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Abbasi E, Akçay E. Host control and species interactions jointly determine microbiome community structure. Theor Popul Biol 2024; 158:185-194. [PMID: 38925487 DOI: 10.1016/j.tpb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.
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Affiliation(s)
- Eeman Abbasi
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA
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2
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Wang Z, Fu X, Kuramae EE. Insight into farming native microbiome by bioinoculant in soil-plant system. Microbiol Res 2024; 285:127776. [PMID: 38820701 DOI: 10.1016/j.micres.2024.127776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.
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Affiliation(s)
- Zhikang Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands; Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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3
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Isidoro-Ayza M, Lorch JM, Klein BS. The skin I live in: Pathogenesis of white-nose syndrome of bats. PLoS Pathog 2024; 20:e1012342. [PMID: 39207947 PMCID: PMC11361426 DOI: 10.1371/journal.ppat.1012342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
The emergence of white-nose syndrome (WNS) in North America has resulted in mass mortalities of hibernating bats and total extirpation of local populations. The need to mitigate this disease has stirred a significant body of research to understand its pathogenesis. Pseudogymnoascus destructans, the causative agent of WNS, is a psychrophilic (cold-loving) fungus that resides within the class Leotiomycetes, which contains mainly plant pathogens and is unrelated to other consequential pathogens of animals. In this review, we revisit the unique biology of hibernating bats and P. destructans and provide an updated analysis of the stages and mechanisms of WNS progression. The extreme life history of hibernating bats, the psychrophilic nature of P. destructans, and its evolutionary distance from other well-characterized animal-infecting fungi translate into unique host-pathogen interactions, many of them yet to be discovered.
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Affiliation(s)
- Marcos Isidoro-Ayza
- Department of Pediatrics, Medicine and Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jeffrey M. Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Bruce S. Klein
- Department of Pediatrics, Medicine and Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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4
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Uberoi A, McCready-Vangi A, Grice EA. The wound microbiota: microbial mechanisms of impaired wound healing and infection. Nat Rev Microbiol 2024; 22:507-521. [PMID: 38575708 DOI: 10.1038/s41579-024-01035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.
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Affiliation(s)
- Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amelia McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Chang YT, Huang WT, Wu PL, Kumar R, Wang HC, Lu HP. Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp. BMC Microbiol 2024; 24:275. [PMID: 39048954 PMCID: PMC11271031 DOI: 10.1186/s12866-024-03407-0] [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: 10/30/2023] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathogens. However, the mechanisms of how low salinity stress induces disease susceptibility remain poorly understood. METHODS We investigated the acute response of shrimp gut microbiota exposed to pathogens under low salinity stress. For comparison, shrimp were exposed to Vibrio infection under two salinity conditions: optimal salinity (Control group) and low salinity stress (Stress group). High throughput 16S rRNA sequencing and real-time PCR were employed to characterize the shrimp gut microbiota and quantify the severity level of Vibrio infection. RESULTS The results showed that low salinity stress increased Vibrio infection levels, reduced gut microbiota species richness, and perturbed microbial functions in the shrimp gut, leading to significant changes in lipopolysaccharide biosynthesis that promoted the growth of pathogens. Gut microbiota of the bacterial genera Candidatus Bacilliplasma, Cellvibrio, and Photobacterium were identified as biomarkers of the Stress group. The functions of the gut microbiota in the Stress group were primarily associated with cellular processes and the metabolism of lipid-related compounds. CONCLUSIONS Our findings reveal how environmental stress, particularly low salinity, increases shrimp susceptibility to Vibrio infection by affecting the gut microbiota. This highlights the importance of avoiding low salinity stress and promoting gut microbiota resilience to maintain the health of shrimp.
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Affiliation(s)
- Yi-Ting Chang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Ting Huang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Lun Wu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ramya Kumar
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Hsiao-Pei Lu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
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Sharma D, Kraft AL, Owade JO, Milicevic M, Yi J, Bergholz TM. Impact of Biotic and Abiotic Factors on Listeria monocytogenes, Salmonella enterica, and Enterohemorrhagic Escherichia coli in Agricultural Soil Extracts. Microorganisms 2024; 12:1498. [PMID: 39065266 PMCID: PMC11278928 DOI: 10.3390/microorganisms12071498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Outbreaks of Enterohemorrhagic Escherichia coli (EHEC), Salmonella enterica, and Listeria monocytogenes linked to fresh produce consumption pose significant food safety concerns. These pathogens can contaminate pre-harvest produce through various routes, including contaminated water. Soil physicochemical properties and flooding can influence pathogen survival in soils. We investigated survival of EHEC, S. enterica, and L. monocytogenes in soil extracts designed to represent soils with stagnant water. We hypothesized pathogen survival would be influenced by soil extract nutrient levels and the presence of native microbes. A chemical analysis revealed higher levels of total nitrogen, phosphorus, and carbon in high-nutrient soil extracts compared to low-nutrient extracts. Pathogen survival was enhanced in high-nutrient, sterile soil extracts, while the presence of native microbes reduced pathogen numbers. A microbiome analysis showed greater diversity in low-nutrient soil extracts, with distinct microbial compositions between extract types. Our findings highlight the importance of soil nutrient composition and microbial dynamics in influencing pathogen behavior. Given key soil parameters, a long short-term memory model (LSTM) effectively predicted pathogen survival. Integrating these factors can aid in developing predictive models for pathogen persistence in agricultural systems. Overall, our study contributes to understanding the complex interplay in agricultural ecosystems, facilitating informed decision-making for crop production and food safety enhancement.
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Affiliation(s)
- Dimple Sharma
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (D.S.)
| | - Autumn L. Kraft
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58105, USA
| | - Joshua O. Owade
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (D.S.)
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA (J.Y.)
| | - Mateja Milicevic
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA (J.Y.)
| | - Jiyoon Yi
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA (J.Y.)
| | - Teresa M. Bergholz
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA; (D.S.)
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7
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Li C, Chen X, Jia Z, Zhai L, Zhang B, Grüters U, Ma S, Qian J, Liu X, Zhang J, Müller C. Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities. Nat Ecol Evol 2024; 8:1270-1284. [PMID: 38849504 DOI: 10.1038/s41559-024-02437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024]
Abstract
Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Xinli Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, USA
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Uwe Grüters
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jing Qian
- Yangzhou China Grand Canal Museum, Yangzhou, China
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Liebig Centre for Agroecology and Climate Impact Research, Justus-Liebig University, Giessen, Germany
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8
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Klümper U, Gionchetta G, Catão E, Bellanger X, Dielacher I, Elena AX, Fang P, Galazka S, Goryluk-Salmonowicz A, Kneis D, Okoroafor U, Radu E, Szadziul M, Szekeres E, Teban-Man A, Coman C, Kreuzinger N, Popowska M, Vierheilig J, Walsh F, Woegerbauer M, Bürgmann H, Merlin C, Berendonk TU. Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation. Commun Biol 2024; 7:706. [PMID: 38851788 PMCID: PMC11162449 DOI: 10.1038/s42003-024-06338-8] [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: 05/25/2023] [Accepted: 05/15/2024] [Indexed: 06/10/2024] Open
Abstract
When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat's microbiome in the long term if they are able to overcome the habitat's biotic resilience towards immigration. This process should become more difficult with increasing biodiversity, as exploitable niches in a given habitat are reduced for immigrants when more diverse competitors are present. Consequently, microbial diversity could provide a natural barrier towards antimicrobial resistance by reducing the persistence time of immigrating ARB and ARG. To test this hypothesis, a pan-European sampling campaign was performed for structured forest soil and dynamic riverbed environments of low anthropogenic impact. In soils, higher diversity, evenness and richness were significantly negatively correlated with relative abundance of >85% of ARGs. Furthermore, the number of detected ARGs per sample were inversely correlated with diversity. However, no such effects were present in the more dynamic riverbeds. Hence, microbiome diversity can serve as a barrier towards antimicrobial resistance dissemination in stationary, structured environments, where long-term, diversity-based resilience against immigration can evolve.
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Affiliation(s)
- Uli Klümper
- Technische Universität Dresden, Institute for Hydrobiology, Dresden, Germany
| | - Giulia Gionchetta
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, Kastanienbaum, Switzerland
| | - Elisa Catão
- Université de Lorraine, Villers-lès-Nancy, France
- Université de Toulon, Toulon, France
| | | | - Irina Dielacher
- TU Wien, Institute of Water Quality and Resource Management, Vienna, Austria
| | - Alan Xavier Elena
- Technische Universität Dresden, Institute for Hydrobiology, Dresden, Germany
| | - Peiju Fang
- Technische Universität Dresden, Institute for Hydrobiology, Dresden, Germany
| | - Sonia Galazka
- AGES - Austrian Agency for Health and Food Safety, Department for Integrative Risk Assessment, Division for Risk Assessment, Data and Statistics, Vienna, Austria
| | - Agata Goryluk-Salmonowicz
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Physiology, Warsaw, Poland
- Warsaw University of Life Sciences, Institute of Biology, Department of Biochemistry and Microbiology, Warsaw, Poland
| | - David Kneis
- Technische Universität Dresden, Institute for Hydrobiology, Dresden, Germany
| | - Uchechi Okoroafor
- Maynooth University, Department of Biology, Kathleen Lonsdale Institute for Human Health, Maynooth, Co. Kildare, Ireland
| | - Elena Radu
- TU Wien, Institute of Water Quality and Resource Management, Vienna, Austria
- Romanian Academy of Science, Institute of Virology Stefan S. Nicolau, Bucharest, Romania
| | - Mateusz Szadziul
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Physiology, Warsaw, Poland
| | - Edina Szekeres
- NIRDBS, Institute of Biological Research Cluj-Napoca, Cluj-Napoca, Romania
| | - Adela Teban-Man
- NIRDBS, Institute of Biological Research Cluj-Napoca, Cluj-Napoca, Romania
| | - Cristian Coman
- NIRDBS, Institute of Biological Research Cluj-Napoca, Cluj-Napoca, Romania
| | - Norbert Kreuzinger
- TU Wien, Institute of Water Quality and Resource Management, Vienna, Austria
| | - Magdalena Popowska
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Physiology, Warsaw, Poland
| | - Julia Vierheilig
- TU Wien, Institute of Water Quality and Resource Management, Vienna, Austria
- Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Fiona Walsh
- Maynooth University, Department of Biology, Kathleen Lonsdale Institute for Human Health, Maynooth, Co. Kildare, Ireland
| | - Markus Woegerbauer
- AGES - Austrian Agency for Health and Food Safety, Department for Integrative Risk Assessment, Division for Risk Assessment, Data and Statistics, Vienna, Austria
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, Kastanienbaum, Switzerland
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9
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Miller IR, Bui H, Wood JB, Fields MW, Gerlach R. Understanding phycosomal dynamics to improve industrial microalgae cultivation. Trends Biotechnol 2024; 42:680-698. [PMID: 38184438 DOI: 10.1016/j.tibtech.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/08/2024]
Abstract
Algal-bacterial interactions are ubiquitous in both natural and industrial systems, and the characterization of these interactions has been reinvigorated by potential applications in biosystem productivity. Different growth conditions can be used for operational functions, such as the use of low-quality water or high pH/alkalinity, and the altered operating conditions likely constrain microbial community structure and function in unique ways. However, research is necessary to better understand whether consortia can be designed to improve the productivity, processing, and sustainability of industrial-scale cultivations through different controls that can constrain microbial interactions for maximal light-driven outputs. The review highlights current knowledge and gaps for relevant operating conditions, as well as suggestions for near-term and longer-term improvements for large-scale cultivation and polyculture engineering.
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Affiliation(s)
- Isaac R Miller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Huyen Bui
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Jessica B Wood
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Matthew W Fields
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; Department of Civil Engineering, Montana State University, Bozeman, MT, USA; Energy Research Institute, Montana State University, Bozeman, MT, USA.
| | - Robin Gerlach
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; Energy Research Institute, Montana State University, Bozeman, MT, USA; Department of Biological and Chemical Engineering, Bozeman, MT, USA
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10
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Maull V, Solé R. Biodiversity as a firewall to engineered microbiomes for restoration and conservation. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231526. [PMID: 39100153 PMCID: PMC11296081 DOI: 10.1098/rsos.231526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 08/06/2024]
Abstract
The possibility of abrupt transitions threatens to poise ecosystems into irreversibly degraded states. Synthetic biology has recently been proposed to prevent them from crossing tipping points. However, there is little understanding of the impact of such intervention on the resident communities. Can such modification have 'unintended consequences', such as loss of species? Here, we address this problem by using a mathematical model that allows us to simulate this intervention scenario explicitly. We show how the indirect effect of damping the decay of shared resources results in biodiversity increase, and last but not least, the successful incorporation of the synthetic within the ecological network and very small-positive changes in the population size of the resident community. Furthermore, extensions and implications for future restoration and terraformation strategies are discussed.
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Affiliation(s)
- Victor Maull
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, Barcelona08003, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, Barcelona08003, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, Barcelona08003, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, Barcelona08003, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM87501, USA
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11
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Zhu Y, Momeni B. Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends. PLoS Comput Biol 2024; 20:e1012193. [PMID: 38865380 PMCID: PMC11198907 DOI: 10.1371/journal.pcbi.1012193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/25/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Host-associated resident microbiota can protect their host from pathogens-a community-level trait called colonization resistance. The effect of the diversity of the resident community in previous studies has shown contradictory results, with higher diversity either strengthening or weakening colonization resistance. To control the confounding factors that may lead to such contradictions, we use mathematical simulations with a focus on species interactions and their impact on colonization resistance. We use a mediator-explicit model that accounts for metabolite-mediated interactions to perform in silico invasion experiments. We show that the relationship between colonization resistance and species richness of the resident community is not monotonic because it depends on two underlying trends as the richness of the resident community increases: a decrease in instances of augmentation (invader species added, without driving out resident species) and an increase in instances of displacement (invader species added, driving out some of the resident species). These trends hold consistently under different parameters, regardless of the number of compounds that mediate interactions between species or the proportion of the facilitative versus inhibitory interactions among species. Our results show a positive correlation between resistance and diversity in low-richness communities and a negative correlation in high-richness communities, offering an explanation for the seemingly contradictory trend in the resistance-diversity relationship in previous reports.
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Affiliation(s)
- Yu Zhu
- Biology Department, Boston College, Chestnut Hill, Massachusetts, Unites States of America
| | - Babak Momeni
- Biology Department, Boston College, Chestnut Hill, Massachusetts, Unites States of America
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12
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Eliette AS, Elodie B, Arnaud M, Tiffany R, Aymé S, Pascal P. Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities. Sci Rep 2024; 14:12375. [PMID: 38811807 PMCID: PMC11137084 DOI: 10.1038/s41598-024-63284-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024] Open
Abstract
Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.
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Affiliation(s)
- Ascensio-Schultz Eliette
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Barbier Elodie
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Mounier Arnaud
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Raynaud Tiffany
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Spor Aymé
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
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13
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Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [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: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
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Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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14
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Algavi YM, Borenstein E. Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics. Nat Commun 2024; 15:4447. [PMID: 38789466 PMCID: PMC11126695 DOI: 10.1038/s41467-024-48717-z] [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: 09/12/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Microorganisms frequently migrate from one ecosystem to another. Yet, despite the potential importance of this process in modulating the environment and the microbial ecosystem, our understanding of the fundamental forces that govern microbial dispersion is still lacking. Moreover, while theoretical models and in-vitro experiments have highlighted the contribution of species interactions to community assembly, identifying such interactions in vivo, specifically in communities as complex as the human gut, remains challenging. To address this gap, here we introduce a robust and rigorous computational framework, termed Relative Dispersion Ratio (RDR) analysis, and leverage data from well-characterized fecal microbiota transplant trials, to rigorously pinpoint dependencies between taxa during the colonization of human gastrointestinal tract. Our analysis identifies numerous pairwise dependencies between co-colonizing microbes during migration between gastrointestinal environments. We further demonstrate that identified dependencies agree with previously reported findings from in-vitro experiments and population-wide distribution patterns. Finally, we explore metabolic dependencies between these taxa and characterize the functional properties that facilitate effective dispersion. Collectively, our findings provide insights into the principles and determinants of community dynamics following ecological translocation, informing potential opportunities for precise community design.
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Affiliation(s)
- Yadid M Algavi
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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15
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Hou D, Li H, Wang S, Weng S, He J. Nitrite nitrogen stress disrupts the intestine bacterial community by altering host-community interactions in shrimp. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171536. [PMID: 38461992 DOI: 10.1016/j.scitotenv.2024.171536] [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: 01/02/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Environmental stress can disrupt the intricate interactions between the host and intestine microbiota, thereby impacting the host health. In this study, we aimed to elucidate the dynamic changes in the bacterial community within shrimp intestines under nitrite nitrogen (nitrite-N) stress and investigate potential host-related factors influencing these changes. Our results revealed a significant reduction in community diversity within the intestine exposed to nitrite-N compared to control conditions. Furthermore, distinct differences in community structures were observed between these two groups at 72 h and 120 h post-stress induction. Nitrite-N stress also altered the abundances of some bacterial species in the intestine dramatically. It is noteworthy that, in comparison to the 72 h, intestine bacterial community structure of stressed shrimp exhibited a significantly higher degree of dispersion after 120 h of nitrite-N stress when compared to control shrimp, and the relative abundance of numerous bacterial species experienced a substantial decrease or even reached 0 %. Moreover, it led to a reduction in bacterial community interactions and decreased competitiveness within the intestine microbiota. Notably, the influence of bacterial community assemblies in the shrimp intestine shifted from a stochastic process to a deterministic one after 24 h and 72 h of nitrite-N stress, returning to a stochastic process at 120 h. We further observed a close association between this phenomenon and host's response to nitrite-N stress. Expression levels of differentially expressed genes in the intestinal tissue significantly impact the intestine bacterial diversity and abundance of species. In particular, the significant decline in bacterial diversity and abundances of quite a few species in intestine was attributed to the up-regulation of peritrophin-48-like. Overall, nitrite-N stress indeed disrupted the intestine microbiota and changed the host-microbiota interactions of shrimp. This study offered novel insights into environment-host-microbiota interactions and also provided practical guidance for promoting healthy shrimp cultivation practices.
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Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haoyang Li
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sheng Wang
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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16
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Vandermaesen J, Daly AJ, Mawarda PC, Baetens JM, De Baets B, Boon N, Springael D. Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship. Ecol Lett 2024; 27:e14433. [PMID: 38712704 DOI: 10.1111/ele.14433] [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: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]
Abstract
The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.
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Affiliation(s)
| | - Aisling J Daly
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Panji Cahya Mawarda
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
- Research Center for Applied Microbiology, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, Indonesia
| | - Jan M Baetens
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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17
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McGrath-Blaser SE, McGathey N, Pardon A, Hartmann AM, Longo AV. Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens. Proc Biol Sci 2024; 291:20232658. [PMID: 38628130 PMCID: PMC11021929 DOI: 10.1098/rspb.2023.2658] [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: 12/07/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). To predict potential dispersal of Bsal spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, Bsal, and an introduced but endemic pathogen, B. dendrobatidis (Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited both Bsal and Bd growth, but inhibitory capacity diminished with increased propagule pressure. Bsal showed greater persistence than Bd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.
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Affiliation(s)
| | - Natalie McGathey
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Allison Pardon
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Arik M. Hartmann
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ana V. Longo
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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18
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Barron AJ, Agrawal S, Lesperance DNA, Doucette J, Calle S, Broderick NA. Microbiome-derived acidity protects against microbial invasion in Drosophila. Cell Rep 2024; 43:114087. [PMID: 38583152 PMCID: PMC11163447 DOI: 10.1016/j.celrep.2024.114087] [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: 10/13/2023] [Revised: 02/16/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Microbial invasions underlie host-microbe interactions resulting in pathogenesis and probiotic colonization. In this study, we explore the effects of the microbiome on microbial invasion in Drosophila melanogaster. We demonstrate that gut microbes Lactiplantibacillus plantarum and Acetobacter tropicalis improve survival and lead to a reduction in microbial burden during infection. Using a microbial interaction assay, we report that L. plantarum inhibits the growth of invasive bacteria, while A. tropicalis reduces this inhibition. We further show that inhibition by L. plantarum is linked to its ability to acidify its environment via lactic acid production by lactate dehydrogenase, while A. tropicalis diminishes the inhibition by quenching acids. We propose that acid from the microbiome is a gatekeeper to microbial invasions, as only microbes capable of tolerating acidic environments can colonize the host. The methods and findings described herein will add to the growing breadth of tools to study microbe-microbe interactions in broad contexts.
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Affiliation(s)
- Alexander J Barron
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Sneha Agrawal
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Danielle N A Lesperance
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jeremy Doucette
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Sthefany Calle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nichole A Broderick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
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19
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Guo Z, Lu Z, Liu Z, Zhou W, Yang S, Lv J, Wei M. Difference in the Effect of Applying Bacillus to Control Tomato Verticillium Wilt in Black and Red Soil. Microorganisms 2024; 12:797. [PMID: 38674740 PMCID: PMC11052436 DOI: 10.3390/microorganisms12040797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In practical applications, the effectiveness of biological control agents such as Bacillus is often unstable due to different soil environments. Herein, we aimed to explore the control effect and intrinsic mechanism of Bacillus in black soil and red soil in combination with tomato Verticillium wilt. Bacillus application effectively controlled the occurrence of Verticillium wilt in red soil, reducing the incidence by 19.83%, but played a limited role in black soil. Bacillus colonized red soil more efficiently. The Verticillium pathogen decreased by 71.13% and 76.09% after the application of Bacillus combinations in the rhizosphere and bulk of the red soil, respectively, while there was no significant difference in the black soil. Additionally, Bacillus application to red soil significantly promoted phosphorus absorption. Furthermore, it significantly altered the bacterial community in red soil and enriched genes related to pathogen antagonism and phosphorus activation, which jointly participated in soil nutrient activation and disease prevention, promoting tomato plant growth in red soil. This study revealed that the shaping of the bacterial community by native soil may be the key factor affecting the colonization and function of exogenous Bacillus.
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Affiliation(s)
| | | | | | | | | | | | - Mi Wei
- School of Agriculture, Shenzhen Campus, Sun Yat-Sen University, Shenzhen 518107, China; (Z.G.); (Z.L.); (Z.L.); (W.Z.); (S.Y.); (J.L.)
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20
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Sha H, Lu J, Chen J, Xiong J. Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis. NPJ Biofilms Microbiomes 2024; 10:40. [PMID: 38605016 PMCID: PMC11009345 DOI: 10.1038/s41522-024-00509-5] [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: 10/03/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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21
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Čaušević S, Dubey M, Morales M, Salazar G, Sentchilo V, Carraro N, Ruscheweyh HJ, Sunagawa S, van der Meer JR. Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions. Nat Commun 2024; 15:2557. [PMID: 38519488 PMCID: PMC10959995 DOI: 10.1038/s41467-024-46933-1] [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: 10/17/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.
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Affiliation(s)
- Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Guillem Salazar
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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22
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Liu X, Salles JF. Lose-lose consequences of bacterial community-driven invasions in soil. MICROBIOME 2024; 12:57. [PMID: 38494494 PMCID: PMC10946201 DOI: 10.1186/s40168-024-01763-7] [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: 06/12/2023] [Accepted: 01/10/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities. RESULTS Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~ 5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community. CONCLUSIONS Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.
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Affiliation(s)
- Xipeng Liu
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG, Groningen, The Netherlands.
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23
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Li C, Li X, Romdhane S, Cheng Y, Li G, Cao R, Li P, Xu J, Zhao Y, Yang Y, Jiao J, Hu F, Wu J, Li H, Philippot L. Deciphering the biotic and abiotic drivers of coalescence asymmetry between soil and manure microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170180. [PMID: 38262533 DOI: 10.1016/j.scitotenv.2024.170180] [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: 10/29/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Manure application improves soil fertility, yet its implications on the success of invasion of manure-borne microorganisms in the soil are poorly understood. Here, we assessed the importance of abiotic and biotic factors in modulating the extent to which manure-borne fungal and bacterial communities can invade resident soil microbial communities. For this purpose, we applied varying frequencies of two different amounts of manure to nine soils differing in physico-chemical properties, as well as in land-use history, over 180 days and monitored changes in bacterial and fungal communities. Variance partitioning revealed differential contributions of abiotic and biotic factors to invasion success, which together accounted for up to 82 % of the variance explained. We showed that the effects of interactions between biotic and abiotic factors increased with coalescence frequency and manure amount for the bacterial and fungal communities, respectively. Both abiotic and biotic factors were important for modulating coalescence asymmetry for the bacterial community, whereas abiotic factors had a greater effect on the fungal community. These results provide new insights into the drivers of coalescence events between manure and resident soil microbial communities. Moreover, our findings highlight the roles of the mixing ratio and frequency of coalescence events in modulating the survival of manure-borne microorganisms.
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Affiliation(s)
- Chunkai Li
- College of Chemical Engineering, Nanjing Forestry University, No. 159, Longpan Road, Nanjing, Jiangsu 210037, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Xianping Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Sana Romdhane
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroécologie, Dijon 21000, France.
| | - Yanhong Cheng
- Key Laboratory of Red Soil Cultivated Land Conservation, Jiangxi Institute of Red Soil and Germplasm Resource, Nanchang, Jiangxi 331717, China
| | - Gen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Rui Cao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Peng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Jingjing Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Yexin Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Yang Yang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Jiaguo Jiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Jun Wu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China.
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Weigang, Nanjing 210014, China.
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroécologie, Dijon 21000, France.
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24
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Bagra K, Kneis D, Padfield D, Szekeres E, Teban-Man A, Coman C, Singh G, Berendonk TU, Klümper U. Contrary effects of increasing temperatures on the spread of antimicrobial resistance in river biofilms. mSphere 2024; 9:e0057323. [PMID: 38323843 PMCID: PMC10900892 DOI: 10.1128/msphere.00573-23] [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: 10/10/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
River microbial communities regularly act as the first barrier of defense against the spread of antimicrobial resistance genes (ARGs) that enter environmental microbiomes through wastewater. However, how the invasion dynamics of wastewater-borne ARGs into river biofilm communities will shift due to climate change with increasing average and peak temperatures remains unknown. Here, we aimed to elucidate the effects of increasing temperatures on the naturally occurring river biofilm resistome, as well as the invasion success of foreign ARGs entering through wastewater. Natural biofilms were grown in a low-anthropogenic impact river and transferred to artificial laboratory recirculation flume systems operated at three different temperatures (20°C, 25°C, and 30°C). After 1 week of temperature acclimatization, significant increases in the abundance of the naturally occurring ARGs in biofilms were detected at higher temperatures. After this acclimatization period, biofilms were exposed to a single pulse of wastewater, and the invasion dynamics of wastewater-borne ARGs were analyzed over 2 weeks. After 1 day, wastewater-borne ARGs were able to invade the biofilms successfully with no observable effect of temperature on their relative abundance. However, thereafter, ARGs were lost at a far increased rate at 30°C, with ARG levels dropping to the initial natural levels after 14 days. Contrary to the lower temperatures, ARGs were either lost at slower rates or even able to establish themselves in biofilms with stable relative abundances above natural levels. Hence, higher temperatures come with contrary effects on river biofilm resistomes: naturally occurring ARGs increase in abundance, while foreign, invading ARGs are lost at elevated speeds.IMPORTANCEInfections with bacteria that gained resistance to antibiotics are taking millions of lives annually, with the death toll predicted to increase. River microbial communities act as a first defense barrier against the spread of antimicrobial resistance genes (ARGs) that enter the environment through wastewater after enrichment in human and animal microbiomes. The global increase in temperature due to climate change might disrupt this barrier effect by altering microbial community structure and functions. We consequently explored how increasing temperatures alter ARG spread in river microbial communities. At higher temperatures, naturally occurring ARGs increased in relative abundance. However, this coincided with a decreased success rate of invading foreign ARGs from wastewater to establish themselves in the communities. Therefore, to predict the effects of climate change on ARG spread in river microbiomes, it is imperative to consider if the river ecosystem and its resistome are dominated by naturally occurring or invading foreign ARGs.
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Affiliation(s)
- Kenyum Bagra
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
- Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - David Kneis
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Daniel Padfield
- Environment and Sustainability Institute, University of Exeter, Exeter, United Kingdom
| | - Edina Szekeres
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
| | - Adela Teban-Man
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
| | - Cristian Coman
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
| | - Gargi Singh
- Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Thomas U. Berendonk
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
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25
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Papin M, Philippot L, Breuil MC, Bru D, Dreux-Zigha A, Mounier A, Le Roux X, Rouard N, Spor A. Survival of a microbial inoculant in soil after recurrent inoculations. Sci Rep 2024; 14:4177. [PMID: 38378706 PMCID: PMC10879113 DOI: 10.1038/s41598-024-54069-x] [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: 10/31/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.
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Affiliation(s)
- M Papin
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - L Philippot
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France.
| | - M C Breuil
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - D Bru
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - A Dreux-Zigha
- GreenCell Biopole Clermont Limagne, 63360, St Beauzire, France
| | - A Mounier
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - X Le Roux
- Universite Claude Bernard Lyon 1, Microbial Ecology Centre LEM, INRAE, CNRS, VetAgroSup, UMR INRAE 1418, 43 Blvd 11 Novembre 1918, 69622, Villeurbanne, France
| | - N Rouard
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - A Spor
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
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26
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Xiao Y, Zhang S, Li H, Teng K, Wu S, Liu Y, Yu F, He Z, Li L, Li L, Meng D, Yin H, Wang Y. Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2024; 15:1325141. [PMID: 38434434 PMCID: PMC10904623 DOI: 10.3389/fpls.2024.1325141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.
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Affiliation(s)
- Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Sai Zhang
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Hongguang Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Kai Teng
- Xiangxi Tobacco Co Hunan Prov, Changsha, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, China
| | - Yongbin Liu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Fahui Yu
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Zhihong He
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Lijuan Li
- Chenzhou Tobacco Company of Hunan Province, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yujie Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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27
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Lee Díaz AS, Minchev Z, Raaijmakers JM, Pozo MJ, Garbeva P. Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress. FEMS Microbiol Ecol 2024; 100:fiad160. [PMID: 38331428 PMCID: PMC10858387 DOI: 10.1093/femsec/fiad160] [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: 01/30/2023] [Revised: 11/16/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024] Open
Abstract
Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.
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Affiliation(s)
- Ana Shein Lee Díaz
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhivko Minchev
- Department of Soil Microbiology and Symbiotic Systems
, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientfícias (CSIC), Calle Prof. Albareda, 1, 18008, Granada, Spain
| | - Jos M Raaijmakers
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - María José Pozo
- Department of Soil Microbiology and Symbiotic Systems
, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientfícias (CSIC), Calle Prof. Albareda, 1, 18008, Granada, Spain
| | - Paolina Garbeva
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
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28
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Wang X, Zhou Z, Zijing L, Xia L, Song S, Meza JVG, Montes ML, Li J. Surge of native rare taxa in tailings soil induced by peat bacterial invasion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168596. [PMID: 37972774 DOI: 10.1016/j.scitotenv.2023.168596] [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: 09/11/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
The pivotal role of the native bacterial community in maintaining soil health, particularly in degraded tailings environments, is often overlooked. This study utilized peat, rich in microorganisms, to investigate its impact on soil function and native bacteria response in copper tailings-soil. Through 16S rRNA gene sequencing, changes in nutrient cycling, organic matter decomposition, and microbial activity were assessed post one-year peat remediation. Results from FEAST and cluster analysis revealed that peat-derived species disproportionately influenced tailings microbial community remediation, supported by the microbial invasion theory. Tailings responded positively to these species, with optimal function achieved at 5 % peat dosage. Peat biomarkers (Actinobacteriota, Bacteroida, Chloroflexi, and Firmicutes) played key roles in heavy metal removal and nutrition fixation. The Random Forest model and co-occurrence network highlighted contributions from native rare species (Dependentiae and Latescibacterota) activated by peat addition. These insights underscore the resilience of rare taxa and provide a foundation for soil health restoration in tailings areas. By emphasizing the importance of peat as a potential exogenous solution for activating indigenous microbial functions, these findings offer valuable insights for developing effective and sustainable remediation strategies in mining-affected regions.
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Affiliation(s)
- Xizhuo Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, Hubei Province 430070, China
| | - Zhou Zhou
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, Hubei Province 430070, China
| | - Lu Zijing
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, Hubei Province 430070, China
| | - Ling Xia
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, Hubei Province 430070, China.
| | - Shaoxian Song
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, Hubei Province 430070, China
| | - J Viridiana García Meza
- Instituto de Física, Universidad Autonoma de San Luis Potosi, Av. Manuel Nava 6, Zona Universitaria, C.P., San Luis Potosí 78290, Mexico
| | | | - Jianbo Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wenzhi Street 34, Wuhan, Hubei Province 430070, China; Instituto de Física, Universidad Autonoma de San Luis Potosi, Av. Manuel Nava 6, Zona Universitaria, C.P., San Luis Potosí 78290, Mexico.
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29
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Custer GF, Mealor BA, Fowers B, van Diepen LTA. Soil microbiome analysis supports claims of ineffectiveness of Pseudomonas fluorescens D7 as a biocontrol agent of Bromus tectorum. Microbiol Spectr 2024; 12:e0177123. [PMID: 38051051 PMCID: PMC10782950 DOI: 10.1128/spectrum.01771-23] [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: 04/28/2023] [Accepted: 10/29/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Cheatgrass is one of North America's most problematic invasive species. Invasion by this annual grass alters ecosystem structure and function and has proven very challenging to remove with traditional approaches. Commercially available bioherbicides, like P. fluorescens D7, are applied with the goal of providing lasting control from a single application. However, experimental results suggest that this bioherbicide has limited efficacy under field conditions. Potential explanations for variable efficacy include a failure of this bioherbicide to establish in the soil microbiome. However, to our knowledge, no data exist to support or refute this hypothesis. Here, we use a deep-sequencing approach to better understand the effects of this bioherbicide on the soil microbiome and screen for P. fluorescens at 18 months post-application.
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Affiliation(s)
- Gordon F. Custer
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- The One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brian A. Mealor
- Department of Plant Sciences, University of Wyoming, Laramie, Wyoming, USA
- Sheridan Research and Extension Center, Sheridan, Wyoming, USA
- Institute for Managing Annual Grasses Invading Natural Ecosystems, Sheridan, Wyoming, USA
| | - Beth Fowers
- Department of Plant Sciences, University of Wyoming, Laramie, Wyoming, USA
- Sheridan Research and Extension Center, Sheridan, Wyoming, USA
- Institute for Managing Annual Grasses Invading Natural Ecosystems, Sheridan, Wyoming, USA
| | - Linda T. A. van Diepen
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
- Institute for Managing Annual Grasses Invading Natural Ecosystems, Sheridan, Wyoming, USA
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30
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Liu C, Shan X, Song L, Wang J, Chen H. Metagenomics-assembled analysis revealed the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167868. [PMID: 37848139 DOI: 10.1016/j.scitotenv.2023.167868] [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: 09/03/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
Antibiotic resistance has received widespread attention in recent years. Soil irrigation and fertilization are routine agricultural practices, but also lead to the spread of antibiotic resistance genes (ARGs) in soil-crop system such as via resistome coalescence. Despite community coalescence being ubiquitous and important in natural ecosystems, little research has been done to investigate resistome coalescence during soil irrigation activities. In this study, the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials (wastewater, wastewater-river water, and wastewater-manure) have been revealed by utilizing microcosm experiments and high-throughput sequencing-based metagenomic assembly approaches. Results showed irrigation and coalescence changed soil quality and resistome. Totally, 789 unique ARGs were identified in the irrigation system, including some emerging ARGs. The abundance and diversity of ARGs increased in the coalesced soils, mainly due to the newly imported ARGs from irrigation materials. Relatively, the soils irrigated with wastewater and manure showed higher level of ARGs. Irrigation with the mixtures containing river water caused greater loss of indigenous taxa, while the community structure of mixing treatment with manure changed more dramatically. Interestingly, the succession of community in coalesced soils was influenced by transient competition for resources and ecological niche width, and the highest abundance and diversity of microorganisms and ARGs were found in the initial phase of coalescence, followed by a gradual succession towards the original community. With increasement of wastewater in the irrigation materials, the soil community showed a stepwise change rather than linear change. Notably, natural deposit of irrigation materials reduced their impacts on the ARGs in the coalesced soils. Findings provide new insights into the resistome coalescence during agricultural practices for reducing the spread risks of ARGs.
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Affiliation(s)
- Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
| | - Jinsheng Wang
- Advanced Institute of Natural Science, Beijing Normal University at Zhuhai, 519087, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
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31
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Zhang Z, Mocanu V, Deehan EC, Hotte N, Zhu Y, Wei S, Kao DH, Karmali S, Birch DW, Walter J, Madsen KL. Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial. Gut Microbes 2024; 16:2345134. [PMID: 38685731 PMCID: PMC11062372 DOI: 10.1080/19490976.2024.2345134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Microbial-based therapeutics in clinical practice are of considerable interest, and a recent study demonstrated fecal microbial transplantation (FMT) followed by dietary fiber supplements improved glucose homeostasis. Previous evidence suggests that donor and recipient compatibility and FMT protocol are key determinants, but little is known about the involvement of specific recipient factors. Using data from our recent randomized placebo-control phase 2 clinical trial in adults with obesity and metabolic syndrome, we grouped participants that received FMT from one of 4 donors with either fiber supplement into HOMA-IR responders (n = 21) and HOMA-IR non-responders (n = 8). We further assessed plasma bile acids using targeted metabolomics and performed subgroup analyzes to evaluate the effects of recipient parameters and gastrointestinal factors on microbiota engraftment and homeostatic model assessment of insulin resistance (HOMA2-IR) response. The baseline fecal microbiota composition at genus level of recipients could predict the improvements in HOMA2-IR at week 6 (ROC-AUC = 0.70). Prevotella was identified as an important predictor, with responders having significantly lower relative abundance than non-responders (p = .02). In addition, recipients displayed a highly individualized degree of microbial engraftment from donors. Compared to the non-responders, the responders had significantly increased bacterial richness (Chao1) after FMT and a more consistent engraftment of donor-specific bacteria ASVs (amplicon sequence variants) such as Faecalibacillus intestinalis (ASV44), Roseburia spp. (ASV103), and Christensenellaceae spp. (ASV140) (p < .05). Microbiota engraftment was strongly associated with recipients' factors at baseline including initial gut microbial diversity, fiber and nutrient intakes, inflammatory markers, and bile acid derivative levels. This study identified that responders to FMT therapy had a higher engraftment rate in the transplantation of specific donor-specific microbes, which were strongly correlated with insulin sensitivity improvements. Further, the recipient baseline gut microbiota and related factors were identified as the determinants for responsiveness to FMT and fiber supplementation. The findings provide a basis for the development of precision microbial therapeutics for the treatment of metabolic syndrome.
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Affiliation(s)
- Zhengxiao Zhang
- College of Ocean Food and Biological Engineering, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian, China
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Valentin Mocanu
- Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Edward C. Deehan
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Naomi Hotte
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Yuanyuan Zhu
- College of Ocean Food and Biological Engineering, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian, China
| | - Shanshan Wei
- College of Ocean Food and Biological Engineering, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian, China
| | - Dina H. Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Shahzeer Karmali
- Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Daniel W. Birch
- Department of Surgery, University of Alberta, Edmonton, AB, Canada
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology and Department of Medicine, University College Cork, Cork, Ireland
| | - Karen L. Madsen
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
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32
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Troitsky TS, Laine VN, Lilley TM. When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation. Anim Microbiome 2023; 5:66. [PMID: 38129884 PMCID: PMC10740296 DOI: 10.1186/s42523-023-00285-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.
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Affiliation(s)
- T S Troitsky
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - V N Laine
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - T M Lilley
- BatLab Finland, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Bagra K, Bellanger X, Merlin C, Singh G, Berendonk TU, Klümper U. Environmental stress increases the invasion success of antimicrobial resistant bacteria in river microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166661. [PMID: 37652387 DOI: 10.1016/j.scitotenv.2023.166661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Environmental microbiomes are constantly exposed to invasion events through foreign, antibiotic resistant bacteria that were enriched in the anthropic sphere. However, the biotic and abiotic factors, as well as the natural barriers that determine the invasion success of these invader bacteria into the environmental microbiomes are poorly understood. A great example of such invasion events are river microbial communities constantly exposed to resistant bacteria originating from wastewater effluents. Here, we aim at gaining comprehensive insights into the key factors that determine their invasion success with a particular focus on the effects of environmental stressors, regularly co-released in wastewater effluents. Understanding invasion dynamics of resistant bacteria is crucial for limiting the environmental spread of antibiotic resistance. To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (Escherichia coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.
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Affiliation(s)
- Kenyum Bagra
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany; Department of Civil Engineering, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Xavier Bellanger
- Université de Lorraine, CNRS, LCPME, UMR 7564, Villers-lès-Nancy, France
| | - Christophe Merlin
- Université de Lorraine, CNRS, LCPME, UMR 7564, Villers-lès-Nancy, France
| | - Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Thomas U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - Uli Klümper
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany.
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Rapp D, Ross C, Cave V, Maclean P, Jauregui R, Brightwell G. Medium-term storage of calf beddings affects bacterial community and effectiveness to inactivate zoonotic bacteria. PLoS One 2023; 18:e0295843. [PMID: 38100478 PMCID: PMC10723701 DOI: 10.1371/journal.pone.0295843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Land-spreading of animal faecal wastes -such as animal beddings- can introduce zoonotic enteropathogens into the food system environment. The study evaluated the effectiveness of animal beddings naturally contaminated by calf manure to reduce E. coli O157:H7 or Salmonella enterica. The two pathogens were introduced separately as a four strains-cocktail and at high (>6.5 Log10 g-1) concentration into bedding materials, and their inactivation over a 10 weeks-period was monitored by using a Most Probable Number (MPN) enumeration method. Inactivation of E. coli O157:H7 was more effective in the bedding inoculated immediately after collection from calf pens than in the beddings inoculated after a 2 months-pre-storage period: E. coli O157:H7 levels were reduced by 6.6 Log10 g-1 in unstored bedding (0.5 Log10 g-1 recovered; 95%CI: 0.0-1.2), and by 4.9 Log10 g-1 in pre-stored bedding (2.2 Log10 g-1 recovered; 95%CI: 1.5-2.8) with a significant (p<0.05) difference between unstored and pre-stored. S. enterica was inactivated less effectively as counts were reduced by one order of magnitude, with no significant difference in inactivation between unstored and pre-stored beddings. Low levels of naturally occurring E. coli O157 and Salmonella spp. were detected in the non-inoculated beddings, as well as in the straw prior to use in the animal facility. To better understand the possible biological processes involved, the bacterial community present in the beddings was characterised by short-read 16S rRNA sequencing. Pre-storage of the bedding affected the composition but not the diversity of the bacterial community. Analyses of the key bacterial phyla suggested that the presence of a diverse and stable bacterial community might facilitate inactivation of the introduced pathogens, and a possible role of bacterial orders associated with lignocellulolytic resources. Overall, the study contributed to the understanding of the fate of zoonotic bacteria introduced in animal beddings during storage and identified bedding storage practices pre-and post-use in animal facilities that could be important to prevent the risk of zoonosis dissemination to the environment or to the dairy herds.
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Affiliation(s)
- Delphine Rapp
- Food System Integrity, AgResearch Ltd, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Colleen Ross
- Food System Integrity, AgResearch Ltd, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Vanessa Cave
- Data Science Team, AgResearch Ltd, Ruakura Research Centre, Hamilton, New Zealand
| | - Paul Maclean
- Data Science Team, AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Ruy Jauregui
- Data Science Team, AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Gale Brightwell
- Food System Integrity, AgResearch Ltd, Hopkirk Research Institute, Palmerston North, New Zealand
- New Zealand Food Safety Science & Research Centre, Hopkirk Research Institute, Palmerston North, New Zealand
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Lu J, Mao J, Qi X, Chen J, Xiong J. The assembly of gut microbiota implicates shrimp acute hepatopancreas necrosis disease progression. Appl Microbiol Biotechnol 2023; 107:7489-7500. [PMID: 37768346 DOI: 10.1007/s00253-023-12810-y] [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: 07/25/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Ample evidence shows dysbiosis in the gut microbiota when comparing healthy shrimp with those affected by severe acute hepatopancreatic necrosis disease (AHPND). However, the static comparison used in available studies leads to the uncertainties regarding how and to what extent the gut microbiota responds to the progressive severity of AHPND. In addition, shrimp AHPND is featured by rapid and massive mortality, thus the initiation of AHPND must be diagnosed for preemptive therapy. For these reasons, we explored the ecological assembly of gut microbiota over shrimp AHPND progression. Increasing AHPND severity was associated with linear increase in the copies of pirAB genes, relative abundance of gut Vibrio and potentially pathogenic, and reduction in the gut bacterial diversity, stability, and relative abundance of Bdellovibrio. Negative and significant association between gut Vibrio and Bdellovibrio were noted, indicating that compromised predation exerts a role in AHPND progression. Notably, the extents of departure to the healthy shrimp gut microbiota were positively coupled with the increasing severity of AHPND. After controlling the temporal variation in the gut microbiota as healthy shrimp age, we constructed a diagnosis model that accurately diagnosed the initial, progressed or moribund stages of AHPND, with an overall accuracy of 86.5%. Shrimp AHPND induced more stochastic gut microbiotas as a consequence of the attenuated ability of diseased shrimp to select their commensals, resulting in convergent bacterial communities between gut and rearing water over AHPND progression. Collectively, our findings provide important step toward the ecological assembly of gut microbiota implicating in AHPND etiology and in diagnosing AHPND stages. KEY POINTS: • The departure of shrimp gut microbiota positively linked with AHPND severity. • The diagnosis model accurately diagnosed the stages of AHPND. • Shrimp AHPND induced more stochastic gut microbiota.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiangning Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xuejing Qi
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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37
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Si H, Cui B, Liu F, Zhao M. Microbial community and chemical composition of cigar tobacco ( Nicotiana tabacum L.) leaves altered by tobacco wildfire disease. PLANT DIRECT 2023; 7:e551. [PMID: 38099080 PMCID: PMC10719477 DOI: 10.1002/pld3.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Tobacco wildfire disease caused by Pseudomonas syringae pv. tabaci is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar tobacco leaves has not been clarified in detail. In this study, the differences in microbiota and chemical factors between wildfire disease-infected leaves and healthy leaves were characterized using high-throughput Illumina sequencing and a continuous-flow analytical system, respectively. The results demonstrated significant alterations in the structure of the phyllosphere microbial community in response to wildfire disease, and the infection of P. syringae pv. tabaci led to a decrease in bacterial richness and diversity. Furthermore, the content of nicotine, protein, total nitrogen, and Cl- in diseased leaves significantly increased by 47.86%, 17.46%, 20.08%, and 72.77% in comparison to healthy leaves, while the levels of total sugar and reducing sugar decreased by 59.59% and 70.0%, respectively. Notably, the wildfire disease had little effect on the content of starch and K+. Redundancy analysis revealed that Pseudomonas, Staphylococcus, Cladosporium, and Wallemia displayed positive correlations with nicotine, protein, total nitrogen, Cl- and K+ contents, while Pantoea, Erwinia, Sphingomonas, Terrisporobacter, Aspergillus, Alternaria, Sampaiozyma, and Didymella displayed positive correlations with total sugar and reducing sugar contents. Brevibacterium, Brachybacterium, and Janibacter were found to be enriched in diseased leaves, suggesting their potential role in disease suppression. Co-occurrence network analysis indicated that positive correlations were prevalent in microbial networks, and the bacterial network of healthy tobacco leaves exhibited greater complexity compared to diseased tobacco leaves. This study revealed the impact of wildfire disease on the microbial community and chemical compositions of tobacco leaves and provides new insights for the biological control of tobacco wildfire disease.
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Affiliation(s)
- Hongyang Si
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Bing Cui
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Fang Liu
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Mingqin Zhao
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
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Shan X, Liu C, Song L, Huan H, Chen H. Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122575. [PMID: 37742860 DOI: 10.1016/j.envpol.2023.122575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/26/2023]
Abstract
Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.
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Affiliation(s)
- Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Huan Huan
- Technical Centre for Soil, Agricultural and Rural Ecology and Environment, Ministry of Ecology and Environment of the People's Republic of China, Beijing, 100012, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China.
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Lear L, Inamine H, Shea K, Buckling A. Diversity loss from multiple interacting disturbances is regime-dependent. Ecol Lett 2023; 26:2056-2065. [PMID: 37847646 DOI: 10.1111/ele.14325] [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: 09/26/2022] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Anthropogenic activities expose many ecosystems to multiple novel disturbances simultaneously. Despite this, how biodiversity responds to simultaneous disturbances remains unclear, with conflicting empirical results on their interactive effects. Here, we experimentally test how one disturbance (an invasive species) affects the diversity of a community over multiple levels of another disturbance regime (pulse mortality). Specifically, we invade stably coexisting bacterial communities under four different pulse frequencies, and compare their final resident diversity to uninvaded communities under the same pulse mortality regimes. Our experiment shows that the disturbances synergistically interact, such that the invader significantly reduces resident diversity at high pulse frequency, but not at low. This work therefore highlights the need to study simultaneous disturbance effects over multiple disturbance regimes as well as to carefully document unmanipulated disturbances, and may help explain the conflicting results seen in previous multiple-disturbance work.
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Affiliation(s)
- Luke Lear
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
| | - Hidetoshi Inamine
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Katriona Shea
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Angus Buckling
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
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Rothschild J, Ma T, Milstein JN, Zilman A. Spatial exclusion leads to "tug-of-war" ecological dynamics between competing species within microchannels. PLoS Comput Biol 2023; 19:e1010868. [PMID: 38039342 PMCID: PMC10718426 DOI: 10.1371/journal.pcbi.1010868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 12/13/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023] Open
Abstract
Competition is ubiquitous in microbial communities, shaping both their spatial and temporal structure and composition. Classical minimal models of competition, such as the Moran model, have been employed in ecology and evolutionary biology to understand the role of fixation and invasion in the maintenance of population diversity. Informed by recent experimental studies of cellular competition in confined spaces, we extend the Moran model to incorporate mechanical interactions between cells that divide within the limited space of a one-dimensional open microchannel. The model characterizes the skewed collective growth of the cells dividing within the channel, causing cells to be expelled at the channel ends. The results of this spatial exclusion model differ significantly from those of its classical well-mixed counterpart. The mean time to fixation of a species is greatly accelerated, scaling logarithmically, rather than algebraically, with the system size, and fixation/extinction probability sharply depends on the species' initial fractional abundance. By contrast, successful takeovers by invasive species, whether through mutation or immigration, are substantially less likely than in the Moran model. We also find that the spatial exclusion tends to attenuate the effects of fitness differences on the fixation times and probabilities. We find that these effects arise from the combination of the quasi-neutral "tug-of-war" diffusion dynamics of the inter-species boundary around an unstable equipoise point and the quasi-deterministic avalanche dynamics away from the fixed point. These results, which can be tested in microfluidic monolayer devices, have implications for the maintenance of species diversity in dense bacterial and cellular ecosystems where spatial exclusion is central to the competition, such as in organized biofilms or intestinal crypts.
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Affiliation(s)
| | - Tianyi Ma
- Department of Physics, University of Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Ontario, Canada
| | - Joshua N. Milstein
- Department of Physics, University of Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Ontario, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, Ontario, Canada
- Institute for Biomedical Engineering, University of Toronto, Ontario, Canada
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41
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Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [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: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
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Wang X, Sun T, Yan S, Chen S, Zhang Y. Sediment microbial community characteristics in sea cucumber restocking area. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106233. [PMID: 37866200 DOI: 10.1016/j.marenvres.2023.106233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.
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Affiliation(s)
- Xiaoling Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Tao Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Shengjun Yan
- National Marine Environmental Monitoring Center, Dalian, 116021, China
| | - Shangyi Chen
- Comprehensive Administrative Law Enforcement Bureau, Qingdao, 266011, China
| | - Yue Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Yang X, Wang C, Wang Q, Zhang Z, Nie W, Shang L. Armored probiotics for oral delivery. SMART MEDICINE 2023; 2:e20230019. [PMID: 39188298 PMCID: PMC11235677 DOI: 10.1002/smmd.20230019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 08/28/2024]
Abstract
As a kind of intestinal flora regulator, probiotics show great potential in the treatment of many diseases. However, orally delivered probiotics are often vulnerable to unfriendly gastrointestinal environments, resulting in a low survival rate and decreased therapeutic efficacy. Decorating or encapsulating probiotics with functional biomaterials has become a facile yet useful strategy, and probiotics can be given different functions by wearing different armors. This review systematically discusses the challenges faced by oral probiotics and the research progress of armored probiotics delivery systems. We focus on how various functional armors help probiotics overcome different obstacles and achieve efficient delivery. We also introduce the applications of armor probiotics in disease treatment and analyze the future trends of developing advanced probiotics-based therapies.
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Affiliation(s)
- Xinyuan Yang
- Zhongshan‐Xuhui Hospital and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Chong Wang
- Zhongshan‐Xuhui Hospital and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Qiao Wang
- Zhongshan‐Xuhui Hospital and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Zhuohao Zhang
- Zhongshan‐Xuhui Hospital and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina
| | - Weimin Nie
- Key Laboratory of Smart Drug DeliverySchool of PharmacyFudan UniversityShanghaiChina
| | - Luoran Shang
- Zhongshan‐Xuhui Hospital and the Shanghai Key Laboratory of Medical Epigenetics, the International Co‐laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology)Institutes of Biomedical SciencesFudan UniversityShanghaiChina
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Van Cauwenberghe J, Simms EL. How might bacteriophages shape biological invasions? mBio 2023; 14:e0188623. [PMID: 37812005 PMCID: PMC10653932 DOI: 10.1128/mbio.01886-23] [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] [Indexed: 10/10/2023] Open
Abstract
Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Ellen L. Simms
- Department of Integrative Biology, University of California, Berkeley, California, USA
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Jiang S, Zhang C, Han Z, Ma W, Wang S, Huo D, Cui W, Zhai Q, Huang S, Zhang J. Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut. NPJ Biofilms Microbiomes 2023; 9:80. [PMID: 37838684 PMCID: PMC10576824 DOI: 10.1038/s41522-023-00447-8] [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: 05/03/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Probiotics often acquire potentially adaptive mutations in vivo, gaining new functional traits through gut selection. While both the host and microbiome can contribute to probiotics' genetic evolution, separating the microbiome and the host's contribution to such selective pressures remains challenging. Here, we introduced germ-free (GF) and specific pathogen-free (SPF) mouse models to track how probiotic strains, i.e., Lactiplantibacillus plantarum HNU082 (Lp082) and Bifidobacterium animalis subsp. lactis V9 (BV9), genetically evolved under selection pressures derived from host factors alone and both host and microbial ecological factors. Notably, compared to the genome of a probiotic strain before consumption, the host only elicited <15 probiotic mutations in probiotic genomes that emerged in the luminal environment of GF mice, while a total of 840 mutations in Lp082 mutants and 21,579 mutations in BV9 were found in SPF mice, <0.25% of those derived from both factors that were never captured by other experimental evolution studies, indicating that keen microbial competitions exhibited the predominant evolutionary force in shaping probiotic genetic composition (>99.75%). For a given probiotic, functional genes occurring in potentially adaptive mutations induced by hosts (GF mice) were all shared with those found in mutants of SPF mice. Collectively, the native microbiome consistently drove a more rapid and divergent genetic evolution of probiotic strains in seven days of colonization than host factors did. Our study further laid a theoretical foundation for genetically engineering probiotics for better gut adaptation through in vitro artificial gut ecosystems without the selection pressures derived from host factors.
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Affiliation(s)
- Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Chengcheng Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhe Han
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Wenyao Ma
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Shunhe Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dongxue Huo
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Weipeng Cui
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Qixiao Zhai
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Jiachao Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, 570228, China.
- One Health Institute, Hainan University, Haikou, Hainan, 570228, China.
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Li M, Chen L, Zhao F, Tang J, Bu Q, Feng Q, Yang L. An innovative risk evaluation method on soil pathogens in urban-rural ecosystem. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132286. [PMID: 37595464 DOI: 10.1016/j.jhazmat.2023.132286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/29/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
The presence and reproduction of pathogens in soil environment have significant negative impacts on soil security and human health in urban-rural ecosystem. Rapid urbanization has dramatically changed the land use, soil ecosystems, and the presence of pathogens in soil environment, however, the risk associated with soil pathogens remains unknown. Identifying the potential risk of pathogens in soils in urban-rural ecosystem has become an urgent issue. In this study, we established a risk evaluation method for soil pathogens based on analytic hierarchy process and entropy methods to quantitatively estimate the potential risk of soil pathogens to children and adults in urban-rural ecosystem. The abundance and species number of soil pathogens, network structure of soil microbial community, and human exposure factors were considered with 12 indicators to establish the risk evaluation system. The results revealed that 19 potential pathogenic bacteria were detected in soils within a typical urban-rural ecosystem. Substantial differences were observed in both abundance and species of soil pathogens as well as network structure of soil microbial community from urban to rural areas. Urban areas exhibited relatively lower levels of soil pathogenic abundance, but the microbial network was considerably unstable. Rural areas supported relatively higher levels of soil pathogenic abundance and stable microbial networks. Notably, peri-urban areas showed relatively unstable microbial networks alongside higher levels of soil pathogenic abundance compared to other areas. The risk evaluation of soil pathogens for both adults and children showed that peri-urban areas presented the highest potential risk, with children being more susceptible than adults to threats posed by soil pathogens in both urban and peri-urban areas. The established evaluation system provides an innovative approach for quantifying risk of soil pathogens at regional scale and can be used as a reference for preventing soil pathogens contamination and enhancing soil health in areas with intense human activities.
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Affiliation(s)
- Min Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liding Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangkai Zhao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Jianfeng Tang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingwei Bu
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing 100083, China
| | - Qingyu Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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Malard LA, Bergk-Pinto B, Layton R, Vogel TM, Larose C, Pearce DA. Snow Microorganisms Colonise Arctic Soils Following Snow Melt. MICROBIAL ECOLOGY 2023; 86:1661-1675. [PMID: 36939866 PMCID: PMC10497451 DOI: 10.1007/s00248-023-02204-y] [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: 05/21/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.
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Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Benoit Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
- BioIT, TAG (Transversal Activities in Applied Genomics) Sciensano, 1050, Brussels, Belgium
| | - Rose Layton
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
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49
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Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
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50
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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