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Gopalakrishnappa C, Li Z, Kuehn S. Environmental modulators of algae-bacteria interactions at scale. Cell Syst 2024:S2405-4712(24)00210-2. [PMID: 39236710 DOI: 10.1016/j.cels.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/29/2023] [Accepted: 08/07/2024] [Indexed: 09/07/2024]
Abstract
Interactions between photosynthetic and heterotrophic microbes play a key role in global primary production. Understanding phototroph-heterotroph interactions remains challenging because these microbes reside in chemically complex environments. Here, we leverage a massively parallel droplet microfluidic platform that enables us to interrogate interactions between photosynthetic algae and heterotrophic bacteria in >100,000 communities across ∼525 environmental conditions with varying pH, carbon availability, and phosphorus availability. By developing a statistical framework to dissect interactions in this complex dataset, we reveal that the dependence of algae-bacteria interactions on nutrient availability is strongly modulated by pH and buffering capacity. Furthermore, we show that the chemical identity of the available organic carbon source controls how pH, buffering capacity, and nutrient availability modulate algae-bacteria interactions. Our study reveals the previously underappreciated role of pH in modulating phototroph-heterotroph interactions and provides a framework for thinking about interactions between phototrophs and heterotrophs in more natural contexts.
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Affiliation(s)
| | - Zeqian Li
- Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA; National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL 60637, USA; Center for Living Systems, The University of Chicago, Chicago, IL 60637, USA.
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2
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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [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: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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3
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Laurich JR, Lash E, O'Brien AM, Pogoutse O, Frederickson ME. Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant. mBio 2024; 15:e0097224. [PMID: 38904411 PMCID: PMC11324027 DOI: 10.1128/mbio.00972-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes. IMPORTANCE There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.
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Affiliation(s)
- Jason R. Laurich
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Emma Lash
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Anna M. O'Brien
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
- Department of
Molecular, Cellular, and Biomedical Sciences, University of New
Hampshire, Durham,
New Hampshire, USA
| | - Oxana Pogoutse
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Megan E. Frederickson
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
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4
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Qin L, Xiao Z, Ming A, Teng J, Zhu H, Qin J, Liang Z. Soil phosphorus cycling microbial functional genes of monoculture and mixed plantations of native tree species in subtropical China. Front Microbiol 2024; 15:1419645. [PMID: 39077738 PMCID: PMC11284607 DOI: 10.3389/fmicb.2024.1419645] [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: 04/18/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Background Transforming coniferous plantation into broadleaved or mixed broadleaved-coniferous plantations is the tendency of forest management strategies in subtropical China. However, the effects of this conversion on soil phosphorus (P) cycling microbial functional genes are still unknown. Methods Soil samples were collected from 0-20, 20-40, and 40-60 cm (topsoil, middle layer, and subsoil, respectively) under coniferous Pinus massoniana (PM), broadleaved Erythrophleum fordii (EF), and their mixed (PM/EF) plantation in subtropical China. Used metagenomic sequencing to examine the alterations of relative abundances and molecular ecological network structure of soil P-cycling functional genes after the conversion of plantations. Results The composition of P-cycling genes in the topsoil of PM stand was significantly different from that of PM/EF and EF stands (p < 0.05), and total phosphorus (TP) was the main factor causing this difference. After transforming PM plantation into EF plantation, the relative abundances of P solubilization and mineralization genes significantly increased in the topsoil and middle layer with the decrease of soil TP content. The abundances of P-starvation response regulation genes also significantly increased in the subsoil (p < 0.05), which may have been influenced by soil organic carbon (SOC). The dominant genes in all soil layers under three plantations were phoR, glpP, gcd, ppk, and ppx. Transforming PM into EF plantation apparently increased gcd abundance in the topsoil (p < 0.05), with TP and NO3 --N being the main influencing factors. After transforming PM into PM/EF plantations, the molecular ecological network structure of P-cycling genes was more complex; moreover, the key genes in the network were modified with the transformation of PM plantation. Conclusion Transforming PM into EF plantation mainly improved the phosphate solubilizing potential of microorganisms at topsoil, while transforming PM into PM/EF plantation may have enhanced structural stability of microbial P-cycling genes react to environmental changes.
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Affiliation(s)
- Lin Qin
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Zhirou Xiao
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Angang Ming
- Experiment Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang, China
- Guangxi Youyiguan Forest Ecosystem Research Station, Pingxiang, China
| | - Jinqian Teng
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Hao Zhu
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Jiaqi Qin
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Zeli Liang
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
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Gupta G, Labrie S, Filteau M. Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening. Microorganisms 2024; 12:1396. [PMID: 39065164 PMCID: PMC11279232 DOI: 10.3390/microorganisms12071396] [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: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose-allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve Labrie
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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6
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Stindt KR, McClean MN. Tuning interdomain conjugation to enable in situ population modification in yeasts. mSystems 2024; 9:e0005024. [PMID: 38747597 PMCID: PMC11326116 DOI: 10.1128/msystems.00050-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/15/2024] [Indexed: 05/28/2024] Open
Abstract
The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.
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Affiliation(s)
- Kevin R Stindt
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Doctoral Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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Wang Y, Fang J, Li X, Li C, Zhao Y, Liu J. Microorganisms Directly Affected Sediment Carbon–Nitrogen Coupling in Two Constructed Wetlands. WATER 2024; 16:1550. [DOI: 10.3390/w16111550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Clarifying the carbon–nitrogen coupling pattern in wetlands is crucial for understanding the driving mechanism of wetland carbon sequestration. However, the impacts of plants and environmental factors on the coupling of carbon–nitrogen in wetland sediments are still unclear. Sediment samples from plant (Typha angustifolia and Phragmites australis)-covered habitats and bare land were collected in two constructed wetlands in northern China. The contents of different forms of carbon and nitrogen in sediments and plants, and the sediment microbial community were detected. It was found that the sediment carbon to nitrogen (C/N) ratios did not differ significantly in the bare sites of different wetlands, but did in the plant-covered sites, which highlighted the different role of plants in shifting the carbon–nitrogen coupling in different constructed wetlands. The effects of plants on the sediment carbon–nitrogen coupling differed in two constructed wetlands, so the structural equation model was used and found that sediment microorganisms directly affected sediment C/N ratios, while water and sediment physicochemical properties indirectly affected sediment C/N ratios by altering sediment microbial functions. Multiple linear regression models showed that water pH, sediment moisture content, water dissolved oxygen, and water depth had a greater influence on the carbon metabolism potential of the sediment microbial community, while sediment moisture content had the greatest impact on the sediment microbial nitrogen metabolism potential. The study indicates that variations in environmental conditions could alter the influence of plants on the carbon and nitrogen cycles of wetland sediments. Water environmental factors mainly affect microbial carbon metabolism functions, while soil physicochemical factors, especially water content, affect microbial carbon and nitrogen metabolism functions.
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Affiliation(s)
- Yan Wang
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jiaohui Fang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Xin Li
- Jinan Environmental Research Academy, Jinan 250000, China
| | - Changchao Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Yongkang Zhao
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao 266237, China
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8
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Dekaj E, Gjini E. Pneumococcus and the stress-gradient hypothesis: A trade-off links R 0 and susceptibility to co-colonization across countries. Theor Popul Biol 2024; 156:77-92. [PMID: 38331222 DOI: 10.1016/j.tpb.2024.02.001] [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: 05/30/2022] [Revised: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across studies and different geographic endemic settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. While the global genomic diversity and serotype distribution of S. pneumoniae have been well-characterized, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of the bacteria. Gathering a rich dataset of cross-sectional pneumococcal colonization studies in the literature, we quantified patterns of transmission intensity and co-colonization prevalence variation in children populations across 17 geographic locations. Linking these data to an SIS model with cocolonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity (R0) and susceptibility to co-colonization (k). In line with expectations from the stress-gradient-hypothesis in ecology (SGH), pneumococcus serotypes appear to compete more in co-colonization in high-transmission settings and compete less in low-transmission settings, a trade-off which ultimately leads to a conserved ratio of single to co-colonization μ=1/(R0-1)k. From the mathematical model's behavior, such conservation suggests preservation of 'stability-diversity-complexity' regimes in coexistence of similar co-colonizing strains. We find no major differences in serotype compositions across studies, pointing to adaptation of the same set of serotypes across variable environments as an explanation for their differential interaction in different transmission settings. Our work highlights that the understanding of transmission patterns of Streptococcus pneumoniae from global scale epidemiological data can benefit from simple analytical approaches that account for quasi-neutrality among strains, co-colonization, as well as variable environmental adaptation.
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Affiliation(s)
- Ermanda Dekaj
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
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Yao J, Zhang Q, Gou M, Tang YQ. High synthetic cost-amino acids reduce member interactions of acetate-degrading methanogenic microbial community. Front Microbiol 2024; 15:1368215. [PMID: 38605716 PMCID: PMC11007023 DOI: 10.3389/fmicb.2024.1368215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction The cooperation among members of microbial communities based on the exchange of public goods such as 20 protein amino acids (AAs) has attracted widespread attention. However, little is known about how AAs availability affects interactions among members of complex microbial communities and the structure and function of a community. Methods To investigate this question, trace amounts of AAs combinations with different synthetic costs (low-cost, medium-cost, high-cost, and all 20 AAs) were supplemented separately to acetate-degrading thermophilic methanogenic reactors, and the differences in microbial community structure and co-occurring networks of main members were compared to a control reactor without AA supplementation. Results The structure of the microbial community and the interaction of community members were influenced by AAs supplementation and the AAs with different synthetic costs had different impacts. The number of nodes, links, positive links, and the average degree of nodes in the co-occurrence network of the microbial communities with AAs supplementation was significantly lower than that of the control without AAs supplementation, especially for all 20 AAs supplementation followed by the medium- and high-cost AAs supplementation. The average proportion of positive interactions of microbial members in the systems supplemented with low-cost, medium-cost, high-cost, all AAs, and the control group were 0.42, 0.38, 0.15, 0.4, and 0.45, respectively. In addition, the ecological functions of community members possibly changed with the supplementation of different cost AAs. Discussion These findings highlight the effects of AAs availability on the interactions among members of complex microbial communities, as well as on community function.
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Affiliation(s)
- Jian Yao
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China
| | - Quan Zhang
- SINOPEC (Dalian) Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian, Liaoning, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China
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10
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Castledine M, Buckling A. Critically evaluating the relative importance of phage in shaping microbial community composition. Trends Microbiol 2024:S0966-842X(24)00057-X. [PMID: 38604881 DOI: 10.1016/j.tim.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial community composition (the relative abundances of species). However, the evidence for the importance of phages is mixed. Here, we critically review the theory and data exploring the role of phages in communities, identifying the conditions when phages are likely to be important drivers of community composition. At ecological scales, we conclude that phages are often followers rather than drivers of microbial population and community dynamics. While phages can affect strain diversity within species, there is yet to be strong evidence suggesting that fluctuations in species' strains affects community composition.
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Affiliation(s)
- Meaghan Castledine
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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11
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Bisesi AT, Möbius W, Nadell CD, Hansen EG, Bowden SD, Harcombe WR. Bacteriophage specificity is impacted by interactions between bacteria. mSystems 2024; 9:e0117723. [PMID: 38376179 PMCID: PMC11237722 DOI: 10.1128/msystems.01177-23] [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: 11/07/2023] [Accepted: 01/20/2024] [Indexed: 02/21/2024] Open
Abstract
Predators play a central role in shaping community structure, function, and stability. The degree to which bacteriophage predators (viruses that infect bacteria) evolve to be specialists with a single bacterial prey species versus generalists able to consume multiple types of prey has implications for their effect on microbial communities. The presence and abundance of multiple bacterial prey types can alter selection for phage generalists, but less is known about how interactions between prey shape predator specificity in microbial systems. Using a phenomenological mathematical model of phage and bacterial populations, we find that the dominant phage strategy depends on prey ecology. Given a fitness cost for generalism, generalist predators maintain an advantage when prey species compete, while specialists dominate when prey are obligately engaged in cross-feeding interactions. We test these predictions in a synthetic microbial community with interacting strains of Escherichia coli and Salmonella enterica by competing a generalist T5-like phage able to infect both prey against P22vir, an S. enterica-specific phage. Our experimental data conform to our modeling expectations when prey species are competing or obligately mutualistic, although our results suggest that the in vitro cost of generalism is caused by a combination of biological mechanisms not anticipated in our model. Our work demonstrates that interactions between bacteria play a role in shaping ecological selection on predator specificity in obligately lytic bacteriophages and emphasizes the diversity of ways in which fitness trade-offs can manifest. IMPORTANCE There is significant natural diversity in how many different types of bacteria a bacteriophage can infect, but the mechanisms driving this diversity are unclear. This study uses a combination of mathematical modeling and an in vitro system consisting of Escherichia coli, Salmonella enterica, a T5-like generalist phage, and the specialist phage P22vir to highlight the connection between bacteriophage specificity and interactions between their potential microbial prey. Mathematical modeling suggests that competing bacteria tend to favor generalist bacteriophage, while bacteria that benefit each other tend to favor specialist bacteriophage. Experimental results support this general finding. The experiments also show that the optimal phage strategy is impacted by phage degradation and bacterial physiology. These findings enhance our understanding of how complex microbial communities shape selection on bacteriophage specificity, which may improve our ability to use phage to manage antibiotic-resistant microbial infections.
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Affiliation(s)
- Ave T. Bisesi
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Wolfram Möbius
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Carey D. Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Eleanore G. Hansen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA
| | - Steven D. Bowden
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA
| | - William R. Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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12
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Denk J, Hallatschek O. Tipping points emerge from weak mutualism in metacommunities. PLoS Comput Biol 2024; 20:e1011899. [PMID: 38442132 PMCID: PMC10942259 DOI: 10.1371/journal.pcbi.1011899] [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: 10/10/2023] [Revised: 03/15/2024] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
The coexistence of obligate mutualists is often precariously close to tipping points where small environmental changes can drive catastrophic shifts in species composition. For example, microbial ecosystems can collapse by the decline of a strain that provides an essential resource on which other strains cross-feed. Here, we show that tipping points, ecosystem collapse, bistability and hysteresis arise even with very weak (non-obligate) mutualism provided the population is spatially structured. Based on numeric solutions of a metacommunity model and mean-field analyses, we demonstrate that weak mutualism lowers the minimal dispersal rate necessary to avoid stochastic extinction, while species need to overcome a mean threshold density to survive in this low dispersal rate regime. Our results allow us to make numerous predictions for mutualistic metacommunities regarding tipping points, hysteresis effects, and recovery from external perturbations, and let us draw general conclusions for ecosystems even with random, not necessarily mutualistic, interactions and systems with density-dependent dispersal rather than direct mutualistic interactions.
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Affiliation(s)
- Jonas Denk
- Department of Physics, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
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13
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Long C, Deng J, Nguyen J, Liu YY, Alm EJ, Solé R, Saavedra S. Structured community transitions explain the switching capacity of microbial systems. Proc Natl Acad Sci U S A 2024; 121:e2312521121. [PMID: 38285940 PMCID: PMC10861894 DOI: 10.1073/pnas.2312521121] [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: 07/24/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Microbial systems appear to exhibit a relatively high switching capacity of moving back and forth among few dominant communities (taxon memberships). While this switching behavior has been mainly attributed to random environmental factors, it remains unclear the extent to which internal community dynamics affect the switching capacity of microbial systems. Here, we integrate ecological theory and empirical data to demonstrate that structured community transitions increase the dependency of future communities on the current taxon membership, enhancing the switching capacity of microbial systems. Following a structuralist approach, we propose that each community is feasible within a unique domain in environmental parameter space. Then, structured transitions between any two communities can happen with probability proportional to the size of their feasibility domains and inversely proportional to their distance in environmental parameter space-which can be treated as a special case of the gravity model. We detect two broad classes of systems with structured transitions: one class where switching capacity is high across a wide range of community sizes and another class where switching capacity is high only inside a narrow size range. We corroborate our theory using temporal data of gut and oral microbiota (belonging to class 1) as well as vaginal and ocean microbiota (belonging to class 2). These results reveal that the topology of feasibility domains in environmental parameter space is a relevant property to understand the changing behavior of microbial systems. This knowledge can be potentially used to understand the relevant community size at which internal dynamics can be operating in microbial systems.
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Affiliation(s)
- Chengyi Long
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jie Deng
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jen Nguyen
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL61801
| | - Eric J. Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Ricard Solé
- Complex Systems Lab, Universitat Pompeu Fabra, Barcelona08003, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona08010, Spain
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Universitat Pompeu Fabra, Barcelona08003, Spain
- Santa Fe Institute, Santa Fe, NM87501
| | - Serguei Saavedra
- Institució Catalana de Recerca i Estudis Avançats, Barcelona08010, Spain
- Santa Fe Institute, Santa Fe, NM87501
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14
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Di Martino R, Picot A, Mitri S. Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative. PLoS Biol 2024; 22:e3002482. [PMID: 38315734 PMCID: PMC10881020 DOI: 10.1371/journal.pbio.3002482] [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: 05/30/2023] [Revised: 02/21/2024] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Knowing how species interact within microbial communities is crucial to predicting and controlling community dynamics, but interactions can depend on environmental conditions. The stress-gradient hypothesis (SGH) predicts that species are more likely to facilitate each other in harsher environments. Even if the SGH gives some intuition, quantitative modeling of the context-dependency of interactions requires understanding the mechanisms behind the SGH. In this study, we show with both experiments and a theoretical analysis that varying the concentration of a single compound, linoleic acid (LA), modifies the interaction between 2 bacterial species, Agrobacterium tumefaciens and Comamonas testosteroni, from competitive at a low concentration, to facilitative at higher concentrations where LA becomes toxic for one of the 2 species. We demonstrate that the mechanism behind facilitation is that one species is able to reduce reactive oxygen species (ROS) that are produced spontaneously at higher concentrations of LA, allowing for short-term rescue of the species that is sensitive to ROS and longer coexistence in serial transfers. In our system, competition and facilitation between species can occur simultaneously, and changing the concentration of a single compound can alter the balance between the two.
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Affiliation(s)
- Rita Di Martino
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aurore Picot
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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15
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Salles LFP, de Aguiar MAM, Marquitti FMD. Evolution of cooperation in a two-species system with a common resource pool. J Theor Biol 2024; 577:111670. [PMID: 37981098 DOI: 10.1016/j.jtbi.2023.111670] [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: 04/19/2023] [Revised: 10/27/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
Understanding the evolution of cooperation is a major question in Evolutionary Biology. Here, we extend a previously proposed mathematical model in Evolutionary Game Theory that investigated how resource use by a single species composed of cooperators and defectors may lead to its maintenance or extinction. We include another species in the model, so as to investigate how different intra and interspecific interactions of cooperative or competitive nature among individuals that share the same essential resource may drive the survival and evolution of the species. Several outcomes emerge from the model, depending on the configuration of the payoff matrix, the individual contribution to the resource pool, the competition intensity between species, and the initial conditions of the system dynamics. Observed results include scenarios in which species thrive due to the action of cooperators, but also scenarios in which both species collapse due to lack of cooperation and, consequently, of resources. In particular, a high initial availability of resources may be the determinant factor to the survival of both species. Interestingly, cooperation may be more favored when individuals have less incentive to cooperate with others, and the survival of their populations may depend crucially on their competitive capacities.
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Affiliation(s)
| | | | - Flavia Maria Darcie Marquitti
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas, Brazil; Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
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16
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Feng J, Ma H, Wang C, Gao J, Zhai C, Jiang L, Wan S. Water rather than nitrogen availability predominantly modulates soil microbial beta-diversity and co-occurrence networks in a secondary forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167996. [PMID: 37871812 DOI: 10.1016/j.scitotenv.2023.167996] [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: 08/12/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Atmospheric nitrogen (N) deposition and changing precipitation regimes greatly affect the structure and functions of terrestrial ecosystems. However, their impacts on the diversity and assembly of soil microbial communities including bacteria, fungi and protists, remain largely unclear. As part of a six-year field experiment in a secondary forest in a warm temperate and subtropical climate transitional zone in China, we aimed to investigate the responses of soil microbial communities to N addition, increased and decreased precipitation. The results showed that N addition had no effect on soil microbial α- or β-diversity, but reduced the complexity of microbial network. Neither increased nor decreased precipitation influenced soil microbial α-diversity, but decreased precipitation rather than increased precipitation elevated bacterial and protistan community dissimilarities (β-diversity), which could have been largely attributed to species replacement processes through reducing soil water availability. In addition, decreased precipitation weakened microbial complexity and stability, but enhanced the node proportion of protists in the co-occurrence network. Our observations suggest the asymmetric responses of soil microbial β-diversity to increased and decreased precipitation, and underscore that water rather than N availability, especially drought condition, plays a predominant role in modulating soil microbial β-diversity. Moreover, the findings imply that global change can strengthen the importance of soil protists and then reshape microbial assembly in forests.
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Affiliation(s)
- Jiayin Feng
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Institute of Life Science and Green Development, Hebei University, Baoding 071002, PR China
| | - Huixia Ma
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Institute of Life Science and Green Development, Hebei University, Baoding 071002, PR China
| | - Chunyu Wang
- School of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Jingjing Gao
- School of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Changchun Zhai
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Institute of Life Science and Green Development, Hebei University, Baoding 071002, PR China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Shiqiang Wan
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Institute of Life Science and Green Development, Hebei University, Baoding 071002, PR China.
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17
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Hu KKY, Suri A, Dumsday G, Haritos VS. Cross-feeding promotes heterogeneity within yeast cell populations. Nat Commun 2024; 15:418. [PMID: 38200012 PMCID: PMC10781747 DOI: 10.1038/s41467-023-44623-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: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Cellular heterogeneity in cell populations of isogenic origin is driven by intrinsic factors such as stochastic gene expression, as well as external factors like nutrient availability and interactions with neighbouring cells. Heterogeneity promotes population fitness and thus has important implications in antimicrobial and anticancer treatments, where stress tolerance plays a significant role. Here, we study plasmid retention dynamics within a population of plasmid-complemented ura3∆0 yeast cells, and show that the exchange of complementary metabolites between plasmid-carrying prototrophs and plasmid-free auxotrophs allows the latter to survive and proliferate in selective environments. This process also affects plasmid copy number in plasmid-carrying prototrophs, further promoting cellular functional heterogeneity. Finally, we show that targeted genetic engineering can be used to suppress cross-feeding and reduce the frequency of plasmid-free auxotrophs, or to exploit it for intentional population diversification and division of labour in co-culture systems.
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Affiliation(s)
- Kevin K Y Hu
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Ankita Suri
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Geoff Dumsday
- Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, 3169, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia.
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18
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Ghadermazi P, Chan SHJ. Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution. Bioinformatics 2024; 40:btae003. [PMID: 38212999 PMCID: PMC10799744 DOI: 10.1093/bioinformatics/btae003] [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: 08/04/2023] [Revised: 12/24/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Abstract
MOTIVATION Microbes are essential part of all ecosystems, influencing material flow and shaping their surroundings. Metabolic modeling has been a useful tool and provided tremendous insights into microbial community metabolism. However, current methods based on flux balance analysis (FBA) usually fail to predict metabolic and regulatory strategies that lead to long-term survival and stability especially in heterogenous communities. RESULTS Here, we introduce a novel reinforcement learning algorithm, Self-Playing Microbes in Dynamic FBA, which treats microbial metabolism as a decision-making process, allowing individual microbial agents to evolve by learning and adapting metabolic strategies for enhanced long-term fitness. This algorithm predicts what microbial flux regulation policies will stabilize in the dynamic ecosystem of interest in the presence of other microbes with minimal reliance on predefined strategies. Throughout this article, we present several scenarios wherein our algorithm outperforms existing methods in reproducing outcomes, and we explore the biological significance of these predictions. AVAILABILITY AND IMPLEMENTATION The source code for this article is available at: https://github.com/chan-csu/SPAM-DFBA.
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Affiliation(s)
- Parsa Ghadermazi
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80521, United States
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80521, United States
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19
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Yang Y, Callaham MA, Wu X, Zhang Y, Wu D, Wang D. Gut microbial communities and their potential roles in cellulose digestion and thermal adaptation of earthworms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166666. [PMID: 37657540 DOI: 10.1016/j.scitotenv.2023.166666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/15/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
Adaptations to temperature and food resources, which can be affected by gut microbiota, are two main adaptive strategies allowing soil fauna to survive in their habitats, especially for cold-blooded animals. Earthworms are often referred to as ecosystem engineers because they make up the biggest component of the animal biomass found in the soil. They are considered as an important indicator in the triangle of soil quality, health and functions. However, the roles of gut microbiota in the environmental adaptation of earthworms at a large scale remain obscure. We explored the gut bacterial communities and their functions in the environmental adaptation of two widespread earthworm species (Eisenia nordenskioldi Eisen and Drawida ghilarovi Gates) in Northeast China (1661 km). Based on our findings, the alpha diversity of gut bacterial communities decreased with the increase of latitude, and the gut bacterial community composition was shaped by both mean annual temperature (MAT) and cellulose. Actinobacteria, Proteobacteria, Firmicutes, and Planctomycetes, recognized as the predominant cellulose degraders, were keystone taxa driving gut bacterial interactions. Actinobacteria, Firmicutes, and Planctomycetes were influenced by MAT and cellulose, and had higher contributions to gut total cellulase activity. The optimal temperature for total cellulase in the gut of E. nordenskioldi (25-30 °C) was lower than that of D ghilarovi (40 °C). The gut microbiota-deleted earthworms had the lowest cellulose degradation rate (1.07 %). The cellulose was degraded faster by gut bacteria from the host they were derived, indicating the presence of home field advantage of cellulose decomposition. This study provides a foundation for understanding the biotic strategies adopted by earthworms when they enter a new habitat, with gut microbiota being central to food digestion and environmental adaptability.
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Affiliation(s)
- Yurong Yang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Mac A Callaham
- USDA, Forest Service, Southern Research Station, Center for Forest Disturbance Science, Athens, GA 30602, USA
| | - Xuefeng Wu
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yufeng Zhang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China; Hebei Key Laboratory of Animal Diversity, Langfang Normal University, Langfang, 065000, China
| | - Donghui Wu
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China; Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, 130024, China.
| | - Deli Wang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China; Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, 130024, China
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20
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Kost C, Patil KR, Friedman J, Garcia SL, Ralser M. Metabolic exchanges are ubiquitous in natural microbial communities. Nat Microbiol 2023; 8:2244-2252. [PMID: 37996708 DOI: 10.1038/s41564-023-01511-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/11/2023] [Indexed: 11/25/2023]
Abstract
Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.
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Affiliation(s)
- Christian Kost
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany.
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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21
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Liu J, Li C, Ma W, Wu Z, Liu W, Wu W. Exploitation alters microbial community and its co-occurrence patterns in ionic rare earth mining sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165532. [PMID: 37454857 DOI: 10.1016/j.scitotenv.2023.165532] [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: 03/30/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The exploitation of ion-adsorption rare earth elements (REEs) deposits results in serious ecological and environmental problems, which has attracted much attention. However, the influences of exploitation on the prokaryotic communities and their complex interactions remain poorly understood. In the present study, bacterial and archaeal communities, as well as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), in and around REEs mining area were investigated through high throughput sequencing and quantitative polymerase chain reaction (qPCR). Our results indicated that mining soil was characterized by poor soil structure, nutrient deficiency, and high concentrations of residual REEs. Oligotrophic bacteria (e.g., Chloroflexi and Acidobacteriota) were dominant in unexploited soil and mining soil, while copiotrophic bacteria (Proteobacteria and Actinobacteriota) were more abundant in surrounding soil. Nutrient was the key factor affecting microbial variation and abundance in mining soil. The bacterial community was more sensitive to REEs, while the archaeal communities were relatively stable. As the key members for ammonia oxidation, AOA outnumbered AOB in all the soil types, and the former was significantly influenced by pH, nutrients, and TREEs in mining soil. The microbial co-occurrence network analysis demonstrated that exploitation significantly influenced topological properties, decreased the complexity, and resulted in a much unstable network, leading to a more fragile microbial ecosystem in mining areas. Notably, the abundance of keystone taxa decreased after exploitation, and oligotrophic groups (Chloroflexi) replaced copiotrophic groups (Proteobacteria and Actinobacteriota) as the key to rebuilt a co-occurrence network, suggesting potentially important roles in maintaining network stability. The current results are of great significance to the ecological risk assessment of REEs exploitation.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China; Jiangxi Key Laboratory of Mining & Metallurgy Environmental Pollution Control, Ganzhou 341099, China.
| | - Chun Li
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China
| | - Wendan Ma
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China
| | - Zengxue Wu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310030, China
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22
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Micali G, Hockenberry AM, Dal Co A, Ackermann M. Minorities drive growth resumption in cross-feeding microbial communities. Proc Natl Acad Sci U S A 2023; 120:e2301398120. [PMID: 37903278 PMCID: PMC10636363 DOI: 10.1073/pnas.2301398120] [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: 02/15/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Microbial communities are fundamental to life on Earth. Different strains within these communities are often connected by a highly connected metabolic network, where the growth of one strain depends on the metabolic activities of other community members. While distributed metabolic functions allow microbes to reduce costs and optimize metabolic pathways, they make them metabolically dependent. Here, we hypothesize that such dependencies can be detrimental in situations where the external conditions change rapidly, as they often do in natural environments. After a shift in external conditions, microbes need to remodel their metabolism, but they can only resume growth once partners on which they depend have also adapted to the new conditions. It is currently not well understood how microbial communities resolve this dilemma and how metabolic interactions are reestablished after an environmental shift. To address this question, we investigated the dynamical responses to environmental perturbation by microbial consortia with distributed anabolic functions. By measuring the regrowth times at the single-cell level in spatially structured communities, we found that metabolic dependencies lead to a growth delay after an environmental shift. However, a minority of cells-those in the immediate neighborhood of their metabolic partners-can regrow quickly and come to numerically dominate the community after the shift. The spatial arrangement of a microbial community is thus a key factor in determining the communities' ability to maintain metabolic interactions and growth in fluctuating conditions. Our results suggest that environmental fluctuations can limit the emergence of metabolic dependencies between microorganisms.
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Affiliation(s)
- Gabriele Micali
- Department of Environmental Systems Science, ETH Zürich, Zurich8092, Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf8600, Switzerland
| | - Alyson M. Hockenberry
- Department of Environmental Systems Science, ETH Zürich, Zurich8092, Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf8600, Switzerland
| | - Alma Dal Co
- Department of Environmental Systems Science, ETH Zürich, Zurich8092, Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf8600, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zurich8092, Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf8600, Switzerland
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23
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Jiang Y, Wu R, Zhang W, Xin F, Jiang M. Construction of stable microbial consortia for effective biochemical synthesis. Trends Biotechnol 2023; 41:1430-1441. [PMID: 37330325 DOI: 10.1016/j.tibtech.2023.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China.
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
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24
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Picot A, Shibasaki S, Meacock OJ, Mitri S. Microbial interactions in theory and practice: when are measurements compatible with models? Curr Opin Microbiol 2023; 75:102354. [PMID: 37421708 DOI: 10.1016/j.mib.2023.102354] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/10/2023]
Abstract
Most predictive models of ecosystem dynamics are based on interactions between organisms: their influence on each other's growth and death. We review here how theoretical approaches are used to extract interaction measurements from experimental data in microbiology, particularly focusing on the generalised Lotka-Volterra (gLV) framework. Though widely used, we argue that the gLV model should be avoided for estimating interactions in batch culture - the most common, simplest and cheapest in vitro approach to culturing microbes. Fortunately, alternative approaches offer a way out of this conundrum. Firstly, on the experimental side, alternatives such as the serial-transfer and chemostat systems more closely match the theoretical assumptions of the gLV model. Secondly, on the theoretical side, explicit organism-environment interaction models can be used to study the dynamics of batch-culture systems. We hope that our recommendations will increase the tractability of microbial model systems for experimentalists and theoreticians alike.
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Affiliation(s)
- Aurore Picot
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shota Shibasaki
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Oliver J Meacock
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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25
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Stindt KR, McClean MN. Tuning Interdomain Conjugation Toward in situ Population Modification in Yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557379. [PMID: 37745509 PMCID: PMC10515866 DOI: 10.1101/2023.09.12.557379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes, and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to widespread use of IDC is its limited efficiency. In this work, we utilize interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture, and model how these tunable controls can predictably yield a range of IDC outcomes. Further, we demonstrate that these lessons can be utilized to lastingly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.
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26
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Shibasaki S, Mitri S. A spatially structured mathematical model of the gut microbiome reveals factors that increase community stability. iScience 2023; 26:107499. [PMID: 37670791 PMCID: PMC10475486 DOI: 10.1016/j.isci.2023.107499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/11/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023] Open
Abstract
Given the importance of gut microbial communities for human health, we may want to ensure their stability in terms of species composition and function. Here, we built a mathematical model of a simplified gut composed of two connected patches where species and metabolites can flow from an upstream patch, allowing upstream species to affect downstream species' growth. First, we found that communities in our model are more stable if they assemble through species invasion over time compared to combining a set of species from the start. Second, downstream communities are more stable when species invade the downstream patch less frequently than the upstream patch. Finally, upstream species that have positive effects on downstream species can further increase downstream community stability. Despite it being quite abstract, our model may inform future research on designing more stable microbial communities or increasing the stability of existing ones.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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27
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Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun 2023; 14:4780. [PMID: 37553336 PMCID: PMC10409746 DOI: 10.1038/s41467-023-40372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
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Affiliation(s)
- Anna S Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa S Niedermeier
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna G Burrichter
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chiara Lincetto
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Hübner
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
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28
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Han L, Qin H, Wang J, Yao D, Zhang L, Guo J, Zhu B. Immediate response of paddy soil microbial community and structure to moisture changes and nitrogen fertilizer application. Front Microbiol 2023; 14:1130298. [PMID: 37547687 PMCID: PMC10400893 DOI: 10.3389/fmicb.2023.1130298] [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: 12/23/2022] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
Water and fertilizer managements are the most common practices to maximize crop yields, and their long-term impact on soil microbial communities has been extensively studied. However, the initial response of microbes to fertilization and soil moisture changes remains unclear. In this study, the immediate effects of nitrogen (N)-fertilizer application and moisture levels on microbial community of paddy soils were investigated through controlled incubation experiments. Amplicon sequencing results revealed that moisture had a stronger influence on the abundance and community composition of total soil bacteria, as well as ammonia oxidizing-archaea (AOA) and -bacteria (AOB). Conversely, fertilizer application noticeably reduced the connectivity and complexity of the total bacteria network, and increasing moisture slightly exacerbated these effects. NH4+-N content emerged as a significant driving force for changes in the structure of the total bacteria and AOB communities, while NO3--N content played more important role in driving shifts in AOA composition. These findings indicate that the initial responses of microbial communities, including abundance and composition, and network differ under water and fertilizer managements. By providing a snapshot of microbial community structure following short-term N-fertilizer and water treatments, this study contributes to a better understanding of how soil microbes respond to long-term agriculture managements.
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Affiliation(s)
- Linrong Han
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi’an, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hongling Qin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Jingyuan Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Dongliang Yao
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
- College of Biodiversity, Conservation Southwest Forestry University, Kunming, China
| | - Leyan Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi’an, China
| | - Baoli Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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29
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Chang CY, Bajić D, Vila JCC, Estrela S, Sanchez A. Emergent coexistence in multispecies microbial communities. Science 2023; 381:343-348. [PMID: 37471535 DOI: 10.1126/science.adg0727] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Understanding the mechanisms that maintain microbial biodiversity is a critical aspiration in ecology. Past work on microbial coexistence has largely focused on species pairs, but it is unclear whether pairwise coexistence in isolation is required for coexistence in a multispecies community. To address this question, we conducted hundreds of pairwise competition experiments among the stably coexisting members of 12 different enrichment communities in vitro. To determine the outcomes of these experiments, we developed an automated image analysis pipeline to quantify species abundances. We found that competitive exclusion was the most common outcome, and it was strongly hierarchical and transitive. Because many species that coexist within a stable multispecies community fail to coexist in pairwise co-culture under identical conditions, we concluded that multispecies coexistence is an emergent phenomenon. This work highlights the importance of community context for understanding the origins of coexistence in complex ecosystems.
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Affiliation(s)
- Chang-Yu Chang
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Microbial Biotechnology. Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Madrid, Spain
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30
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Lu C, Zhang Z, Guo P, Wang R, Liu T, Luo J, Hao B, Wang Y, Guo W. Synergistic mechanisms of bioorganic fertilizer and AMF driving rhizosphere bacterial community to improve phytoremediation efficiency of multiple HMs-contaminated saline soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163708. [PMID: 37105481 DOI: 10.1016/j.scitotenv.2023.163708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/28/2023] [Accepted: 04/20/2023] [Indexed: 06/03/2023]
Abstract
The addition of Arbuscular mycorrhizal fungi (AMF) or bioorganic fertilizer (BOF) alone has been reported to enhance plant tolerance to heavy metals and salt stress and promote plant growth, while their synergistic effects on plant growth and rhizosphere microorganism are largely unknown. This study explored the effects of AMF (Rhizophagus intraradices), BOF and BOF + RI assisted phytoremediation on heavy metals contaminated saline soil improvement and revealed the microbial mechanism. For this purpose, a pot trial consisting of four treatments (CK, RI, BOF and BOF + RI) was carried out. The results showed that the biomass, nutrient element contents, the accumulation of heavy metals and Na of Astragalus adsurgens and soil properties were most significantly improved by BOF + RI. BOF + RI significantly impacted rhizosphere microbial diversity, abundance and community composition. Chloroflexi and Patescibacteria at the phylum level and Actinomadura, Iamia, and Desulfosporosinus at the genus level were significantly enriched in BOF + RI. Network analysis revealed that BOF + RI significantly changed the keystone and enhanced complexity and interaction. Most of the keystones had roles in promoting plant growth and stress resistance. This study suggested that phytoremediation assisted by BOF and AMF is an attractive approach to ameliorate heavy metals contaminated saline soil.
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Affiliation(s)
- Chengyan Lu
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Zhechao Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Peiran Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Run Wang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Tai Liu
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Junqing Luo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Baihui Hao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yuchen Wang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
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31
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An R, Liu Y, Pan C, Da Z, Zhang P, Qiao N, Zhao F, Ba S. Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163308. [PMID: 37028668 DOI: 10.1016/j.scitotenv.2023.163308] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/26/2023] [Accepted: 04/01/2023] [Indexed: 05/27/2023]
Abstract
Alpine wetland is a natural laboratory for studying the Earth's third polar ecosphere. Protist communities are key components of wetland ecosystems which are extremely vulnerable to environmental change. It is of great importance to study the protist community in relation to environment, which might be the key to understand the ecosystem of the alpine wetlands under global change. In this study, we investigated the composition of protist communities across the Mitika Wetland, a unique alpine wetland hosting tremendous endemic diversity. Using 18S rRNA gene high-throughput sequencing, we evaluated how protist taxonomic and functional group composition is structured by seasonal climate and environmental variation. We found a high relative abundance of Ochrophyta, Ciliophora, and Cryptophyta, each of which showcased a unique spatial pattern in the wet and dry seasons. The proportion of consumers, parasites and phototrophs groups were stable among the functional zones and also between the seasons, with consumers dominating communities in terms of richness, while phototrophic taxa dominated in terms of relative abundance. Protist and each functional group were rather regulated by deterministic than stochastic processes, with water quality having a strong control on communities. Salinity and pH were the most important environmental factors at shaping protistan community. The protist co-occurrence network dominated by the positive edge indicating the communities resisted extreme environmental conditions through close cooperation, and more consumers were determined as the keystones in wet season and more phototrophic taxa in dry season. Our results provided the baseline of the protist taxonomic and functional group composition in the highest wetland, and highlighted environmental selections drive protist distribution, implying the alpine wetland ecosystem are sensitive to climate changes and human activities.
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Affiliation(s)
- Ruizhi An
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Yang Liu
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Chengmei Pan
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Zhen Da
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Peng Zhang
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Nanqian Qiao
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Sang Ba
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China.
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32
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Li M, Yao J, Sunahara G, Duran R, Liu B, Cao Y, Li H, Pang W, Liu H, Jiang S, Zhu J, Zhang Q. Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131153. [PMID: 36893604 DOI: 10.1016/j.jhazmat.2023.131153] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/20/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.
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Affiliation(s)
- Miaomiao Li
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Jun Yao
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Geoffrey Sunahara
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China; Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Drive, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Bang Liu
- Universite de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Ying Cao
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Hao Li
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Wancheng Pang
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Houquan Liu
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shun Jiang
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Junjie Zhu
- Science and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
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33
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Amarnath K, Narla AV, Pontrelli S, Dong J, Reddan J, Taylor BR, Caglar T, Schwartzman J, Sauer U, Cordero OX, Hwa T. Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. Nat Commun 2023; 14:3165. [PMID: 37258505 DOI: 10.1038/s41467-023-38913-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that extensive excretion of key metabolites following growth arrest provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities progress through distinct phases of growth-dilution cycles, comprising of exponential growth, acidification-triggered growth arrest, collaborative deacidification, and growth recovery, with each phase involving different combinations of physiological states of individual species. Our findings challenge the steady-state view of ecosystems commonly portrayed in ecological models, offering an alternative dynamical view based on growth advantages of complementary species in different phases.
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Affiliation(s)
- Kapil Amarnath
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Avaneesh V Narla
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Sammy Pontrelli
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Jiajia Dong
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA, 17837, USA
| | - Jack Reddan
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA
| | - Brian R Taylor
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Tolga Caglar
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Uwe Sauer
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA.
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34
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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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Zhan J, Li Y, Zhao X, Yang H, Ning Z, Zhang R. Effects of nitrogen addition and plant litter manipulation on soil fungal and bacterial communities in a semiarid sandy land. Front Microbiol 2023; 14:1013570. [PMID: 37051518 PMCID: PMC10083410 DOI: 10.3389/fmicb.2023.1013570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The plant and soil microbial communities are influenced by variability in environmental conditions (e.g., nitrogen addition); however, it is unclear how long-term nitrogen addition and litter manipulation affect soil microbial communities in a semiarid sandy grassland. Therefore, we simulated the impact of N addition and litter manipulation (litter removal, litter doubling) on plant and soil microbial communities in Horqin grassland, northern China through an experiment from 2014 to 2019. Our results revealed that in the case of non-nitrogen (N0), litter manipulation significantly reduced vegetation coverage (V) (p < 0.05); soil bacterial communities have higher alpha diversity than that of the fungi, and the beta diversity of soil fungi was higher than that of the bacteria; soil microbial alpha diversity was significantly decreased by nitrogen addition (N10) (p < 0.05); N addition and litter manipulation had significantly interactive influences on soil microbial beta diversity, and litter manipulation (C0 and C2) had significantly decreased soil microbial beta diversity (p < 0.05) in the case of nitrogen addition (N10) (p < 0.05). Moreover, bacteria were mostly dominated by the universal phyla Proteobacteria, Actinobacteria, and Acidobacteria, and fungi were only dominated by Ascomycota. Furthermore, the correlation analysis, redundancy analysis (RDA), and variation partitioning analysis indicated that the soil fungi community was more apt to be influenced by plant community diversity. Our results provide evidence that plant and soil microbial community respond differently to the treatments of the 6-year N addition and litter manipulation in a semiarid sandy land.
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Affiliation(s)
- Jin Zhan
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yulin Li
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Yulin Li,
| | - Xueyong Zhao
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Hongling Yang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiying Ning
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
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36
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Bhandari R, Sanz-Saez A, Leisner CP, Potnis N. Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere. ISME COMMUNICATIONS 2023; 3:24. [PMID: 36973329 PMCID: PMC10043289 DOI: 10.1038/s43705-023-00232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.
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Affiliation(s)
- Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
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Liu YY. Controlling the human microbiome. Cell Syst 2023; 14:135-159. [PMID: 36796332 PMCID: PMC9942095 DOI: 10.1016/j.cels.2022.12.010] [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: 06/06/2022] [Revised: 10/18/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
We coexist with a vast number of microbes that live in and on our bodies. Those microbes and their genes are collectively known as the human microbiome, which plays important roles in human physiology and diseases. We have acquired extensive knowledge of the organismal compositions and metabolic functions of the human microbiome. However, the ultimate proof of our understanding of the human microbiome is reflected in our ability to manipulate it for health benefits. To facilitate the rational design of microbiome-based therapies, there are many fundamental questions to be addressed at the systems level. Indeed, we need a deep understanding of the ecological dynamics associated with such a complex ecosystem before we rationally design control strategies. In light of this, this review discusses progress from various fields, e.g., community ecology, network science, and control theory, that are helping us make progress toward the ultimate goal of controlling the human microbiome.
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Affiliation(s)
- Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
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38
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Jiang C, Zeng H. Unique Habitat of Karst Tiankengs Changes the Taxonomy and Potential Metabolism of Soil Microbial Communities. Microbiol Spectr 2023; 11:e0231622. [PMID: 36648219 PMCID: PMC9927240 DOI: 10.1128/spectrum.02316-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Microbial communities in karst ecosystems have been extensively studied. However, in a class of deep-lying habitats with unique climates (karst tiankeng), the structure and ecological functions of microorganisms receive little attention, which is essential for understanding the biogeochemistry of karst tiankeng. Herein, microorganisms from inside (ITK) and outside (OTK) karst tiankengs were analyzed by high-throughput sequencing and multivariate statistical analysis. The results showed that the structure and function of soil bacterial communities inside and outside karst tiankengs were significantly different. The ITK microbial communities presented significantly higher Shannon diversity due to the abundant nutrients in karst tiankeng soil. Random molecular ecological network analysis revealed that the ITK network was simpler and more vulnerable and may be susceptible to environmental changes. More positive links within the network indicate that microorganisms adapt to the karst tiankeng through synergies. The keystones in karst tiankeng were mainly involved in the decomposition of soil organic matter and carbon/nitrogen cycles. Although soil total phosphorus and available potassium regulate microbial community structure variation, dispersal limitation is the predominant ecological process within the microbial community in karst tiankeng. In addition, the functional profiles of the microbial communities reveal that some human diseases (such as infectious diseases) exist in OTK. Collectively, these findings have enhanced our understanding of microbial interactions, ecological functions, and community composition processes in karst tiankeng ecosystems. IMPORTANCE Constrained by the trapped terrain, a unique ecosystem has formed in karst tiankeng. Soil microorganisms are essential for the formation and maintenance of ecosystems, but soil microbial ecology research in karst tiankeng is still lacking. In this study, representative habitats inside and outside karst tiankeng were selected to study the taxonomy and potential metabolism of soil microbial communities. The results show that the unique habitat of karst tiankeng reshapes the composition, structure, and function of soil microbial communities. Our results contribute to enhancing our understanding of sustainable recovery strategies in fragile ecosystems and understanding the biodiversity value of karst tiankeng under climate change.
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Affiliation(s)
- Cong Jiang
- School of Urban Planning and Design, Peking University Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Hui Zeng
- School of Urban Planning and Design, Peking University Shenzhen Graduate School, Peking University, Shenzhen, China
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39
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Zhou X, Liu L, Zhao J, Zhang J, Cai Z, Huang X. High carbon resource diversity enhances the certainty of successful plant pathogen and disease control. THE NEW PHYTOLOGIST 2023; 237:1333-1346. [PMID: 36305241 DOI: 10.1111/nph.18582] [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: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The host-associated microbiome highly determines plant health. Available organic resources, such as food for microbes, are important in shaping microbial community structure and multifunctionality. However, how using organic resources precisely manipulates the soil microbiome and makes it supportive of plant health remains unclear. Here, we experimentally tested the influence of carbon resource diversity on the microbial trophic network and pathogen invasion success in a microcosm study. We further explored how resource diversity affects microbial evenness, community functions, and plant disease outcomes in systems involving tomato plants and the in vivo soil microbiome. Increasing available resource diversity altered trophic network architecture, increased microbial evenness, and thus increased the certainty of successful pathogen control. By contrast, the invasion resistance effects of low resource diversity were less effective and highly varied. Accordingly, increases in the evenness and connection of dominant species induced by high resource diversity significantly contributed to plant disease suppression. Furthermore, high carbohydrate diversity upregulated plant immune system regulation-related microbial functions. Our results deepen the biodiversity-invasion resistance theory and provide practical guidance for the control of plant pathogens and diseases by using organic resource-mediated approaches, such as crop rotation, intercropping, and organic amendments.
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Affiliation(s)
- Xing Zhou
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
| | - Liangliang Liu
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
| | - Jun Zhao
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Xinqi Huang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
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40
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Sun M, Li M, Zhou Y, Liu J, Shi W, Wu X, Xie B, Deng Y, Gao Z. Nitrogen deposition enhances the deterministic process of the prokaryotic community and increases the complexity of the microbial co-network in coastal wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158939. [PMID: 36170917 DOI: 10.1016/j.scitotenv.2022.158939] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/15/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Global nitrogen deposition has increased significantly in recent years. At present, research on the effects of different amounts and types of nitrogen deposition on soil microorganisms in coastal wetlands is scarce. In this study, based on 7 years of simulated nitrogen deposition at multiple levels (low, medium, high) and of multiple types (NH4NO3, NH4Cl, KNO3), the effects of different nitrogen deposition conditions on the diversity, community assembly processes, co-networks, and community function of soil prokaryotes in coastal wetlands were examined. The results showed that, compared with that in control, the microbial α diversity increased significantly under nitrogen deposition (P < 0.05). However, it decreased significantly in the high-NH4NO3 and high-NH4Cl treatments (P < 0.05). The deterministic process of community assembly was strengthened under the different types of nitrogen deposition. Compared with that under NH4+-N deposition, the microbial co-network under NO3--N deposition was more complex. Network stability significantly decreased under different NH4+-N deposition levels. In addition, the results of FAPROTAX functional prediction showed that microbial community functional groups associated with carbon and nitrogen cycling changed significantly (P < 0.05). In conclusion, our results emphasize that nitrogen deposition environments cause changes in soil microbial community structure and interactions, and may also affect soil carbon and nitrogen cycling, but the effects of different forms and levels of nitrogen deposition are not consistent. This study provides new insights for evaluating the changes in soil microbial communities in coastal wetlands caused by different types of long-term nitrogen deposition, and has scientific significance for assessing the ecological effects of long-term nitrogen deposition.
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Affiliation(s)
- Mengyue Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Tai'an 271018, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jiai Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Wenchong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | | | - Baohua Xie
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, CAS, Shandong provincial Key Laboratory of Coastal Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, Shandong, China; Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Dongying 257500, China.
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-alkali Land, Tai'an 271018, China.
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41
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Wang H, Liu H, Yang T, Lv G, Li W, Chen Y, Wu D. Mechanisms underlying the succession of plant rhizosphere microbial community structure and function in an alpine open-pit coal mining disturbance zone. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116571. [PMID: 36308787 DOI: 10.1016/j.jenvman.2022.116571] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/25/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Elucidating the responses and potential functions of soil microbial communities during succession is important for understanding biogeochemical processes and the sustainable development of plant communities after environmental disturbances. However, studies of such dynamics during post-mining ecological restoration in alpine areas remain poorly understood. Microbial diversity, nitrogen, and phosphorus cycle functional gene potential in the Heishan mining area of Northwest China was studied, including primitive succession, secondary succession, and artificial succession disturbed by mining. The results revealed that: (1) The dominant bacteria in both categories (non-remediated and ecologically restored) of mining area rhizosphere soil were Proteobacteria, adopting the r strategy, whereas in naturally occurring soil outside the mining area, the dominant bacteria were actinomycetes and Acidobacteria, adopting the k strategy. Notably, mining perturbation significantly reduced the relative abundance of archaea. (2) After restoration, more bacterial network node connections were observed in mining areas than were originally present, whereas the archaeal network showed the opposite trend. (3) The networks of microbial genes related to nitrogen and phosphorus cycle potential differed significantly, depending on the succession type. Namely, prior to restoration, there were more phosphorus related functional gene network connections; these were also more strongly correlated, and the network was more aggregated. (4) Soil factors such as pH and NO3-N affected both the mining area remediation soil and the soil outside the mining area, but did not affect the soil of the original vegetation in the mining area. The changes in the structure and function of plant rhizosphere microorganisms after mining disturbance can provide a theoretical basis for the natural restoration of mining areas.
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Affiliation(s)
- Hengfang Wang
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
| | - Honglin Liu
- School of Geology and Mining Engineering, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Environmental Protection Mining for Mineral Resources at Universities of Education Department of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830017, China.
| | - Tianhong Yang
- School of Resources and Civil Engineering, Northeastern University, 110004, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
| | - Wenjing Li
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
| | - Yuncai Chen
- School of Geology and Mining Engineering, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Environmental Protection Mining for Mineral Resources at Universities of Education Department of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830017, China
| | - Deyan Wu
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
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42
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Sadiq FA, De Reu K, Burmølle M, Maes S, Heyndrickx M. Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries. Front Microbiol 2023; 14:1159434. [PMID: 37125177 PMCID: PMC10133454 DOI: 10.3389/fmicb.2023.1159434] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Most biofilms within the food industry are formed by multiple bacterial species which co-exist on surfaces as a result of interspecies interactions. These ecological interactions often make these communities tolerant against antimicrobials. Our previous work led to the identification of a large number (327) of highly diverse bacterial species on food contact surfaces of the dairy, meat, and egg industries after routine cleaning and disinfection (C&D) regimes. In the current study, biofilm-forming ability of 92 bacterial strains belonging to 26 genera and 42 species was assessed and synergistic interactions in biofilm formation were investigated by coculturing species in all possible four-species combinations. Out of the total 455 four-species biofilm combinations, greater biofilm mass production, compared to the sum of biofilm masses of individual species in monoculture, was observed in 34 combinations. Around half of the combinations showed synergy in biofilm mass > 1.5-fold and most of the combinations belonged to dairy strains. The highest synergy (3.13-fold) was shown by a combination of dairy strains comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus. The observed synergy in mixed biofilms turned out to be strain-specific rather than species-dependent. All biofilm combinations showing remarkable synergy appeared to have certain common species in all combinations which shows there are keystone industry-specific bacterial species which stimulate synergy or antagonism and this may have implication for biofilm control in the concerned food industries.
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Affiliation(s)
- Faizan Ahmed Sadiq
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Faizan Ahmed Sadiq,
| | - Koen De Reu
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sharon Maes
- The Department of Ecotechnology and Sustainable Building Engineering, Mid Sweden University, Östersund, Sweden
| | - Marc Heyndrickx
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- *Correspondence: Marc Heyndrickx,
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43
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George AB, Korolev KS. Ecological landscapes guide the assembly of optimal microbial communities. PLoS Comput Biol 2023; 19:e1010570. [PMID: 36626403 PMCID: PMC9831326 DOI: 10.1371/journal.pcbi.1010570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023] Open
Abstract
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.
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Affiliation(s)
- Ashish B. George
- Department of Physics and Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Carl R. Woese Institute for Genomic Biology and Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Kirill S. Korolev
- Department of Physics and Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
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44
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Li M, Pommier T, Yin Y, Cao W, Zhang X, Hu J, Hautier Y, Yang T, Xu Y, Shen Q, Kowalchuk GA, Jousset A, Wei Z. Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions. Environ Microbiol 2022; 24:5680-5689. [PMID: 36053873 DOI: 10.1111/1462-2920.16184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here, we use resource availability (RA) as a model parameter altering the resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.
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Affiliation(s)
- Mei Li
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.,Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Yue Yin
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Wenhui Cao
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Xiaohui Zhang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Jie Hu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands.,UMR 6553 Ecobio, CNRS-University of Rennes, Rennes Cedex, France
| | - Yann Hautier
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Tianjie Yang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yangchun Xu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qirong Shen
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Zhong Wei
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
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45
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Zhang M, Zhang R, Song R, An X, Chu G, Jia H. Soil pqqC-harboring bacterial community response to increasing aridity in semi-arid grassland ecosystems: Diversity, co-occurrence network, and assembly process. Front Microbiol 2022; 13:1019023. [PMID: 36338099 PMCID: PMC9633997 DOI: 10.3389/fmicb.2022.1019023] [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: 08/14/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2023] Open
Abstract
Aridity is increasing in several regions because of global climate change, which strongly affects the soil microbial community. The soil pqqC-harboring bacterial community plays a vital role in soil P cycling and P availability. However, the effect of shifts in aridity on the pqqC community is largely unknown. Here, based on high-throughput sequencing technology, we investigated the response patterns of the diversity, co-occurrence networks, and assembly mechanisms of the soil pqqC communities along a natural aridity gradient in adjacent pairs of natural and disturbed grasslands in Inner Mongolia, China. The results showed that the α-diversity of the pqqC community first increased and then decreased with increasing aridity in the natural grassland, while it linearly increased as aridity increased in the disturbed grassland. The pqqC community dissimilarity significantly increased with increased aridity, exhibiting a steeper change rate in the disturbed grassland than in the natural grassland. Increased aridity altered the pqqC community composition, leading to increases in the relative abundance of Actinobacteria but decreases in Proteobacteria. The composition and structure of the pqqC community showed significant differences between natural and disturbed grasslands. In addition, the network analysis revealed that aridity improved the interactions among pqqC taxa and promoted the interspecific competition of pqqC microorganisms. The pqqC community assembly was primarily governed by stochastic processes, and the relative contribution of stochastic processes increased with increasing aridity. Furthermore, disturbances could affect pqqC-harboring bacterial interactions and assembly processes. Overall, our findings fill an important knowledge gap in our understanding of the influence of aridity on the diversity and assembly mechanism of the soil pqqC community in grassland ecosystems, and this work is thus conducive to predicting the pqqC community and its ecological services in response to future climate change.
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Affiliation(s)
- Mei Zhang
- College of Grassland Science, Xinjiang Agricultural University, Urumqi, China
- School of Life Science, Shaoxing University, Shaoxing, China
| | - Ruixi Zhang
- Inner Mongolia Autonomous Region Water Conservancy and Hydropower Survey and Design Institute Co., Ltd., Hohhot, China
| | - Riquan Song
- Inner Mongolia Institute of Water Conservancy Science Research, Hohhot, China
| | - Xilong An
- Xilin Gol League Bureau of Agriculture and Animal Husbandry, Xilinhot, China
| | - Guixin Chu
- School of Life Science, Shaoxing University, Shaoxing, China
| | - Hongtao Jia
- College of Grassland Science, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
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46
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Murillo-Roos M, Abdullah HSM, Debbar M, Ueberschaar N, Agler MT. Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability. THE ISME JOURNAL 2022; 16:2280-2289. [PMID: 35768644 PMCID: PMC9381498 DOI: 10.1038/s41396-022-01271-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/20/2022] [Accepted: 06/10/2022] [Indexed: 12/27/2022]
Abstract
Leaf microbiomes play crucial roles in plant health, making it important to understand the origins and functional relevance of their diversity. High strain-level leaf bacterial genetic diversity is known to be relevant for interactions with hosts, but little is known about its relevance for interactions with the multitude of diverse co-colonizing microorganisms. In leaves, nutrients like amino acids are major regulators of microbial growth and activity. Using metabolomics of leaf apoplast fluid, we found that different species of the plant genus Flaveria considerably differ in the concentrations of high-cost amino acids. We investigated how these differences affect bacterial community diversity and assembly by enriching leaf bacteria in vitro with only sucrose or sucrose + amino acids as possible carbon sources. Enrichments from F. robusta were dominated by Pantoea sp. and Pseudomonas sp., regardless of carbon source. The latter was unable to grow on sucrose alone but persisted in the sucrose-only enrichment thanks to exchange of diverse metabolites from Pantoea sp. Individual Pseudomonas strains in the enrichments had high genetic similarity but still displayed clear niche partitioning, enabling distinct strains to cross-feed in parallel. Pantoea strains were also closely related, but individuals enriched from F. trinervia fed Pseudomonas more poorly than those from F. robusta. This can be explained in part by the plant environment, since some cross-feeding interactions were selected for, when experimentally evolved in a poor (sucrose-only) environment but selected against in a rich (sucrose + amino acids) one. Together, our work shows that leaf bacterial diversity is functionally relevant in cross-feeding interactions and strongly suggests that the leaf resource environment can shape these interactions and thereby indirectly drive bacterial diversity.
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Affiliation(s)
- Mariana Murillo-Roos
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hafiz Syed M Abdullah
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Mossaab Debbar
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Friedrich Schiller University Jena, Jena, Germany
| | - Matthew T Agler
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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47
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Gao C, Xu L, Montoya L, Madera M, Hollingsworth J, Chen L, Purdom E, Singan V, Vogel J, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, Taylor JW. Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities. Nat Commun 2022; 13:3867. [PMID: 35790741 PMCID: PMC9256619 DOI: 10.1038/s41467-022-31343-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
Plant response to drought stress involves fungi and bacteria that live on and in plants and in the rhizosphere, yet the stability of these myco- and micro-biomes remains poorly understood. We investigate the resistance and resilience of fungi and bacteria to drought in an agricultural system using both community composition and microbial associations. Here we show that tests of the fundamental hypotheses that fungi, as compared to bacteria, are (i) more resistant to drought stress but (ii) less resilient when rewetting relieves the stress, found robust support at the level of community composition. Results were more complex using all-correlations and co-occurrence networks. In general, drought disrupts microbial networks based on significant positive correlations among bacteria, among fungi, and between bacteria and fungi. Surprisingly, co-occurrence networks among functional guilds of rhizosphere fungi and leaf bacteria were strengthened by drought, and the same was seen for networks involving arbuscular mycorrhizal fungi in the rhizosphere. We also found support for the stress gradient hypothesis because drought increased the relative frequency of positive correlations.
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Affiliation(s)
- Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Mary Madera
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Joy Hollingsworth
- University of California Kearney Agricultural Research & Extension Center, Parlier, CA, 93648, USA
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- Department of Energy Joint Genome Institute, 1 Cyclotron Rd., Berkeley, CA, 94720, USA
| | - John Vogel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Energy Joint Genome Institute, 1 Cyclotron Rd., Berkeley, CA, 94720, USA
| | - Robert B Hutmacher
- UC Davis Department of Plant Sciences, University of California West Side Research & Extension Center, Five Points, CA, 93624, US
| | - Jeffery A Dahlberg
- University of California Kearney Agricultural Research & Extension Center, Parlier, CA, 93648, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA, 94710, USA
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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48
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van den Berg NI, Machado D, Santos S, Rocha I, Chacón J, Harcombe W, Mitri S, Patil KR. Ecological modelling approaches for predicting emergent properties in microbial communities. Nat Ecol Evol 2022; 6:855-865. [PMID: 35577982 PMCID: PMC7613029 DOI: 10.1038/s41559-022-01746-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/23/2022] [Indexed: 12/20/2022]
Abstract
Recent studies have brought forward the critical role of emergent properties in shaping microbial communities and the ecosystems of which they are a part. Emergent properties-patterns or functions that cannot be deduced linearly from the properties of the constituent parts-underlie important ecological characteristics such as resilience, niche expansion and spatial self-organization. While it is clear that emergent properties are a consequence of interactions within the community, their non-linear nature makes mathematical modelling imperative for establishing the quantitative link between community structure and function. As the need for conservation and rational modulation of microbial ecosystems is increasingly apparent, so is the consideration of the benefits and limitations of the approaches to model emergent properties. Here we review ecosystem modelling approaches from the viewpoint of emergent properties. We consider the scope, advantages and limitations of Lotka-Volterra, consumer-resource, trait-based, individual-based and genome-scale metabolic models. Future efforts in this research area would benefit from capitalizing on the complementarity between these approaches towards enabling rational modulation of complex microbial ecosystems.
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Affiliation(s)
| | - Daniel Machado
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sophia Santos
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Isabel Rocha
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jeremy Chacón
- Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - William Harcombe
- Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Sara Mitri
- Département de Microbiologie Fondamentale, University of Lausanne, Lausanne, Switzerland
| | - Kiran R Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
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49
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Wagner A. Competition for nutrients increases invasion resistance during assembly of microbial communities. Mol Ecol 2022; 31:4188-4203. [PMID: 35713370 PMCID: PMC9542400 DOI: 10.1111/mec.16565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 12/02/2022]
Abstract
The assembly of microbial communities through sequential invasions of microbial species is challenging to study experimentally. Here, I used genome‐scale metabolic models of multiple species to model community assembly. Each such model represents all known biochemical reactions that a species uses to build biomass from nutrients in the environment. Species interactions in such models emerge from first biochemical principles, either through competition for environmental nutrients, or through cross‐feeding on metabolic by‐products excreted by resident species. I used these models to study 250 community assembly sequences. In each such sequence, a community changes through successive species invasions. During the 250 assembly sequences, communities become more species‐rich and invasion‐resistant. Resistance against both constructive and destructive invasions – those that entail species extinction – is associated with high community productivity, high biomass, and low concentrations of unused carbon. Competition for nutrients outweighs the influence of cross‐feeding on the growth rate of individual species. In a community assembly network of all communities that arise during the 250 assembly sequences, some communities occur more often than expected by chance. These include invasion resistant “attractor” communities with high biomass that arise late in community assembly and persist preferentially because of their invasion resistance. Genome‐scale metabolic models can reveal generic properties of microbial communities that are independent of the resident species and the environment.
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Affiliation(s)
- Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, New Mexico, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
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50
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Dang Q, Zhao X, Yang T, Gong T, He X, Tan W, Xi B. Coordination of bacterial biomarkers with the dominant microbes enhances triclosan biodegradation in soil amended with food waste compost and cow dung compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153837. [PMID: 35181369 DOI: 10.1016/j.scitotenv.2022.153837] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Increasing concerns regarding the micropollutant triclosan (TCS) derive from its potential threats to human health and ecological security. Compost addition have been verified to be effective in soil remediation, however, the biodegradation of TCS under compost amendment in soil remain unclear. This study investigated the removal of TCS in soils amended with food waste compost (FS), cow dung compost (CS) and sludge compost (SS), respectively, explored the key TCS-degraders and biological mechanisms of TCS removal. Compost addition significantly enhanced the removal of TCS (p < 0.05) in the order of FS > CS > SS. The dosage of 20% (w/w) was the most efficient one and the ultimate concentrations of TCS were decreased by 76.67%, 67.90% and 56.79% compared with CK, respectively. The abundance of key dominant bacterial genus (7 in FS and 4 in CS) and fungal genus (3 in FS and CS) was stimulated due to the increase of soil nutrient factors (including dissolved organic carbon, DOC; soil organic matter, SOM; ammonium nitrogen, NH4+; nitrate nitrogen, NO3-) and the decrease of pH. A negative correlation between these dominant microbes and TCS concentration indicated their potential effect on TCS degradation. A total of four bacterial biomarkers, namely Saccharomonospora, Aequorivita, Bacillaceae and Fodinicurvataceae (both at family level) were the key TCS-degraders. Structural equation model (SEM) indicated that the improvement of soil nutrient factors in FS and CS promoted TCS biodegradation by improving the activity of bacterial biomarkers, as while, the key dominant microbes showed good tolerance to TCS stress. However, there were no significant biological effects on TCS in SS group. Network analysis further confirmed that it was the coordination of bacterial biomarkers with the dominant microbes that enhanced TCS biodegradation in soil amended with food waste compost and cow dung compost.
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Affiliation(s)
- Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tianxue Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tiancheng Gong
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiaosong He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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