaofang Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Keming Yang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Chunxia Lu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Bryden Fields
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Yangchun Xu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhong Wei
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Ville-Petri Friman
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, Wentworth Way, York , United Kingdom
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4
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Bottery MJ, Johansen HK, Pitchford JW, Friman VP. Co-occurring microflora and mucin drive Pseudomonas aeruginosa diversification and pathoadaptation. ISME Commun 2024; 4:ycae043. [PMID: 38707844 PMCID: PMC11067959 DOI: 10.1093/ismeco/ycae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 05/07/2024]
Abstract
While several environmental factors contribute to the evolutionary diversification of the pathogenic bacterium Pseudomonas aeruginosa during cystic fibrosis lung infections, relatively little is known about the impact of the surrounding microbiota. By using in vitro experimental evolution, we show that the presence of Stenotrophomonas maltophilia, Staphylococcus aureus, or them both, prevent the evolution of loss of virulence, which repeatedly occurs in the absence of these species due to mutations in regulators of the Pseudomonas Quinolone Signal quorum sensing system, vqsM and pqsR. Moreover, the strength of the effect of co-occurring species is attenuated through changes in the physical environment by the addition of mucin, resulting in selection for phenotypes resembling those evolved in the absence of the co-occurring species. Together, our findings show that variation in mucosal environment and the surrounding polymicrobial environment can determine the evolutionary trajectory of P. aeruginosa, partly explaining its diversification and pathoadaptation from acute to chronic phenotype during cystic fibrosis lung infections.
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Affiliation(s)
- Michael J Bottery
- Division of Evolution Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Helle Krogh Johansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 9301, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jon W Pitchford
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
- Department of Mathematics, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
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5
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Gu Y, Li Z, Lei P, Wang R, Xu H, Friman VP. Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities. Environ Microbiol 2023; 25:1940-1954. [PMID: 37254577 DOI: 10.1111/1462-2920.16437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.
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Affiliation(s)
- Yian Gu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, China
| | - Zhidan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, York, UK
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6
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Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
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Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
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7
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Yang K, Fu R, Feng H, Jiang G, Finkel O, Sun T, Liu M, Huang B, Li S, Wang X, Yang T, Wang Y, Wang S, Xu Y, Shen Q, Friman VP, Jousset A, Wei Z. RIN enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota. Mol Plant 2023; 16:1379-1395. [PMID: 37563832 DOI: 10.1016/j.molp.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 05/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The RIPENING-INHIBITOR (RIN) transcriptional factor is a key regulator governing fruit ripening. While RIN also affects other physiological processes, its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppress the soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared with the wild-type (WT) plant, RIN mutants had different root exudate profiles, which were associated with distinct changes in microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity, and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin, which were exuded in much lower concentrations by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria, and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Collectively, our work suggests that, while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome, and the pathogen, it can be indirectly manipulated using "prebiotic" compounds that promote the recruitment of disease-suppressive microbiota.
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Affiliation(s)
- Keming Yang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ruixin Fu
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; School of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China
| | - Haichao Feng
- College of Agriculture, Henan University, Zhengzhou 450046, China
| | - Gaofei Jiang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Omri Finkel
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tianyu Sun
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Shan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China.
| | - Shimei Wang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Department of Biology, University of York, York YO10 5DD, UK; Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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8
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Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Influence of insertion sequences on population structure of phytopathogenic bacteria in the Ralstonia solanacearum species complex. Microbiology (Reading) 2023; 169:001364. [PMID: 37458734 PMCID: PMC10433421 DOI: 10.1099/mic.0.001364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Ralstonia solanacearum species complex (RSSC) is a destructive group of plant pathogenic bacteria and the causative agent of bacterial wilt disease. Experimental studies have attributed RSSC virulence to insertion sequences (IS), transposable genetic elements which can both disrupt and activate host genes. Yet, the global diversity and distribution of RSSC IS are unknown. In this study, IS were bioinformatically identified in a diverse collection of 356 RSSC isolates representing five phylogenetic lineages and their diversity investigated based on genetic distance measures and comparisons with the ISFinder database. IS phylogenetic associations were determined based on their distribution across the RSSC phylogeny. Moreover, IS positions within genomes were characterised and their potential gene disruptions determined based on IS proximity to coding sequences. In total, we found 24732 IS belonging to eleven IS families and 26 IS subgroups with over half of the IS found in the megaplasmid. While IS families were generally widespread across the RSSC phylogeny, IS subgroups showed strong lineage-specific distributions and genetically similar bacterial isolates had similar IS contents. Similar associations with bacterial host genetic background were also observed with IS insertion positions which were highly conserved in closely related bacterial isolates. Finally, IS were found to disrupt genes with predicted functions in virulence, stress tolerance, and metabolism suggesting that they might be adaptive. This study highlights that RSSC insertion sequences track the evolution of their bacterial hosts potentially contributing to both intra- and inter-lineage genetic diversity.
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Affiliation(s)
- Samuel T. E. Greenrod
- Department of Biology, University of York, York, UK
- Present address: Department of Biology, University of Oxford, Oxford, UK
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
| | - Ville-Petri Friman
- Department of Biology, University of York, York, UK
- Present address: Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
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9
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Fields B, Moeskjaer S, Deakin WJ, Moffat EK, Roulund N, Andersen SU, Young JPW, Friman VP. Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions. Mol Ecol 2023. [PMID: 37248617 DOI: 10.1111/mec.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023]
Abstract
While shaping of plant microbiome composition through 'host filtering' is well documented in legume-rhizobium symbioses, it is less clear to what extent different varieties and genotypes of the same plant species differentially influence symbiont community diversity and composition. Here, we compared how clover host varieties and genotypes affect the structure of Rhizobium populations in root nodules under conventional field and controlled greenhouse conditions. We first grew four Trifolium repens (white clover) F2 crosses and one variety in a conventional field trial and compared differences in root nodule Rhizobium leguminosarum symbiovar trifolii (Rlt) genotype diversity using high-throughput amplicon sequencing of chromosomal housekeeping (rpoB and recA) genes and auxiliary plasmid-borne symbiosis genes (nodA and nodD). We found that Rlt nodule diversities significantly differed between clover crosses, potentially due to host filtering. However, variance in Rlt diversity largely overlapped between crosses and was also explained by the spatial distribution of plants in the field, indicative of the role of local environmental conditions for nodule diversity. To test the effect of host filtering, we conducted a controlled greenhouse trial with a diverse Rlt inoculum and several host genotypes. We found that different clover varieties and genotypes of the same variety selected for significantly different Rlt nodule communities and that the strength of host filtering (deviation from the initial Rhizobium inoculant composition) was positively correlated with the efficiency of symbiosis (rate of plant greenness colouration). Together, our results suggest that selection by host genotype and local growth conditions jointly influence white clover Rlt nodule diversity and community composition.
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Affiliation(s)
| | - Sara Moeskjaer
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Emma K Moffat
- Department of Biology, University of York, York, UK
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Ville-Petri Friman
- Department of Biology, University of York, York, UK
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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10
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Liao H, Liu C, Ai C, Gao T, Yang QE, Yu Z, Gao S, Zhou S, Friman VP. Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting. ISME J 2023; 17:916-930. [PMID: 37031344 DOI: 10.1038/s41396-023-01404-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/10/2023]
Abstract
While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaofan Ai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Gao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiu-E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhen Yu
- Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Shaoming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, YO10 5DD, York, UK.
- Department of Microbiology, University of Helsinki, Helsinki, 00014, Finland.
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11
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Rehm K, Vollenweider V, Gu S, Friman VP, Kümmerli R, Wei Z, Bigler L. Chryseochelins-structural characterization of novel citrate-based siderophores produced by plant protecting Chryseobacterium spp. Metallomics 2023; 15:7040575. [PMID: 36792066 PMCID: PMC9989332 DOI: 10.1093/mtomcs/mfad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/29/2023] [Indexed: 02/17/2023]
Abstract
Bacteria secrete siderophores whose function is to acquire iron. In recent years, the siderophores of several Chryseobacterium species were shown to promote the health and growth of various plants such as tomato or rice. However, the chemical nature of Chryseobacterium siderophores remained unexplored despite great interest. In this work, we present the purification and structure elucidation by nuclear magnetic resonance (NMR) spectroscopy and tandem mass spectrometry (MS/MS) of chryseochelin A, a novel citrate-based siderophore secreted by three Chryseobacterium strains involved in plant protection. It contains the unusual building blocks 3-hydroxycadaverine and fumaric acid. Furthermore, the unstable structural isomer chryseochelin B and its stable derivative containing fatty acid chains, named chryseochelin C, were identified by mass spectrometric methods. The latter two incorporate an unusual ester connectivity to the citrate moiety showing similarities to achromobactin from the plant pathogen Dickeya dadantii. Finally, we show that chryseochelin A acts in a concentration-dependent manner against the plant-pathogenic Ralstonia solanacearum strain by reducing its access to iron. Thus, our study provides valuable knowledge about the siderophores of Chryseobacterium strains, which have great potential in various applications.
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Affiliation(s)
- Karoline Rehm
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vera Vollenweider
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ville-Petri Friman
- University of York, Department of Biology, Wentworth Way, York YO10 5DD, UK
| | - Rolf Kümmerli
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, PR China
| | - Laurent Bigler
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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12
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Wang J, Raza W, Jiang G, Yi Z, Fields B, Greenrod S, Friman VP, Jousset A, Shen Q, Wei Z. Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs. ISME J 2023; 17:443-452. [PMID: 36635489 PMCID: PMC9938241 DOI: 10.1038/s41396-023-01356-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.
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Affiliation(s)
- Jianing Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Waseem Raza
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China.
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Zhang Yi
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Bryden Fields
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Samuel Greenrod
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China.
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
- Department of Microbiology, University of Helsinki, Helsinki, 00014, Finland.
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China.
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13
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Yang K, Wang X, Hou R, Lu C, Fan Z, Li J, Wang S, Xu Y, Shen Q, Friman VP, Wei Z. Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease. Microbiome 2023; 11:16. [PMID: 36721270 PMCID: PMC9890766 DOI: 10.1186/s40168-023-01463-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/09/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. 'primary phages') and (2) that 'secondary phages' that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly 'helping' the pathogen. RESULTS Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, 'secondary phages' that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and 'secondary phages' were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen. CONCLUSIONS Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Video Abstract.
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Affiliation(s)
- Keming Yang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiaofang Wang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Rujiao Hou
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chunxia Lu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhe Fan
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jingxuan Li
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shuo Wang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yangchun Xu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qirong Shen
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ville-Petri Friman
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland.
| | - Zhong Wei
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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14
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Law JP, Wood AJ, Friman VP. The Effects of Antibiotic Combination Treatments on Pseudomonas aeruginosa Tolerance Evolution and Coexistence with Stenotrophomonas maltophilia. Microbiol Spectr 2022; 10:e0184222. [PMID: 36453898 PMCID: PMC9769631 DOI: 10.1128/spectrum.01842-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
The Pseudomonas aeruginosa bacterium is a common pathogen of cystic fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. While P. aeruginosa resistance evolution is well-characterized in monocultures, it is less well-understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-minimum inhibitory concentration (MIC) doses, both alone and in combination, shaped the tolerance evolution of P. aeruginosa (PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species, Stenotrophomonas maltophilia. The increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and, when combined, the selected antibiotics increased the MICs for all of the antibiotics. Though the presence of S. maltophilia did not affect the tolerance or the MIC evolution, it drove P. aeruginosa into extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast, P. aeruginosa dominated and drove S. maltophilia extinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multispecies communities. IMPORTANCE Cystic fibrosis (CF) is a genetic condition that results in thick mucus secretions in the lungs that are susceptible to chronic bacterial infections. The bacterial pathogen Pseudomonas aeruginosa is often associated with morbidity in CF and is difficult to treat due to its high resistance to antibiotics. The resistance evolution of Pseudomonas aeruginosa is poorly understood in polymicrobial infections that are typical of CF. To study this, we exposed P. aeruginosa to sublethal concentrations of ciprofloxacin, colistin, or tobramycin antibiotics in the absence and presence of a commonly co-occurring CF species, Stenotrophomonas maltophilia. We found that low-level antibiotic concentrations selected for high-level antibiotic resistance. While P. aeruginosa dominated in most antibiotic treatments, S. maltophilia drove it into extinction in the presence of tobramycin due to an innately higher tobramycin resistance. Our findings suggest that, besides driving high-level antibiotic tolerance evolution, sublethal antibiotic exposure can magnify competition in bacterial communities, which can lead to target pathogen extinctions in multispecies communities.
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Affiliation(s)
- Jack P. Law
- Department of Biology, University of York, York, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
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15
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Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex. BMC Genomics 2022; 23:689. [PMID: 36199029 PMCID: PMC9535894 DOI: 10.1186/s12864-022-08909-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents. Results Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria. Conclusions Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08909-7.
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Affiliation(s)
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
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16
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Quinn AM, Bottery MJ, Thompson H, Friman VP. Resistance evolution can disrupt antibiotic exposure protection through competitive exclusion of the protective species. ISME J 2022; 16:2433-2447. [PMID: 35859161 PMCID: PMC9477885 DOI: 10.1038/s41396-022-01285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/05/2022]
Abstract
Antibiotic degrading bacteria can reduce the efficacy of drug treatments by providing antibiotic exposure protection to pathogens. While this has been demonstrated at the ecological timescale, it is unclear how exposure protection might alter and be affected by pathogen antibiotic resistance evolution. Here, we utilised a two-species model cystic fibrosis (CF) community where we evolved the bacterial pathogen Pseudomonas aeruginosa in a range of imipenem concentrations in the absence or presence of Stenotrophomonas maltophilia, which can detoxify the environment by hydrolysing β-lactam antibiotics. We found that P. aeruginosa quickly evolved resistance to imipenem via parallel loss of function mutations in the oprD porin gene. While the level of resistance did not differ between mono- and co-culture treatments, the presence of S. maltophilia increased the rate of imipenem resistance evolution in the four μg/ml imipenem concentration. Unexpectedly, imipenem resistance evolution coincided with the extinction of S. maltophilia due to increased production of pyocyanin, which was cytotoxic to S. maltophilia. Together, our results show that pathogen resistance evolution can disrupt antibiotic exposure protection due to competitive exclusion of the protective species. Such eco-evolutionary feedbacks may help explain changes in the relative abundance of bacterial species within CF communities despite intrinsic resistance to anti-pseudomonal drugs.
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17
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Greenrod S, Stoycheva M, Friman VP. Global diversity and potential functioning of prophages in plant pathogenic Ralstonia solanacearum bacterium. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ralstonia solanacearum is a destructive plant pathogenic bacterium which harbours a wide variety of virulence genes allowing it to infect over 200 plant species worldwide. Its virulence is also affected by the presence of integrated bacteriophages, termed prophages. While several such prophages have been identified, the global distribution and diversity of R. solanacearum prophages is unknown.
To study this, we first identified prophages present in a diverse collection of 192 assembled R. solanacearum genomes. Prophage diversity was explored by calculating prophage genetic distances and clustering with characterised prophages in a neighbour-joining tree. Prophage clusters were further verified by assessing gene content, GC content, and prophage length. Prophage identities were determined using the NCBI Virus database, and prophage-encoded virulence genes identified by analysing pangenome content.
343 intact prophages were identified, forming ten prophage clusters with distinct gene content, GC content, and length profiles. Five prophage clusters, containing 159 prophages, belonged to the Inoviridae, Myoviridae, and Siphoviridae phage families. The remaining 184 prophages were uncharacterised and may therefore represent novel prophages. Transcriptional regulators with potential virulence effects were identified in three prophage clusters, including one uncharacterised cluster. These prophage clusters were unequally distributed throughout the R. solanacearum population being host genotype specific.
This research demonstrates that R. solanacearum contains a high level of uncharacterised prophage diversity and highlights novel prophages that could contribute to pathogen virulence. Given their potential host-genotype-specific virulence effects, R. solanacearumprophages could be co-evolving with their hosts, and may contribute to global variation in R. solanacearum virulence.
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18
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Zhu C, Friman VP, Li L, Xu Q, Guo J, Guo S, Shen Q, Ling N. Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale. Environ Microbiol 2022; 24:2013-2028. [PMID: 35362656 DOI: 10.1111/1462-2920.15984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth's terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.
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Affiliation(s)
- Chen Zhu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ling Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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19
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Castledine M, Padfield D, Sierocinski P, Soria Pascual J, Hughes A, Mäkinen L, Friman VP, Pirnay JP, Merabishvili M, de Vos D, Buckling A. Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro. eLife 2022; 11:73679. [PMID: 35188102 PMCID: PMC8912922 DOI: 10.7554/elife.73679] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/20/2022] [Indexed: 12/02/2022] Open
Abstract
With rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolves to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct ‘in vitro evolutionary simulations’ using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria—evolved in vitro and in vivo—had lower virulence. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro phage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection on de novo mutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolve in vivo, and how in vitro experiments may give useful insights for clinical evolutionary outcomes.
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Affiliation(s)
- Meaghan Castledine
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Daniel Padfield
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Pawel Sierocinski
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Jesica Soria Pascual
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Adam Hughes
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Lotta Mäkinen
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | | | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel de Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Angus Buckling
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
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20
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Abstract
Phage therapy is a promising alternative to traditional antibiotics for treating bacterial infections. Such phage-based therapeutics typically contain multiple phages, but how the efficacy of phage combinations scales with phage richness, identity and functional traits is unclear. Here, we experimentally tested the efficacy of 827 unique phage combinations ranging in phage richness from one to 12 phages. The efficacy of phage combinations increased with phage richness. However, complementarity between functionally diverse phages allowed efficacy to be maximized at lower levels of phage richness in functionally diverse combinations. These findings suggest that phage functional diversity is the key property of effective phage combinations, enabling the design of simple but effective phage therapies that overcome the practical and regulatory hurdles that limit development of more diverse phage therapy cocktails.
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Affiliation(s)
- Rosanna C T Wright
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Department of Biology, University of York, York, UK.,Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | | | - Michael A Brockhurst
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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21
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Hu J, Yang T, Friman VP, Kowalchuk GA, Hautier Y, Li M, Wei Z, Xu Y, Shen Q, Jousset A. Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome. Proc Biol Sci 2021; 288:20211396. [PMID: 34641724 PMCID: PMC8511750 DOI: 10.1098/rspb.2021.1396] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant-associated microbiomes to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimized and how their effects are mediated. Here, we sought to enhance tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.
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Affiliation(s)
- Jie Hu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Yann Hautier
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
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22
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Fields B, Moffat EK, Harrison E, Andersen SU, Young JPW, Friman VP. Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex. Environ Microbiol 2021; 24:3463-3485. [PMID: 34398510 DOI: 10.1111/1462-2920.15720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/08/2021] [Accepted: 08/10/2021] [Indexed: 12/01/2022]
Abstract
Competitive and facilitative interactions influence bacterial community composition, diversity and functioning. However, the role of genetic diversity for determining interactions between coexisting strains of the same, or closely related, species remains poorly understood. Here, we investigated the type (facilitative/inhibitory) and potential underlying mechanisms of pairwise interactions between 24 genetically diverse bacterial strains belonging to three genospecies (gsA,C,E) of the Rhizobium leguminosarum species complex. Interactions were determined indirectly, based on secreted compounds in cell-free supernatants, and directly, as growth inhibition in cocultures. We found supernatants mediated both facilitative and inhibitory interactions that varied greatly between strains and genospecies. Overall, gsE strains indirectly suppressed growth of gsA strains, while their own growth was facilitated by other genospecies' supernatants. Similar genospecies-level patterns were observed in direct competition, where gsA showed the highest susceptibility and gsE the highest inhibition capacity. At the genetic level, increased gsA susceptibility was associated with a non-random distribution of quorum sensing and secondary metabolite genes across genospecies. Together, our results suggest that genetic variation is associated with facilitative and competitive interactions, which could be important ecological mechanisms explaining R. leguminosarum diversity.
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Affiliation(s)
| | - Emma K Moffat
- Department of Biology, University of York, York, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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23
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Liao H, Li X, Yang Q, Bai Y, Cui P, Wen C, Liu C, Chen Z, Tang J, Che J, Yu Z, Geisen S, Zhou S, Friman VP, Zhu YG. Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes. Mol Biol Evol 2021; 38:2337-2350. [PMID: 33592098 PMCID: PMC8136491 DOI: 10.1093/molbev/msab029] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Herbicides are one of the most widely used chemicals in agriculture. While they are known to be harmful to nontarget organisms, the effects of herbicides on the composition and functioning of soil microbial communities remain unclear. Here we show that application of three widely used herbicides—glyphosate, glufosinate, and dicamba—increase the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil microbiomes without clear changes in the abundance, diversity and composition of bacterial communities. Mechanistically, these results could be explained by a positive selection for more tolerant genotypes that acquired several mutations in previously well-characterized herbicide and ARGs. Moreover, herbicide exposure increased cell membrane permeability and conjugation frequency of multidrug resistance plasmids, promoting ARG movement between bacteria. A similar pattern was found in agricultural soils across 11 provinces in China, where herbicide application, and the levels of glyphosate residues in soils, were associated with increased ARG and MGE abundances relative to herbicide-free control sites. Together, our results show that herbicide application can enrich ARGs and MGEs by changing the genetic composition of soil microbiomes, potentially contributing to the global antimicrobial resistance problem in agricultural environments.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xi Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yudan Bai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Cui
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Wen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhi Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahuan Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiangang Che
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhen Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen 6700AA, Netherlands
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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24
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Wang X, Wan J, Jiang G, Yang T, Banerjee S, Wei Z, Mei X, Friman VP, Xu Y, Shen Q. Compositional and functional succession of bacterial and fungal communities is associated with changes in abiotic properties during pig manure composting. Waste Manag 2021; 131:350-358. [PMID: 34237529 DOI: 10.1016/j.wasman.2021.06.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
While both bacteria and fungi are important for the degradation and humification of organic matter during composting, it is unclear to what extent their roles are associated with abiotic compost properties. This study evaluated changes in abiotic compost properties and the succession of bacterial and fungal communities during pig manure composting for 90 days. The compost rapidly reached thermophilic phase (>58 ℃), which lasted for 15 days. Both bacterial and fungal community compositions changed drastically during composting and while bacterial diversity increased, the fungal diversity decreased during the thermophilic phase of composting. Two taxa dominated both bacterial (Bacillales and Clostridiales) and fungal (Eurotiales and Glomerellales) communities and these showed alternating abundance fluctuations following different phases of composting. The abundance fluctuations of most dominant bacterial and fungal taxa could be further associated with decreases in the concentrations of fulvic acid, cellulose, hemicellulose and overall biodegradation potential in the compost. Moreover, bacterial predicted metabolic gene abundances dominated the first three phases of composting, while predicted fungal saprotrophic functional genes increased consistently, reaching highest abundances towards the end of composting. Finally, redundancy analysis (RDA) showed that changes in abiotic compost properties correlated with the bacterial community diversity and carbohydrate metabolism and fungal wood saprotrophic function. Together these results suggests that bacterial and fungal community succession was associated with temporal changes in abiotic compost properties, potentially explaining alternating taxa abundance patterns during pig manure composting.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jinxin Wan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Zhong Wei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Xinlan Mei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | | | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
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25
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Liao H, Bai Y, Liu C, Wen C, Yang Q, Chen Z, Banerjee S, Zhou S, Friman VP. Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage. Environ Microbiol 2021; 23:7483-7496. [PMID: 34259375 DOI: 10.1111/1462-2920.15672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 11/27/2022]
Abstract
Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yudan Bai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chang Wen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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26
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Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021; 12:3829. [PMID: 34158504 PMCID: PMC8219802 DOI: 10.1038/s41467-021-24005-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Affiliation(s)
- Erqin Li
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.14095.390000 0000 9116 4836Freie Universität Berlin, Institut für Biologie, Berlin, Germany ,grid.452299.1Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
| | - Chen Liu
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Ville-Petri Friman
- grid.5685.e0000 0004 1936 9668University of York, Department of Biology, York, UK
| | - Corné M. J. Pieterse
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- grid.5477.10000000120346234Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands
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27
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Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021. [PMID: 34158504 DOI: 10.1038/s41467-012-24005-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Affiliation(s)
- Erqin Li
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
| | - Chen Liu
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | | | - Corné M J Pieterse
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A H M Bakker
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands.
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Duyvejonck H, Merabishvili M, Vaneechoutte M, de Soir S, Wright R, Friman VP, Verbeken G, De Vos D, Pirnay JP, Van Mechelen E, Vermeulen SJT. Evaluation of the Stability of Bacteriophages in Different Solutions Suitable for the Production of Magistral Preparations in Belgium. Viruses 2021; 13:v13050865. [PMID: 34066841 PMCID: PMC8151234 DOI: 10.3390/v13050865] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 01/20/2023] Open
Abstract
In Belgium, the incorporation of phages into magistral preparations for human application has been permitted since 2018. The stability of such preparations is of high importance to guarantee quality and efficacy throughout treatments. We evaluated the ability to preserve infectivity of four different phages active against three different bacterial species in five different buffer and infusion solutions commonly used in medicine and biotechnological manufacturing processes, at two different concentrations (9 and 7 log pfu/mL), stored at 4 °C. DPBS without Ca2+ and Mg2+ was found to be the best option, compared to the other solutions. Suspensions with phage concentrations of 7 log pfu/mL were unsuited as their activity dropped below the effective therapeutic dose (6–9 log pfu/mL), even after one week of storage at 4 °C. Strong variability between phages was observed, with Acinetobacter baumannii phage Acibel004 being stable in four out of five different solutions. We also studied the long term storage of lyophilized staphylococcal phage ISP, and found that the titer could be preserved during a period of almost 8 years when sucrose and trehalose were used as stabilizers. After rehydration of the lyophilized ISP phage in saline, the phage solutions remained stable at 4 °C during a period of 126 days.
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Affiliation(s)
- Hans Duyvejonck
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium; (H.D.); (E.V.M.)
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (M.M.); (M.V.)
| | - Maya Merabishvili
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (M.M.); (M.V.)
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (M.M.); (M.V.)
| | - Steven de Soir
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Rosanna Wright
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (R.W.); (V.-P.F.)
- Division of Evolution and Genomic Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (R.W.); (V.-P.F.)
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, 1120 Brussel, Belgium; (S.d.S.); (G.V.); (D.D.V.); (J.-P.P.)
| | - Els Van Mechelen
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium; (H.D.); (E.V.M.)
| | - Stefan J. T. Vermeulen
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium; (H.D.); (E.V.M.)
- Correspondence: ; Tel.: +32-498-496-997
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Abstract
Rhizobia - nitrogen-fixing, root-nodulating bacteria - play a critical role in both plant ecosystems and sustainable agriculture. Rhizobia form intracellular infections within legumes roots where they produce plant accessible nitrogen from atmospheric nitrogen and thus reduce the reliance on industrial inputs. The rhizobia-legume symbiosis is often treated as a pairwise relationship between single genotypes, both in research and in the production of rhizobial inoculants. However in nature individual plants are infected by a high diversity of rhizobia symbionts. How this diversity affects productivity within the symbiosis is unclear. Here, we use a powerful statistical approach to assess the impact of diversity within the Rhizobium leguminosarum - clover symbiosis using a biodiversity-ecosystem function framework. Statistically, we found no significant impact of rhizobium diversity. However this relationship was weakly positive - rather than negative - indicating that there is no significant cost to increasing inoculant diversity. Productivity was influenced by the identity of the strains within an inoculant; strains with the highest individual performance showed a significant positive contribution within mixed inoculants. Overall, inoculant effectiveness was best predicted by the individual performance of the best inoculant member, and only weakly predicted by the worst performing member. Collectively, our data suggest that the Rhizobium leguminosarum - clover symbiosis displays a weak diversity-function relationship, but that inoculant performance can be improved through the inclusion of high performing strains. Given the wide environmental dependence of rhizobial inoculant quality, multi-strain inoculants could be highly successful as they increase the likelihood of including a strain well adapted to local conditions across different environments.
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Affiliation(s)
- Bryden Fields
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Emma K Moffat
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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30
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Wan J, Wang X, Yang T, Wei Z, Banerjee S, Friman VP, Mei X, Xu Y, Shen Q. Livestock Manure Type Affects Microbial Community Composition and Assembly During Composting. Front Microbiol 2021; 12:621126. [PMID: 33828537 PMCID: PMC8019744 DOI: 10.3389/fmicb.2021.621126] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/25/2021] [Indexed: 12/17/2022] Open
Abstract
Composting is an environmentally friendly way to turn plant and animal wastes into organic fertilizers. However, it is unclear to what extent the source of animal waste products (such as manure) affects the physicochemical and microbiological properties of compost. Here, we experimentally tested how the type of livestock manure of herbivores (sheep and cattle) and omnivores (pig and chicken) influences the bacterial and fungal communities and physicochemical properties of compost. Higher pH, NO3-N, Total carbon (TC) content and C/N were found in sheep and cattle manure composts, while higher EC, NH4-N, Total nitrogen (TN) and total phosphorus (TP) content were measured in pig and chicken manure composts. Paired clustering between herbivore and omnivore manure compost metataxonomy composition was also observed at both initial and final phases of composting. Despite this clear clustering, all communities changed drastically during the composting leading to reduced bacterial and fungal diversity and large shifts in community composition and species dominance. While Proteobacteria and Chloroflexi were the major phyla in sheep and cattle manure composts, Firmicutes dominated in pig and chicken manure composts. Together, our results indicate that feeding habits of livestock can determine the biochemical and biological properties of manures, having predictable effects on microbial community composition and assembly during composting. Manure metataxonomy profiles could thus potentially be used to steer and manage composting processes.
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Affiliation(s)
- Jinxin Wan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xiaofang Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China.,Department of Biology, University of York, York, United Kingdom
| | - Xinlan Mei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, China
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31
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Fields B, Moeskjaer S, Friman VP, Andersen SU, Young JPW. MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction. Mol Ecol Resour 2020; 21:703-720. [PMID: 33171018 DOI: 10.1111/1755-0998.13294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/22/2020] [Accepted: 11/05/2020] [Indexed: 12/18/2022]
Abstract
Sequencing and PCR errors are a major challenge when characterizing genetic diversity using high-throughput amplicon sequencing (HTAS). We have developed a multiplexed HTAS method, MAUI-seq, which uses unique molecular identifiers (UMIs) to improve error correction by exploiting variation among sequences associated with a single UMI. Erroneous sequences are recognized because, across the data set, they are over-represented among the minor sequences associated with UMIs. We show that two main advantages of this approach are efficient elimination of chimeric and other erroneous reads, outperforming dada2 and unoise3, and the ability to confidently recognize genuine alleles that are present at low abundance or resemble chimeras. The method provides sensitive and flexible profiling of diversity and is readily adaptable to most HTAS applications, including microbial 16S rRNA profiling and metabarcoding of environmental DNA.
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Affiliation(s)
| | - Sara Moeskjaer
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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32
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Gu S, Wei Z, Shao Z, Friman VP, Cao K, Yang T, Kramer J, Wang X, Li M, Mei X, Xu Y, Shen Q, Kümmerli R, Jousset A. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nat Microbiol 2020; 5:1002-1010. [PMID: 32393858 DOI: 10.1038/s41564-020-0719-8] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/03/2020] [Indexed: 01/26/2023]
Abstract
Plant pathogenic bacteria cause high crop and economic losses to human societies1-3. Infections by such pathogens are challenging to control as they often arise through complex interactions between plants, pathogens and the plant microbiome4,5. Experimental studies of this natural ecosystem at the microbiome-wide scale are rare, and consequently we have a poor understanding of how the taxonomic and functional microbiome composition and the resulting ecological interactions affect pathogen growth and disease outbreak. Here, we combine DNA-based soil microbiome analysis with in vitro and in planta bioassays to show that competition for iron via secreted siderophore molecules is a good predictor of microbe-pathogen interactions and plant protection. We examined the ability of 2,150 individual bacterial members of 80 rhizosphere microbiomes, covering all major phylogenetic lineages, to suppress the bacterium Ralstonia solanacearum, a global phytopathogen capable of infecting various crops6,7. We found that secreted siderophores altered microbiome-pathogen interactions from complete pathogen suppression to strong facilitation. Rhizosphere microbiome members with growth-inhibitory siderophores could often suppress the pathogen in vitro as well as in natural and greenhouse soils, and protect tomato plants from infection. Conversely, rhizosphere microbiome members with growth-promotive siderophores were often inferior in competition and facilitated plant infection by the pathogen. Because siderophores are a chemically diverse group of molecules, with each siderophore type relying on a compatible receptor for iron uptake8-12, our results suggest that pathogen-suppressive microbiome members produce siderophores that the pathogen cannot use. Our study establishes a causal mechanistic link between microbiome-level competition for iron and plant protection and opens promising avenues to use siderophore-mediated interactions as a tool for microbiome engineering and pathogen control.
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Affiliation(s)
- Shaohua Gu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.
| | - Zhengying Shao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.,Department of Biology, University of York, York, UK
| | - Kehao Cao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Xiaofang Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Xinlan Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, P R China.,Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
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Raza W, Wang J, Jousset A, Friman VP, Mei X, Wang S, Wei Z, Shen Q. Bacterial community richness shifts the balance between volatile organic compound-mediated microbe-pathogen and microbe-plant interactions. Proc Biol Sci 2020; 287:20200403. [PMID: 32290797 DOI: 10.1098/rspb.2020.0403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant-bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to 12 strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe-pathogen and microbe-plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems.
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Affiliation(s)
- Waseem Raza
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Jianing Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Xinlan Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Shimei Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
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34
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Wang X, Wei Z, Yang K, Wang J, Jousset A, Xu Y, Shen Q, Friman VP. Phage combination therapies for bacterial wilt disease in tomato. Nat Biotechnol 2019; 37:1513-1520. [PMID: 31792408 DOI: 10.1038/s41587-019-0328-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022]
Abstract
Bacteriophages have been proposed as an alternative to pesticides to kill bacterial pathogens of crops. However, the efficacy of phage biocontrol is variable and poorly understood in natural rhizosphere microbiomes. We studied biocontrol efficacy of different phage combinations on Ralstonia solanacearum infection in tomato. Increasing the number of phages in combinations decreased the incidence of disease by up to 80% in greenhouse and field experiments during a single crop season. The decreased incidence of disease was explained by a reduction in pathogen density and the selection for phage-resistant but slow-growing pathogen strains, together with enrichment for bacterial species that were antagonistic toward R. solanacearum. Phage treatment did not affect the existing rhizosphere microbiota. Specific phage combinations have potential as precision tools to control plant pathogenic bacteria.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China
| | - Zhong Wei
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China.
| | - Keming Yang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China
| | - Jianing Wang
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China
| | - Alexandre Jousset
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China.,Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, the Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China.
| | - Ville-Petri Friman
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang, Nanjing, China. .,Department of Biology, University of York, York, UK.
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35
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Liao H, Zhao Q, Cui P, Chen Z, Yu Z, Geisen S, Friman VP, Zhou S. Efficient reduction of antibiotic residues and associated resistance genes in tylosin antibiotic fermentation waste using hyperthermophilic composting. Environ Int 2019; 133:105203. [PMID: 31665678 DOI: 10.1016/j.envint.2019.105203] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Insufficient removal of antibiotics and antibiotic resistance genes (ARGs) from waste products can increase the risk of selection for antibiotic resistance in non-clinical environments. While composting is an efficient way to reduce ARGs, most conventional methods are ineffective at processing highly contaminated antibiotic fermentation waste. Here we explored the efficacy and underlying mechanisms of hyperthermophilic composting at removing tylosin antibiotic fermentation residues (TFR) and associated ARGs and mobile genetic elements (MGEs; plasmids, integrons and transposon). Hyperthermophilic composting removed 95.0% of TFR, 75.8% of ARGs and 98.5% of MGEs and this reduction mainly occurred after extended exposure to temperatures above 60 °C for at least 6 days. Based on sequencing and culture-dependent experiments, reduction in ARGs and MGEs was strongly associated with a decrease in the number of bacterial taxa that were initially associated with ARGs and MGEs. Moreover, we found 94.1% reduction in plasmid genes abundances (ISCR1 and IncQ-oriV) that significantly correlated with reduced ARGs during the composting, which suggests that plasmids were the main carriers for ARGs. We verified this using direct culturing to show that ARGs were more often found in plasmids during the early phase of composting. Together these results suggest that hyperthermophilic composting is efficient at removing ARGs and associated resistance genes from antibiotic fermentation waste by decreasing the abundance of antibiotic resistance plasmids and associated host bacteria.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian Zhao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peng Cui
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, YO10 5DD York, UK
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
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Wright RCT, Friman VP, Smith MCM, Brockhurst MA. Resistance Evolution against Phage Combinations Depends on the Timing and Order of Exposure. mBio 2019; 10:e01652-19. [PMID: 31551330 PMCID: PMC6759759 DOI: 10.1128/mbio.01652-19] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/29/2019] [Indexed: 01/07/2023] Open
Abstract
Phage therapy is a promising alternative to chemotherapeutic antibiotics for the treatment of bacterial infections. However, despite recent clinical uses of combinations of phages to treat multidrug-resistant infections, a mechanistic understanding of how bacteria evolve resistance against multiple phages is lacking, limiting our ability to deploy phage combinations optimally. Here, we show, using Pseudomonas aeruginosa and pairs of phages targeting shared or distinct surface receptors, that the timing and order of phage exposure determine the strength, cost, and mutational basis of resistance. Whereas sequential exposure allowed bacteria to acquire multiple resistance mutations effective against both phages, this evolutionary trajectory was prevented by simultaneous exposure, resulting in quantitatively weaker resistance. The order of phage exposure determined the fitness costs of sequential resistance, such that certain sequential orders imposed much higher fitness costs than the same phage pair in the reverse order. Together, these data suggest that phage combinations can be optimized to limit the strength of evolved resistances while maximizing their associated fitness costs to promote the long-term efficacy of phage therapy.IMPORTANCE Globally rising rates of antibiotic resistance have renewed interest in phage therapy where combinations of phages have been successfully used to treat multidrug-resistant infections. To optimize phage therapy, we first need to understand how bacteria evolve resistance against combinations of multiple phages. Here, we use simple laboratory experiments and genome sequencing to show that the timing and order of phage exposure determine the strength, cost, and mutational basis of resistance evolution in the opportunistic pathogen Pseudomonas aeruginosa These findings suggest that phage combinations can be optimized to limit the emergence and persistence of resistance, thereby promoting the long-term usefulness of phage therapy.
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Affiliation(s)
- Rosanna C T Wright
- Department of Biology, University of York, York, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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Wei Z, Gu Y, Friman VP, Kowalchuk GA, Xu Y, Shen Q, Jousset A. Initial soil microbiome composition and functioning predetermine future plant health. Sci Adv 2019; 5:eaaw0759. [PMID: 31579818 PMCID: PMC6760924 DOI: 10.1126/sciadv.aaw0759] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 08/27/2019] [Indexed: 05/18/2023]
Abstract
Plant-pathogen interactions are shaped by multiple environmental factors, making it difficult to predict disease dynamics even in relatively simple agricultural monocultures. Here, we explored how variation in the initial soil microbiome predicts future disease outcomes at the level of individual plants. We found that the composition and functioning of the initial soil microbiome predetermined whether the plants survived or succumbed to disease. Surviving plant microbiomes were associated with specific rare taxa, highly pathogen-suppressing Pseudomonas and Bacillus bacteria, and high abundance of genes encoding antimicrobial compounds. Microbiome-mediated plant protection could subsequently be transferred to the next plant generation via soil transplantation. Together, our results suggest that small initial variation in soil microbiome composition and functioning can determine the outcomes of plant-pathogen interactions under natural field conditions.
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Affiliation(s)
- Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
| | - Yian Gu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, 223300, P.R. China
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
- Department of Biology, University of York, York, UK
| | - George A. Kowalchuk
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, P.R. China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, Netherlands
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Liao H, Friman VP, Geisen S, Zhao Q, Cui P, Lu X, Chen Z, Yu Z, Zhou S. Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting. Sci Total Environ 2019; 660:841-850. [PMID: 30743970 DOI: 10.1016/j.scitotenv.2018.12.353] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/02/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
About 1.3 billion tons of food waste (FW) is annually produced at a global scale. A major fraction of FW is deposited into landfills thereby contributing to environmental pollution and emission of greenhouse gasses. While increasing amounts of FW are recycled more sustainably into fertilizers in industrial-scale composting, very little is known about the antibiotic resistance genes (ARGs) present in FW and how their abundance is affected by composting. To study this, we quantified the diversity and abundance of ARGs, mobile genetic elements (MGEs) and bacterial communities in the beginning, during and at the end of the FW composting. All targeted 27 ARGs and 5 MGEs were detected in every sample suggesting that composted FW remains a reservoir of ARGs and MGEs. While the composting drastically changed the abundance, composition and diversity of bacterial communities, an increase in total ARG and MGE abundances was observed. Changes in ARGs were linked with shifts in the composition of bacterial communities as revealed by a Procrustes analysis (P < 0.01). Crucially, even though the high composting temperatures reduced the abundance and diversity of initially ARG-associated bacterial taxa, ARG abundances were maintained in other associated bacterial taxa. This was likely driven by horizontal gene transfer and physicochemical composting properties as revealed by a clear positive correlation between ARGs, MGEs, pH, NO3- and moisture. Together our findings suggest that traditional composting is not efficient at removing ARGs and MGEs from FW. More effective composting strategies are thus needed to minimize ARG release from composted FW into agricultural environments.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ville-Petri Friman
- Department of Biology, Wentworth Way, YO10 5DD, University of York, York, UK
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Qian Zhao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Cui
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaomei Lu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhi Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhen Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Yang T, Han G, Yang Q, Friman VP, Gu S, Wei Z, Kowalchuk GA, Xu Y, Shen Q, Jousset A. Resource stoichiometry shapes community invasion resistance via productivity-mediated species identity effects. Proc Biol Sci 2018; 285:20182035. [PMID: 30963908 PMCID: PMC6304049 DOI: 10.1098/rspb.2018.2035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/17/2018] [Indexed: 11/12/2022] Open
Abstract
Diversity-invasion resistance relationships are often variable and sensitive to environmental conditions such as resource availability. Resource stoichiometry, the relative concentration of different elements in the environment, has been shown to have strong effects on the physiology and interactions between different species. Yet, its role for diversity-invasion resistance relationships is still poorly understood. Here, we explored how the ratio of nitrogen (N) and phosphorus affects the productivity and invasion resistance of constructed microbial communities by a plant pathogenic bacterium, Ralstonia solanacearum. We found that resource stoichiometry and species identity effects affected the invasion resistance of communities. Both high N concentration and resident community diversity constrained invasions, and two resident species, in particular, had strong negative effects on the relative density of the invader and the resident community productivity. While resource stoichiometry did not affect the mean productivity of the resident community, it favoured the growth of two species that strongly constrained invasions turning the slope of productivity-invasion resistance relationship more negative. Together our findings suggest that alterations in resource stoichiometry can change the community resistance to invasions by having disproportionate effects on species growth, potentially explaining changes in microbial community composition under eutrophication.
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Affiliation(s)
- Tianjie Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gang Han
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Qingjun Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
- Department of Biology, University of York, Wentworth Way, YO10 5DD, York, UK
| | - Shaohua Gu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Zhong Wei
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - George A. Kowalchuk
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Li M, Wei Z, Wang J, Jousset A, Friman VP, Xu Y, Shen Q, Pommier T. Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett 2018; 22:149-158. [PMID: 30460736 DOI: 10.1111/ele.13177] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/12/2018] [Accepted: 10/08/2018] [Indexed: 12/31/2022]
Abstract
While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant-pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.
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Affiliation(s)
- Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jianing Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China.,Institute for Environmental Biology, Ecology& Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China.,Department of Biology, University of York, Wentworth Way, YO10 5DD, York, UK
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China
| | - Thomas Pommier
- Ecologie Microbienne, UMR1418, French National Institute for Agricultural Research (INRA), University Lyon I, F-69622, Villeurbanne, France
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Wright RCT, Friman VP, Smith MCM, Brockhurst MA. Cross-resistance is modular in bacteria-phage interactions. PLoS Biol 2018; 16:e2006057. [PMID: 30281587 PMCID: PMC6188897 DOI: 10.1371/journal.pbio.2006057] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/15/2018] [Accepted: 09/24/2018] [Indexed: 01/21/2023] Open
Abstract
Phages shape the structure of natural bacterial communities and can be effective therapeutic agents. Bacterial resistance to phage infection, however, limits the usefulness of phage therapies and could destabilise community structures, especially if individual resistance mutations provide cross-resistance against multiple phages. We currently understand very little about the evolution of cross-resistance in bacteria–phage interactions. Here we show that the network structure of cross-resistance among spontaneous resistance mutants of Pseudomonas aeruginosa evolved against each of 27 phages is highly modular. The cross-resistance network contained both symmetric (reciprocal) and asymmetric (nonreciprocal) cross-resistance, forming two cross-resistance modules defined by high within- but low between-module cross-resistance. Mutations conferring cross-resistance within modules targeted either lipopolysaccharide or type IV pilus biosynthesis, suggesting that the modularity of cross-resistance was structured by distinct phage receptors. In contrast, between-module cross-resistance was provided by mutations affecting the alternative sigma factor, RpoN, which controls many lifestyle-associated functions, including motility, biofilm formation, and quorum sensing. Broader cross-resistance range was not associated with higher fitness costs or weaker resistance against the focal phage used to select resistance. However, mutations in rpoN, providing between-module cross-resistance, were associated with higher fitness costs than mutations associated with within-module cross-resistance, i.e., in genes encoding either lipopolysaccharide or type IV pilus biosynthesis. The observed structure of cross-resistance predicted both the frequency of resistance mutations and the ability of phage combinations to suppress bacterial growth. These findings suggest that the evolution of cross-resistance is common, is likely to play an important role in the dynamic structure of bacteria–phage communities, and could inform the design principles for phage therapy treatments. Phage therapy is a promising alternative to antibiotics for treating bacterial infections. Yet as with antibiotics, bacteria readily evolve resistance to phage attack, including cross-resistance that protects against multiple phages at once and so limits the usefulness of phage cocktails. Here we show, using laboratory experimental evolution of resistance against 27 phages in P. aeruginosa, that cross-resistance is common and determines the ability of phage combinations to suppress bacterial growth. Using whole-genome sequencing, we show that cross-resistance is most common against multiple phages that use the same receptor but that global regulator mutations provide generalist resistance, probably by simultaneously affecting the expression of multiple different phage receptors. Future trials should test if these features of cross-resistance evolution translate to more complex in vivo environments and can therefore be exploited to design more effective phage therapies for the clinic.
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Affiliation(s)
- Rosanna C. T. Wright
- Department of Biology, University of York, York, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Michael A. Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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Flanagan L, Steen RR, Saxby K, Klatter M, Aucott BJ, Winstanley C, Fairlamb IJS, Lynam JM, Parkin A, Friman VP. The Antimicrobial Activity of a Carbon Monoxide Releasing Molecule (EBOR-CORM-1) Is Shaped by Intraspecific Variation within Pseudomonas aeruginosa Populations. Front Microbiol 2018; 9:195. [PMID: 29472912 PMCID: PMC5809400 DOI: 10.3389/fmicb.2018.00195] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
Carbon monoxide releasing molecules (CORMs) have been suggested as a new synthetic class of antimicrobials to treat bacterial infections. Here we utilized a novel EBOR-CORM-1 ([NEt4][MnBr2(CO)4]) capable of water-triggered CO-release, and tested its efficacy against a collection of clinical Pseudomonas aeruginosa strains that differ in infection-related virulence traits. We found that while EBOR-CORM-1 was effective in clearing planktonic and biofilm cells of P. aeruginosa strain PAO1 in a concentration dependent manner, this effect was less clear and varied considerably between different P. aeruginosa cystic fibrosis (CF) lung isolates. While a reduction in cell growth was observed after 8 h of CORM application, either no effect or even a slight increase in cell densities and the amount of biofilm was observed after 24 h. This variation could be partly explained by differences in bacterial virulence traits: while CF isolates showed attenuated in vivo virulence and growth compared to strain PAO1, they formed much more biofilm, which could have potentially protected them from the CORM. Even though no clear therapeutic benefits against a subset of isolates was observed in an in vivo wax moth acute infection model, EBOR-CORM-1 was more efficient at reducing the growth of CF isolate co-culture populations harboring intraspecific variation, in comparison with efficacy against more uniform single isolate culture populations. Together these results suggest that CORMs could be effective at controlling genetically diverse P. aeruginosa populations typical for natural chronic CF infections and that the potential benefits of some antibiotics might not be observed if tested only against clonal bacterial populations.
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Affiliation(s)
- Lindsey Flanagan
- Department of Biology, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
| | - Rachel R. Steen
- Department of Chemistry, University of York, York, United Kingdom
| | - Karinna Saxby
- Department of Biology, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
| | - Mirre Klatter
- Department of Biology, University of York, York, United Kingdom
| | | | - Craig Winstanley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - Jason M. Lynam
- Department of Chemistry, University of York, York, United Kingdom
| | - Alison Parkin
- Department of Chemistry, University of York, York, United Kingdom
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Moreau P, Diggle SP, Friman VP. Bacterial cell-to-cell signaling promotes the evolution of resistance to parasitic bacteriophages. Ecol Evol 2017; 7:1936-1941. [PMID: 28331600 PMCID: PMC5355186 DOI: 10.1002/ece3.2818] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/19/2016] [Accepted: 01/28/2017] [Indexed: 12/21/2022] Open
Abstract
The evolution of host–parasite interactions could be affected by intraspecies variation between different host and parasite genotypes. Here we studied how bacterial host cell‐to‐cell signaling affects the interaction with parasites using two bacteria‐specific viruses (bacteriophages) and the host bacterium Pseudomonas aeruginosa that communicates by secreting and responding to quorum sensing (QS) signal molecules. We found that a QS‐signaling proficient strain was able to evolve higher levels of resistance to phages during a short‐term selection experiment. This was unlikely driven by demographic effects (mutation supply and encounter rates), as nonsignaling strains reached higher population densities in the absence of phages in our selective environment. Instead, the evolved nonsignaling strains suffered relatively higher growth reduction in the absence of the phage, which could have constrained the phage resistance evolution. Complementation experiments with synthetic signal molecules showed that the Pseudomonas quinolone signal (PQS) improved the growth of nonsignaling bacteria in the presence of a phage, while the activation of las and rhl quorum sensing systems had no effect. Together, these results suggest that QS‐signaling can promote the evolution of phage resistance and that the loss of QS‐signaling could be costly in the presence of phages. Phage–bacteria interactions could therefore indirectly shape the evolution of intraspecies social interactions and PQS‐mediated virulence in P. aeruginosa.
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Affiliation(s)
- Pierre Moreau
- Imperial College London, Silwood Park Campus Ascot Berkshire UK
| | - Stephen P Diggle
- School of Life Sciences Centre for Biomolecular Sciences University of Nottingham Nottingham UK
| | - Ville-Petri Friman
- Imperial College London, Silwood Park Campus Ascot Berkshire UK; Department of Biology The University of York York UK
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Aminov R, Caplin J, Chanishvili N, Coffey A, Cooper I, De Vos D, Doškař J, Friman VP, Kurtböke İ, Pantucek R, Pirnay JP, Resch G, Rohde C, Sybesma W, Wittmann J. Application of bacteriophages. Microbiol Aust 2017. [DOI: 10.1071/ma17029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The emergence of antibiotic-resistant bacteria and decrease in the discovery rate of novel antibiotics takes mankind back to the ‘pre-antibiotic era' and search for alternative treatments. Bacteriophages have been one of promising alternative agents which can be utilised for medicinal and biological control purposes in agriculture and related fields. The idea to treat bacterial infections with phages came out of the pioneering work of Félix d‘Hérelle but this was overshadowed by the success of antibiotics. Recent renewed interest in phage therapy is dictated by its advantages most importantly by their specificity against the bacterial targets. This prevents complications such as antibiotic-induced dysbiosis and secondary infections. This article is compiled by the participants of the Expert Round Table conference ‘Bacteriophages as tools for therapy, prophylaxis and diagnostics' (19–21 October 2015) at the Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia. The first paper from the Round Table was published in the Biotechnology Journal1. This In Focus article expands from this paper and includes recent developments reported since then by the Expert Round Table participants, including the implementation of the Nagoya Protocol for the applications of bacteriophages.
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Mumford R, Friman VP. Bacterial competition and quorum-sensing signalling shape the eco-evolutionary outcomes of model in vitro phage therapy. Evol Appl 2016; 10:161-169. [PMID: 28127392 PMCID: PMC5253424 DOI: 10.1111/eva.12435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/25/2016] [Indexed: 12/12/2022] Open
Abstract
The rapid rise of antibiotic resistance has renewed interest in phage therapy – the use of bacteria‐specific viruses (phages) to treat bacterial infections. Even though phages are often pathogen‐specific, little is known about the efficiency and eco‐evolutionary outcomes of phage therapy in polymicrobial infections. We studied this experimentally by exposing both quorum‐sensing (QS) signalling PAO1 and QS‐deficient lasR Pseudomonas aeruginosa genotypes (differing in their ability to signal intraspecifically) to lytic PT7 phage in the presence and absence of two bacterial competitors: Staphylococcus aureus and Stenotrophomonas maltophilia–two bacteria commonly associated with P. aeruginosa in polymicrobial cystic fibrosis lung infections. Both the P. aeruginosa genotype and the presence of competitors had profound effects on bacteria and phage densities and bacterial resistance evolution. In general, competition reduced the P. aeruginosa frequencies leading to a lower rate of resistance evolution. This effect was clearer with QS signalling PAO1 strain due to lower bacteria and phage densities and relatively larger pleiotropic growth cost imposed by both phages and competitors. Unexpectedly, phage selection decreased the total bacterial densities in the QS‐deficient lasR pathogen communities, while an increase was observed in the QS signalling PAO1 pathogen communities. Together these results suggest that bacterial competition can shape the eco‐evolutionary outcomes of phage therapy.
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Affiliation(s)
- Rachel Mumford
- Silwood Park Campus Imperial College London Ascot Berkshire UK
| | - Ville-Petri Friman
- Silwood Park Campus Imperial College London Ascot Berkshire UK; Department of Biology University of York York UK
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Sun M, Ye M, Schwab AP, Li X, Wan J, Wei Z, Wu J, Friman VP, Liu K, Tian D, Liu M, Li H, Hu F, Jiang X. Human migration activities drive the fluctuation of ARGs: Case study of landfills in Nanjing, eastern China. J Hazard Mater 2016; 315:93-101. [PMID: 27179703 DOI: 10.1016/j.jhazmat.2016.04.077] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/27/2016] [Accepted: 04/30/2016] [Indexed: 05/22/2023]
Abstract
Landfills are perfect sites to study the effect of human migration on fluctuation of antibiotic resistance genes (ARGs) as they are the final destination of municipal waste. For example, large-scale human migration during the holidays is often accompanied by changes in waste dumping having potential effects on ARG abundance. Three landfills were selected to examine fluctuation in the abundance of fifteen ARGs and Intl1 genes for 14 months in Nanjing, eastern China. Mass human migration, the amount of dumped waste and temperature exerted the most significant effects on bimonthly fluctuations of ARG levels in landfill sites. As a middle-sized cosmopolitan city in China, millions of college students and workers migrate during holidays, contributing to the dramatic increases in waste production and fluctuation in ARG abundances. In line with this, mass migration explained most of the variation in waste dumping. The waste dumping also affected the bioaccessibility of mixed-compound pollutants that further positively impacted the level of ARGs. The influence of various bioaccessible compounds on ARG abundance followed the order: antibiotics>nutrients>metals>organic pollutants. Concentrations of bioaccessible compounds were more strongly correlated with ARG levels compared to total compound concentrations. Improved waste classification and management strategies could thus help to decrease the amount of bioaccessible pollutants leading to more effective control for urban ARG dissemination.
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Affiliation(s)
- Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Mao Ye
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Arthur P Schwab
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 88743, United States
| | - Xu Li
- Department of Civil Engineering, University of Nebraska-Lincoln, 844 North 16th Street, Lincoln, NE 68588-6105, United States
| | - Jinzhong Wan
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection of China, Nanjing 210042, PR China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Jun Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Ville-Petri Friman
- University of York, Department of Biology, Wentworth Way, York YO105DD, United Kingdom
| | - Kuan Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Da Tian
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huixin Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
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Friman VP, Guzman LM, Reuman DC, Bell T. Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities. Proc Biol Sci 2016; 282:20142920. [PMID: 25833854 DOI: 10.1098/rspb.2014.2920] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.
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Affiliation(s)
- Ville-Petri Friman
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Laura Melissa Guzman
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Daniel C Reuman
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK Department of Ecology and Evolutionary Biology and Kansas Biological Survey, University of Kansas, Lawrence, KS 66047, USA Laboratory of Populations, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thomas Bell
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
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Wei Z, Huang JF, Hu J, Gu YA, Yang CL, Mei XL, Shen QR, Xu YC, Friman VP. Altering Transplantation Time to Avoid Periods of High Temperature Can Efficiently Reduce Bacterial Wilt Disease Incidence with Tomato. PLoS One 2015; 10:e0139313. [PMID: 26441225 PMCID: PMC4595502 DOI: 10.1371/journal.pone.0139313] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/10/2015] [Indexed: 02/02/2023] Open
Abstract
Tomato bacterial wilt caused by Ralstonia solanacearum bacterium is a severe problem in Southern China, where relatively high environmental temperatures commonly prevails during the crop seasons. Previous research has indicated that bacterial wilt disease incidence generally increases during the warm months of summer leading to reduced tomato yield. Moreover, the efficacy of bio-organic fertilizers (BOFs)-organic compost fortified with pathogen-suppressive bacteria-is often lost during the periods of high environmental temperatures. Here we studied if the disease incidence could be reduced and the BOF performance enhanced by simply preponing and postponing the traditional seedling transplantation times to avoid tomato plant development during periods of high environmental temperature. To this end, a continuous, two-year field experiment was conducted to evaluate the performance of BOF in two traditional (late-spring [LS] and early-autumn [EA]) and two alternative (early-spring [ES] and late-autumn [LA]) crop seasons. We found that changing the transplantation times reduced the mean disease incidence from 33.9% (LS) and 54.7% (EA) to 11.1% (ES) and 7.1% (LA), respectively. Reduction in disease incidence correlated with the reduction in R. Solanacearum pathogen density in the tomato plant rhizosphere and stem base. Applying BOF during alternative transplantation treatments improved biocontrol efficiency from 43.4% (LS) and 3.1% (EA) to 67.4% (ES) and 64.8% (LA). On average, the mean maximum air temperatures were positively correlated with the disease incidence, and negatively correlated with the BOF biocontrol efficacy over the crop seasons. Crucially, even though preponing the transplantation time reduced the tomato yield in general, it was still economically more profitable compared to LS season due to reduced crop losses and relatively higher market prices. Preponing and postponing traditional tomato transplantation times to cooler periods could thus offer simple but effective way to control R. solanacearum disease outbreaks.
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Affiliation(s)
- Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Jian-Feng Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
- Institute of Agricultural Resources and the Environment, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou, PR China
| | - Jie Hu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Yi-An Gu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Chun-Lan Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Xin-Lan Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Qi-Rong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Yang-Chun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, PR China
| | - Ville-Petri Friman
- University of York, Department of Biology, Wentworth Way, York, YO10 5DD, London, United Kingdom
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Wei Z, Yang T, Friman VP, Xu Y, Shen Q, Jousset A. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nat Commun 2015; 6:8413. [PMID: 26400552 PMCID: PMC4598729 DOI: 10.1038/ncomms9413] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 08/19/2015] [Indexed: 02/06/2023] Open
Abstract
Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity-invasion resistance relationships in bacterial rhizosphere communities.
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Affiliation(s)
- Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Ville-Petri Friman
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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Friman VP, Ghoul M, Molin S, Johansen HK, Buckling A. Pseudomonas aeruginosa adaptation to lungs of cystic fibrosis patients leads to lowered resistance to phage and protist enemies. PLoS One 2013; 8:e75380. [PMID: 24069407 PMCID: PMC3777905 DOI: 10.1371/journal.pone.0075380] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 08/12/2013] [Indexed: 01/21/2023] Open
Abstract
Pathogenic life styles can lead to highly specialized interactions with host species, potentially resulting in fitness trade-offs in other ecological contexts. Here we studied how adaptation of the environmentally transmitted bacterial pathogen, Pseudomonas aeruginosa, to cystic fibrosis (CF) patients affects its survival in the presence of natural phage (14/1, ΦKZ, PNM and PT7) and protist (Tetrahymena thermophila and Acanthamoebae polyphaga) enemies. We found that most of the bacteria isolated from relatively recently intermittently colonised patients (1–25 months), were innately phage-resistant and highly toxic for protists. In contrast, bacteria isolated from long time chronically infected patients (2–23 years), were less efficient in both resisting phages and killing protists. Moreover, chronic isolates showed reduced killing of wax moth larvae (Galleria mellonella) probably due to weaker in vitro growth and protease expression. These results suggest that P. aeruginosa long-term adaptation to CF-lungs could trade off with its survival in aquatic environmental reservoirs in the presence of microbial enemies, while lowered virulence could reduce pathogen opportunities to infect insect vectors; factors that are both likely to result in poorer environmental transmission. From an applied perspective, phage therapy could be useful against chronic P. aeruginosa lung infections that are often characterized by multidrug resistance: chronic isolates were least resistant to phages and their poor growth will likely slow down the emergence of beneficial resistance mutations.
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Affiliation(s)
- Ville-Petri Friman
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Biosciences, University of Exeter, Penryn, United Kingdom
- * E-mail:
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Søren Molin
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | - Angus Buckling
- Biosciences, University of Exeter, Penryn, United Kingdom
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