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Laurich JR, Lash E, O'Brien AM, Pogoutse O, Frederickson ME. Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant. mBio 2024; 15:e0097224. [PMID: 38904411 PMCID: PMC11324027 DOI: 10.1128/mbio.00972-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes. IMPORTANCE There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.
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Affiliation(s)
- Jason R. Laurich
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Emma Lash
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Anna M. O'Brien
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
- Department of
Molecular, Cellular, and Biomedical Sciences, University of New
Hampshire, Durham,
New Hampshire, USA
| | - Oxana Pogoutse
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Megan E. Frederickson
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
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Sadiq FA, De Reu K, Yang N, Burmølle M, Heyndrickx M. Interspecies interactions in dairy biofilms drive community structure and response against cleaning and disinfection. Biofilm 2024; 7:100195. [PMID: 38639000 PMCID: PMC11024912 DOI: 10.1016/j.bioflm.2024.100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024] Open
Abstract
Interspecies interactions within a biofilm community influence population dynamics and community structure, which in turn may affect the bacterial stress response to antimicrobials. This study was conducted to assess the impact of interactions between Kocuria salsicia and a three-species biofilm community (comprising Stenotrophomonas rhizophila, Bacillus licheniformis, and Microbacterium lacticum) on biofilm mass, the abundance of individual species, and their survival under a laboratory-scale cleaning and disinfection (C&D) regime. The presence of K. salsicia enhanced the cell numbers of all three species in pairwise interactions. The outcomes derived from summing up pairwise interactions did not accurately predict the bacterial population dynamics within communities of more than two species. In four-species biofilms, we observed the dominance of S. rhizophila and B. licheniformis, alongside a concurrent reduction in the cell counts of K. salsicia and M. lacticum. This pattern suggests that the underlying interactions are not purely non-transitive; instead, a more complex interplay results in the dominance of specific species. We observed that bacterial spatial organization and matrix production in different mixed-species combinations affected survival in response to C&D. Confocal microscopy analysis of spatial organization showed that S. rhizophila localized on the biofilm formed by B. licheniformis and M. lacticum, and S. rhizophila was more susceptible to C&D. Matrix production in B. licheniformis, evidenced by alterations in biofilm mass and by scanning electron microscopy, demonstrated its protective role against C&D, not only for this species itself, but also for neighbouring species. Our findings emphasise that various social interactions within a biofilm community not only affect bacterial population dynamics but also influence the biofilm community's response to C&D stress.
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Affiliation(s)
- Faizan Ahmed Sadiq
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
- Advanced Therapies Group, School of Dentistry, Cardiff University, Cardiff, UK
| | - Koen De Reu
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Nan Yang
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
- Ghent University, Department of Pathobiology, Pharmacology and Zoological Medicine, Salisburylaan 133, B-9820, Merelbeke, Belgium
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Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
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Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Lee SM, Thapa Magar R, Jung MK, Kong HG, Song JY, Kwon JH, Choi M, Lee HJ, Lee SY, Khan R, Kim JF, Lee SW. Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health. THE ISME JOURNAL 2024; 18:wrae120. [PMID: 38952008 PMCID: PMC11253211 DOI: 10.1093/ismejo/wrae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
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Affiliation(s)
- Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Roniya Thapa Magar
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Min Kyeong Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Joo Hwan Kwon
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Minseo Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Jihyun F Kim
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Microbiome Initiative, Yonsei University, Seoul 03722, Republic of Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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5
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Kost C, Patil KR, Friedman J, Garcia SL, Ralser M. Metabolic exchanges are ubiquitous in natural microbial communities. Nat Microbiol 2023; 8:2244-2252. [PMID: 37996708 DOI: 10.1038/s41564-023-01511-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/11/2023] [Indexed: 11/25/2023]
Abstract
Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.
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Affiliation(s)
- Christian Kost
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany.
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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6
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Abstract
The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.
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Affiliation(s)
- James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA;
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7
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Guo H, Ji M, Du T, Xu W, Liu J, Bai R, Teng Z, Li T. Salt stress altered anaerobic microbial community and carbon metabolism characteristics: The trade-off between methanogenesis and chain elongation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 341:118111. [PMID: 37156025 DOI: 10.1016/j.jenvman.2023.118111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Discharge of saline organic wastewater is increasing worldwide, yet how salt stress disrupts the microbial community's structure and metabolism in bioreactors has not been systematically investigated. The non-adapted anaerobic granular sludge was inoculated into wastewater with varying salt concentration (ranging from 0% to 5%) to examine the effects of salt stress on the structure and function of the anaerobic microbial community. Result indicated that salt stress had a significant impact on the metabolic function and community structure of the anaerobic granular sludge. Specifically, we observed a notable reduction in methane production in response to all salt stress treatments (r = -0.97, p < 0.01), while an unexpected increase in butyrate production (r = 0.91, p < 0.01) under moderate salt stress (1-3%) with ethanol and acetate as carbon sources. In addition, analysis of microbiome structures and networks demonstrated that as the degree of salt stress increased, the networks exhibited lower connectance and increased compartmentalization. The abundance of interaction partners (methanogenic archaea and syntrophic bacteria) decreased under salt stress. In contrast, the abundance of chain elongation bacteria, specifically Clostridium kluyveri, increased under moderate salt stress (1-3%). As a consequence, the microbial carbon metabolism patterns shifted from cooperative mode (methanogenesis) to independent mode (carbon chain elongation) under moderate salt stress. This study provides evidence that salt stress altered the anaerobic microbial community and carbon metabolism characteristics, and suggests potential guidance for steering the microbiota to promote resource conversion in saline organic wastewater treatment.
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Affiliation(s)
- Huiyuan Guo
- CAS Key Laboratory of Green Process and Engineering, Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Beijing Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meina Ji
- CAS Key Laboratory of Green Process and Engineering, Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Beijing Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; Wuhan Institute of Technology, Wuhan, 430205, China
| | - Tianxiao Du
- CAS Key Laboratory of Green Process and Engineering, Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Beijing Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weichao Xu
- CAS Key Laboratory of Green Process and Engineering, Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Beijing Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianwei Liu
- Beijing Research Center of Sustainable Urban Drainage System and Risk Control, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Renbi Bai
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, 215009, China
| | - Zedong Teng
- CAS Key Laboratory of Green Process and Engineering, Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Beijing Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tinggang Li
- CAS Key Laboratory of Green Process and Engineering, Innovation Academy for Green Manufacture, National Engineering Research Center of Green Recycling for Strategic Metal Resources, Beijing Engineering Research Centre of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Ganjiang Innovation Academy, Jiangxi Province Key Laboratory of Cleaner Production of Rare Earths, Chinese Academy of Sciences, Ganzhou, 341000, China.
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