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Wang Z, Fu X, Kuramae EE. Insight into farming native microbiome by bioinoculant in soil-plant system. Microbiol Res 2024; 285:127776. [PMID: 38820701 DOI: 10.1016/j.micres.2024.127776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.
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Affiliation(s)
- Zhikang Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands; Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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2
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McEnany JD, Good BH. Predicting the First Steps of Evolution in Randomly Assembled Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.15.571925. [PMID: 38168431 PMCID: PMC10760118 DOI: 10.1101/2023.12.15.571925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Microbial communities can self-assemble into highly diverse states with predictable statistical properties. However, these initial states can be disrupted by rapid evolution of the resident strains. When a new mutation arises, it competes for resources with its parent strain and with the other species in the community. This interplay between ecology and evolution is difficult to capture with existing community assembly theory. Here, we introduce a mathematical framework for predicting the first steps of evolution in large randomly assembled communities that compete for substitutable resources. We show how the fitness effects of new mutations and the probability that they coexist with their parent depends on the size of the community, the saturation of its niches, and the metabolic overlap between its members. We find that successful mutations are often able to coexist with their parent strains, even in saturated communities with low niche availability. At the same time, these invading mutants often cause extinctions of metabolically distant species. Our results suggest that even small amounts of evolution can produce distinct genetic signatures in natural microbial communities.
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3
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Woelfel S, Silva MS, Stecher B. Intestinal colonization resistance in the context of environmental, host, and microbial determinants. Cell Host Microbe 2024; 32:820-836. [PMID: 38870899 DOI: 10.1016/j.chom.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
Microbial communities that colonize the human gastrointestinal (GI) tract defend against pathogens through a mechanism known as colonization resistance (CR). Advances in technologies such as next-generation sequencing, gnotobiotic mouse models, and bacterial cultivation have enhanced our understanding of the underlying mechanisms and the intricate microbial interactions involved in CR. Rather than being attributed to specific microbial clades, CR is now understood to arise from a dynamic interplay between microbes and the host and is shaped by metabolic, immune, and environmental factors. This evolving perspective underscores the significance of contextual factors, encompassing microbiome composition and host conditions, in determining CR. This review highlights recent research that has shifted its focus toward elucidating how these factors interact to either promote or impede enteric infections. It further discusses future research directions to unravel the complex relationship between host, microbiota, and environmental determinants in safeguarding against GI infections to promote human health.
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Affiliation(s)
- Simon Woelfel
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig Maximilian University of Munich, 80336 Munich, Germany
| | - Marta Salvado Silva
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig Maximilian University of Munich, 80336 Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute for Hygiene and Clinical Microbiology, Ludwig Maximilian University of Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
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4
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Chen Y, Niu L, Li Y, Wang Y, Shen J, Zhang W, Wang L. Distribution characteristics and microbial synergistic degradation potential of polyethylene and polypropylene in freshwater estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134328. [PMID: 38643575 DOI: 10.1016/j.jhazmat.2024.134328] [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: 02/14/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
The microbial degradation of polyethylene (PE) and polypropylene (PP) resins in rivers and lakes has emerged as a crucial issue in the management of microplastics. This study revealed that as the flow rate decreased longitudinally, ammonia nitrogen (NH4+-N), heavy fraction of organic carbon (HFOC), and small-size microplastics (< 1 mm) gradually accumulated in the deep and downstream estuarine sediments. Based on their surface morphology and carbonyl index, these sediments were identified as the potential hot zone for PE/PP degradation. Within the identified hot zone, concentrations of PE/PP-degrading genes, enzymes, and bacteria were significantly elevated compared to other zones, exhibiting strong intercorrelations. Analysis of niche differences revealed that the accumulation of NH4+-N and HFOC in the hot zone facilitated the synergistic coexistence of key bacteria responsible for PE/PP degradation within biofilms. The findings of this study offer a novel insight and comprehensive understanding of the distribution characteristics and synergistic degradation potential of PE/PP in natural freshwater environments.
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Affiliation(s)
- Yamei Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Yingjie Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Jiayan Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing 210098, PR China
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5
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Gibbs TL, Gellner G, Levin SA, McCann KS, Hastings A, Levine JM. When can higher-order interactions produce stable coexistence? Ecol Lett 2024; 27:e14458. [PMID: 38877741 DOI: 10.1111/ele.14458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Most ecological models are based on the assumption that species interact in pairs. Diverse communities, however, can have higher-order interactions, in which two or more species jointly impact the growth of a third species. A pitfall of the common pairwise approach is that it misses the higher-order interactions potentially responsible for maintaining natural diversity. Here, we explore the stability properties of systems where higher-order interactions guarantee that a specified set of abundances is a feasible equilibrium of the dynamics. Even these higher-order interactions which lead to equilibria do not necessarily produce stable coexistence. Instead, these systems are more likely to be stable when the pairwise interactions are weak or facilitative. Correlations between the pairwise and higher-order interactions, however, do permit robust coexistence even in diverse systems. Our work not only reveals the challenges in generating stable coexistence through higher-order interactions but also uncovers interaction patterns that can enable diversity.
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Affiliation(s)
- Theo L Gibbs
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Gabriel Gellner
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kevin S McCann
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alan Hastings
- Department of Environmental Science and Policy, University of California at Davis, Davis, California, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
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6
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Li P, Dini-Andreote F, Jiang J. Exploiting microbial competition to promote plant health. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00121-3. [PMID: 38760241 DOI: 10.1016/j.tplants.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
The host-associated microbiota can promote colonization resistance against pathogens via a mechanism termed 'nutrient blocking', as highlighted in a recent article by Spragge et al. This implies that greater metabolic overlap between commensal taxa and pathogens leads to disease suppression. Here, we discuss future avenues for how this principle can be exploited in the rhizosphere microbiota to promote plant health.
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Affiliation(s)
- Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China.
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Meyer C, Jeanbille M, Breuil MC, Bru D, Höfer K, Screpanti C, Philippot L. Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134231. [PMID: 38598881 DOI: 10.1016/j.jhazmat.2024.134231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.
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Affiliation(s)
- Cara Meyer
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France; Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Mathilde Jeanbille
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - Marie-Christine Breuil
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - David Bru
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France
| | - Kristin Höfer
- Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Claudio Screpanti
- Syngenta Crop Protection Research Stein, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, 17 rue Sully, 21000 Dijon, France.
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8
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Li Y, Liu Y, Cui J, Zhu M, Wang W, Chen K, Huang L, Liu Y. Oral-gut microbial transmission promotes diabetic coronary heart disease. Cardiovasc Diabetol 2024; 23:123. [PMID: 38581039 PMCID: PMC10998415 DOI: 10.1186/s12933-024-02217-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Diabetes is a predominant driver of coronary artery disease worldwide. This study aims to unravel the distinct characteristics of oral and gut microbiota in diabetic coronary heart disease (DCHD). Simultaneously, we aim to establish a causal link between the diabetes-driven oral-gut microbiota axis and increased susceptibility to diabetic myocardial ischemia-reperfusion injury (MIRI). METHODS We comprehensively investigated the microbial landscape in the oral and gut microbiota in DCHD using a discovery cohort (n = 183) and a validation chohort (n = 68). Systematically obtained oral (tongue-coating) and fecal specimens were subjected to metagenomic sequencing and qPCR analysis, respectively, to holistically characterize the microbial consortia. Next, we induced diabetic MIRI by administering streptozotocin to C57BL/6 mice and subsequently investigated the potential mechanisms of the oral-gut microbiota axis through antibiotic pre-treatment followed by gavage with specific bacterial strains (Fusobacterium nucleatum or fecal microbiota from DCHD patients) to C57BL/6 mice. RESULTS Specific microbial signatures such as oral Fusobacterium nucleatum and gut Lactobacillus, Eubacterium, and Roseburia faecis, were identified as potential microbial biomarkers in DCHD. We further validated that oral Fusobacterium nucleatum and gut Lactobacillus are increased in DCHD patients, with a positive correlation between the two. Experimental evidence revealed that in hyperglycemic mice, augmented Fusobacterium nucleatum levels in the oral cavity were accompanied by an imbalance in the oral-gut axis, characterized by an increased coexistence of Fusobacterium nucleatum and Lactobacillus, along with elevated cardiac miRNA-21 and a greater extent of myocardial damage indicated by TTC, HE, TUNEL staining, all of which contributed to exacerbated MIRI. CONCLUSION Our findings not only uncover dysregulation of the oral-gut microbiota axis in diabetes patients but also highlight the pivotal intermediary role of the increased abundance of oral F. nucleatum and gut Lactobacillus in exacerbating MIRI. Targeting the oral-gut microbiota axis emerges as a potent strategy for preventing and treating DCHD. Oral-gut microbial transmission constitutes an intermediate mechanism by which diabetes influences myocardial injury, offering new insights into preventing acute events in diabetic patients with coronary heart disease.
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Affiliation(s)
- Yiwen Li
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100078, China
| | - Yanfei Liu
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Jing Cui
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Mengmeng Zhu
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Wenting Wang
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Keji Chen
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Luqi Huang
- China Academy of Chinese Medical Sciences, Beijing, 100078, China
| | - Yue Liu
- National Clinical Research Center for TCM Cardiology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
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Daniel BBJ, Steiger Y, Sintsova A, Field CM, Nguyen BD, Schubert C, Cherrak Y, Sunagawa S, Hardt WD, Vorholt JA. Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags. Nat Microbiol 2024; 9:1103-1116. [PMID: 38503975 PMCID: PMC10994841 DOI: 10.1038/s41564-024-01634-9] [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: 09/19/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.
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Affiliation(s)
| | - Yves Steiger
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anna Sintsova
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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10
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Geesink P, ter Horst J, Ettema TJG. More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities. FEMS Microbiol Ecol 2024; 100:fiae029. [PMID: 38444203 PMCID: PMC10950044 DOI: 10.1093/femsec/fiae029] [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: 11/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.
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Affiliation(s)
- Patricia Geesink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jolanda ter Horst
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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11
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Yue H, Sun X, Wang T, Zhang A, Han D, Wei G, Song W, Shu D. Host genotype-specific rhizosphere fungus enhances drought resistance in wheat. MICROBIOME 2024; 12:44. [PMID: 38433268 PMCID: PMC10910722 DOI: 10.1186/s40168-024-01770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.
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Affiliation(s)
- Hong Yue
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuming Sun
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Wang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ali Zhang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dejun Han
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Weining Song
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
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12
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McCain JSP. Mapping combinatorial expression perturbations to growth in Escherichia coli. Cell Syst 2024; 15:106-108. [PMID: 38387440 DOI: 10.1016/j.cels.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
The connection between growth and gene expression has often been considered in a single gene. Repurposing a drug-drug interaction model, the multidimensional effects of several simultaneous gene expression perturbations on growth have been examined in the model bacteria Escherichia coli.
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Affiliation(s)
- J Scott P McCain
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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13
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Deng J, Taylor W, Levin SA, Saavedra S. On the limits to invasion prediction using coexistence outcomes. J Theor Biol 2024; 577:111674. [PMID: 38008157 DOI: 10.1016/j.jtbi.2023.111674] [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: 04/20/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
The dynamics of ecological communities in nature are typically characterized by probabilistic processes involving invasion dynamics. Because of technical challenges, however, the majority of theoretical and experimental studies have focused on coexistence dynamics. Therefore, it has become central to understand the extent to which coexistence outcomes can be used to predict analogous invasion outcomes relevant to systems in nature. Here, we study the limits to this predictability under a geometric and probabilistic Lotka-Volterra framework. We show that while individual survival probability in coexistence dynamics can be fairly closely translated into invader colonization probability in invasion dynamics, the translation is less precise between community persistence and community augmentation, and worse between exclusion probability and replacement probability. These results provide a guiding and testable theoretical framework regarding the translatability of outcomes between coexistence and invasion outcomes when communities are represented by Lotka-Volterra dynamics under environmental uncertainty.
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Affiliation(s)
- Jie Deng
- Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Washington Taylor
- Center for Theoretical Physics, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Simon A Levin
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA; High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| | - Serguei Saavedra
- Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
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14
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Dooley KD, Bergelson J. Richness and density jointly determine context dependence in bacterial interactions. iScience 2024; 27:108654. [PMID: 38188527 PMCID: PMC10770726 DOI: 10.1016/j.isci.2023.108654] [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: 04/27/2023] [Revised: 08/30/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Pairwise interactions are often used to predict features of complex microbial communities due to the challenge of measuring multi-species interactions in high dimensional contexts. This assumes that interactions are unaffected by community context. Here, we used synthetic bacterial communities to investigate that assumption by observing how interactions varied across contexts. Interactions were most often weakly negative and showed a phylogenetic signal among genera. Community richness and total density emerged as strong predictors of interaction strength and contributed to an attenuation of interactions as richness increased. Population level and per-capita measures of interactions both displayed such attenuation, suggesting factors beyond systematic changes in population size were involved; namely, changes to the interactions themselves. Nevertheless, pairwise interactions retained some explanatory power across contexts, provided those contexts were not substantially divergent in richness. These results suggest that understanding the emergent properties of microbial interactions can improve our ability to predict the features of microbial communities.
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Affiliation(s)
- Keven D. Dooley
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Joy Bergelson
- Center for Genomics and System Biology, Department of Biology, New York University, New York, NY 10003, USA
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15
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Liu G, Sun J, Xie P, Guo C, Zhu K, Tian K. Climate warming enhances microbial network complexity by increasing bacterial diversity and fungal interaction strength in litter decomposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168444. [PMID: 37949122 DOI: 10.1016/j.scitotenv.2023.168444] [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: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Microbial communities are important drivers of plant litter decomposition; however, the mechanisms of microbial co-occurrence networks and their network interaction dynamics in response to climate warming in wetlands remain unclear. Here, we conducted a 1.5-year warming experiment on the bacterial and fungal communities involved in litter decomposition in a typical wetland. The results showed that warming accelerated the decomposition of litter and had a greater effect on the diversity of bacteria than on that of fungi. Dominant bacterial communities, such as Bacteroidia, Alphaproteobacteria, and Actinobacteria, and dominant fungal communities, such as Leotiomycetes and Sordariomycetes, showed significant positive correlations with lignin and cellulose. Co-occurrence networks revealed that the average path length and betweenness centrality under warming conditions increased in the bacterial community but decreased in the fungal community. Both bacterial and fungal networks in the 2.0 °C warming treatment had the highest ratio of positive links (58.53 % and 98.14 %), indicating that moderate warming can promote the positive correlations and symbiotic relationships observed in the microbial community. This also suggests that small-world characteristics and weak-link advantages accelerate diffusion, and scale-free features facilitate propagation in microbial communities in response to climate warming. Logistic growth and Lotka-Volterra competition models revealed that climate warming enhances microbial network complexity mainly by increasing bacterial diversity and fungal interaction strength in litter decomposition. However, the symbiotic relationship decreased slightly under 4.0 °C warming, indicating that climate warming is a random attack rather than a targeted attack, and the microbial network has strong resistance to random attack, as shown by the highly robust dynamic performance of the microbial network in litter decomposition. Overall, the microbial community in litter decomposition responded to climate warming and shifted its network interactions, leading to further changes in emergent network topology and dynamics, thus accelerating litter decomposition in wetlands.
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Affiliation(s)
- Guodong Liu
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China; Key Laboratory of Lake Nansi Wetland Ecological and Environmental Protection, Rizhao 276826, China.
| | - Jinfang Sun
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China; Key Laboratory of Lake Nansi Wetland Ecological and Environmental Protection, Rizhao 276826, China.
| | - Peng Xie
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Chao Guo
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Kaixiang Zhu
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Kun Tian
- National Plateau Wetlands Research Center/Southwest Forestry University, Kunming 650224, China
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16
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Lepori VJ, Loeuille N, Rohr RP. Robustness versus productivity during evolutionary community assembly: short-term synergies and long-term trade-offs. Proc Biol Sci 2024; 291:20232495. [PMID: 38196359 PMCID: PMC10777152 DOI: 10.1098/rspb.2023.2495] [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: 11/06/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
The realization that evolutionary feedbacks need to be considered to fully grasp ecological dynamics has sparked interest in the effect of evolution on community properties like coexistence and productivity. However, little is known about the evolution of community robustness and productivity along diversification processes in species-rich systems. We leverage the recent structural approach to coexistence together with adaptive dynamics to study such properties and their relationships in a general trait-based model of competition on a niche axis. We show that the effects of coevolution on coexistence are two-fold and contrasting depending on the time scale considered. In the short term, evolution of niche differentiation strengthens coexistence, while long-term diversification leads to niche packing and decreased robustness. Moreover, we find that coevolved communities tend to be on average more robust and more productive than non-evolutionary assemblages. We illustrate how our theoretical predictions echo in observed empirical patterns and the implications of our results for empiricists and applied ecologists. We suggest that some of our results such as the improved robustness of Evolutionarily Stable Communities could be tested experimentally in suitable model systems.
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Affiliation(s)
- Vasco J. Lepori
- Department of Biology – Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Nicolas Loeuille
- Institute of Ecology and Environmental Sciences, IEES, Sorbonne Université, UPEC, CNRS, IRD, INRA, 75005 Paris, France
| | - Rudolf P. Rohr
- Department of Biology – Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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17
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Risely A, Byrne PG, Hoye BJ, Silla AJ. Dietary carotenoid supplementation has long-term and community-wide effects on the amphibian skin microbiome. Mol Ecol 2024; 33:e17203. [PMID: 37962103 DOI: 10.1111/mec.17203] [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: 04/21/2023] [Revised: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
The amphibian skin microbiome plays a crucial role in host immunity and pathogen defence, yet we know little about the environmental drivers of skin microbial variation across host individuals. Inter-individual variation in the availability of micro-nutrients such as dietary carotenoids, which are involved in amphibian immunity, may be one factor that influences skin microbial assembly across different life history stages. We compared the effect of four carotenoid supplementation regimes during different life stages on the adult skin microbiome using a captive population of the critically endangered southern corroboree frog, Pseudophryne corroboree. We applied 16S rRNA sequencing paired with joint-species distribution models to examine the effect of supplementation on taxon abundances. We found that carotenoid supplementation had subtle yet taxonomically widespread effects on the skin microbiome, even 4.5 years post supplementation. Supplementation during any life-history stage tended to have a positive effect on the number of bacterial taxa detected, although explanatory power was low. Some genera were sensitive to supplementation pre-metamorphosis, but most demonstrated either additive or dominant effects, whereby supplementation during one life history stage had intermediate or similar effects, respectively, to supplementation across life. Carotenoid supplementation increased abundances of taxa belonging to lactic acid bacteria, including Lactococcus and Enterococcus, a group of bacteria that have previously been linked to protection against the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). While the fitness benefits of these microbial shifts require further study, these results suggest a fundamental relationship between nutrition and the amphibian skin microbiome which may be critical to amphibian health and the development of novel conservation strategies.
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Affiliation(s)
- A Risely
- School of Science, Engineering and Environment, Salford University, Manchester, UK
| | - Phillip G Byrne
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Aimee J Silla
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
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18
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Goldman DA, Xue KS, Parrott AB, Jeeda RR, Franzese LR, Lopez JG, Vila JCC, Petrov DA, Good BH, Relman DA, Huang KC. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569120. [PMID: 38076867 PMCID: PMC10705444 DOI: 10.1101/2023.11.29.569120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The long-term success of introduced populations depends on their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization. Here, we investigate how initial population (propagule) size and resource competition interact during community coalescence by systematically mixing eight pairs of in vitro microbial communities at ratios that vary over six orders of magnitude, and we compare our results to a neutral ecological model. Although the composition of the resulting co-cultures deviated substantially from neutral expectations, each co-culture contained species whose relative abundance depended on propagule size even after ~40 generations of growth. Using a consumer-resource model, we show that this dose-dependent colonization can arise when resident and introduced species have high niche overlap and consume shared resources at similar rates. This model predicts that propagule size will have larger, longer-lasting effects in diverse communities in which niche overlap is higher, and we experimentally confirm that strain isolates show stronger dose dependence when introduced into diverse communities than in pairwise co-culture. This work shows how neutral-like colonization dynamics can emerge from non-neutral resource competition and have lasting effects on the outcomes of community coalescence.
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Affiliation(s)
- Doran A. Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katherine S. Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Autumn B. Parrott
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Rashi R. Jeeda
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauryn R. Franzese
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jaime G. Lopez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jean C. C. Vila
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H. Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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19
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Couso LL, Soler-Bistué A, Aptekmann AA, Sánchez IE. Ecology theory disentangles microbial dichotomies. Environ Microbiol 2023; 25:3052-3063. [PMID: 37658654 DOI: 10.1111/1462-2920.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.
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Affiliation(s)
- Luciana L Couso
- Facultad de Agronomía. Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas "Rodolfo A. Ugalde", IIB-IIBIO, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignacio E Sánchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Universidad de Buenos Aires, Buenos Aires, Argentina
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20
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Fei N, Xie B, Long TJ, StGeorge M, Tan A, Manzoor S, Sidebottom AM, Spedale M, Theriault BR, Sulakhe D, Chang EB. The Host-specific Microbiota is Required for Diet-Specific Metabolic Homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565654. [PMID: 37986759 PMCID: PMC10659342 DOI: 10.1101/2023.11.05.565654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
In complex mammals, the importance and host-specificity of microbial communities have been demonstrated through their positive effects on host immune fitness or performance. However, whether host metabolic physiology homeostasis depends on a specific bacterial community exclusive to the host remains unclear. Here, we show that the coevolved host-specific microbiota is required to maintain diet-specific flexible and sufficient metabolic homeostasis through a high colonization rate, modulating gut metabolites, and related targets. Using germ-free (GF) mice, we tested whether the fitness benefiting the host metabolic phenotype of microbiota was host-specific. We demonstrated that GF mice associated with exogenous microbiota (human microbiota (HM)), which exhibited different and reduced gut microbial species diversity, significantly elevated metabolic rate, and exhibited metabolic insufficiency, all characteristics of GF mice. Strikingly, the absence of the host-specific microbiome attenuated high-fat diet-specific metabolism features. Different diets caused different metabolic changes in only host-specific microbiota-associated mice, not the host-microbiota mismatched mice. While RNA sequencing revealed subtle changes in the expression of genes in the liver, GF mice and HM mice showed considerably altered expression of genes associated with metabolic physiology compared to GF mice associated with host-specific microbiota. The effect of diet outweighed microbiota in the liver transcriptome. These changes occurred in the setting of decreased luminal short-chain fatty acids (SCFAs) and the secondary bile acid (BAs) pool and downstream gut signaling targets in HM and GF mice, which affects whole-body metabolism. These data indicate that a foreign microbial community provides little metabolic benefit to the host when compared to a host-specific microbiome, due to the colonization selection pressure and microbiota-derived metabolites dysfunction. Overall, microbiome fitness effects on the host metabolic phenotype were host-specific. Understanding the impact of the host-specificity of the microbiome on metabolic homeostasis may provide important insights for building a better probiotic. Highlights Microbiome fitness effects on the host metabolic phenotype were host-specific in mammals.Human microbiota-associated mice exhibited lower host metabolic fitness or performance, and similar functional costs in GF mice.Different diets cause different metabolic changes only in host-specific microbiota-associated mice, not the host-microbiota mismatched mice.The defective gut microbiota in host-specific microbiota, microbial metabolites and related targets likely drive the metabolic homeostasis.
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21
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Spaak JW, Schreiber SJ. Building modern coexistence theory from the ground up: The role of community assembly. Ecol Lett 2023; 26:1840-1861. [PMID: 37747362 DOI: 10.1111/ele.14302] [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: 01/23/2023] [Revised: 08/06/2023] [Accepted: 08/12/2023] [Indexed: 09/26/2023]
Abstract
Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates-the average, per-capita growth rate of a rare species-to identify when and why species coexist. Despite significant advances in dissecting coexistence mechanisms when coexistence occurs, MCT relies on a 'mutual invasibility' condition designed for two-species communities but poorly defined for species-rich communities. Here, we review well-known issues with this component of MCT and propose a solution based on recent mathematical advances. We propose a clear framework for expanding MCT to species-rich communities and for understanding invasion resistance as well as coexistence, especially for communities that could not be analysed with MCT so far. Using two data-driven community models from the literature, we illustrate the utility of our framework and highlight the opportunities for bridging the fields of community assembly and species coexistence.
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Affiliation(s)
- Jurg W Spaak
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Institute for Environmental Sciences, Rheinland-Pfälzische Technische Univerität Kaiserslautern-Landau, Landau, Germany
| | - Sebastian J Schreiber
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California, USA
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22
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Vila JC, Goldford J, Estrela S, Bajic D, Sanchez-Gorostiaga A, Damian-Serrano A, Lu N, Marsland R, Rebolleda-Gomez M, Mehta P, Sanchez A. Metabolic similarity and the predictability of microbial community assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564019. [PMID: 37961608 PMCID: PMC10634833 DOI: 10.1101/2023.10.25.564019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
When microbial communities form, their composition is shaped by selective pressures imposed by the environment. Can we predict which communities will assemble under different environmental conditions? Here, we hypothesize that quantitative similarities in metabolic traits across metabolically similar environments lead to predictable similarities in community composition. To that end, we measured the growth rate and by-product profile of a library of proteobacterial strains in a large number of single nutrient environments. We found that growth rates and secretion profiles were positively correlated across environments when the supplied substrate was metabolically similar. By analyzing hundreds of in-vitro communities experimentally assembled in an array of different synthetic environments, we then show that metabolically similar substrates select for taxonomically similar communities. These findings lead us to propose and then validate a comparative approach for quantitatively predicting the effects of novel substrates on the composition of complex microbial consortia.
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Affiliation(s)
- Jean C.C. Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joshua Goldford
- Division of Geophysical and Planetary sciences,California Institute of Technology, Pasadena, CA, USA
| | - Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Djordje Bajic
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Section of Industrial Microbiology, Department of Biotechnology, Technical University Delft, Delft, The Netherlands
| | - Alicia Sanchez-Gorostiaga
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcalá de Henares, Spain
| | - Alejandro Damian-Serrano
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Department of Biology, University of Oregon, Eugene, OR, USA
| | - Nanxi Lu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Robert Marsland
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Maria Rebolleda-Gomez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbial Biotechnology, National Center for Biotechnology CNB-CSIC; Madrid, Spain
- New address: Institute of Functional Biology & Genomics IBFG, CSIC & University of Salamanca; Salamanca, Spain
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23
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Takano S, Vila JCC, Miyazaki R, Sánchez Á, Bajić D. The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies. Mol Biol Evol 2023; 40:msad187. [PMID: 37619982 PMCID: PMC10476156 DOI: 10.1093/molbev/msad187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Microbial strategies for resource use are an essential determinant of their fitness in complex habitats. When facing environments with multiple nutrients, microbes often use them sequentially according to a preference hierarchy, resulting in well-known patterns of diauxic growth. In theory, the evolutionary diversification of metabolic hierarchies could represent a mechanism supporting coexistence and biodiversity by enabling temporal segregation of niches. Despite this ecologically critical role, the extent to which substrate preference hierarchies can evolve and diversify remains largely unexplored. Here, we used genome-scale metabolic modeling to systematically explore the evolution of metabolic hierarchies across a vast space of metabolic network genotypes. We find that only a limited number of metabolic hierarchies can readily evolve, corresponding to the most commonly observed hierarchies in genome-derived models. We further show how the evolution of novel hierarchies is constrained by the architecture of central metabolism, which determines both the propensity to change ranks between pairs of substrates and the effect of specific reactions on hierarchy evolution. Our analysis sheds light on the genetic and mechanistic determinants of microbial metabolic hierarchies, opening new research avenues to understand their evolution, evolvability, and ecology.
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Affiliation(s)
- Sotaro Takano
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Jean C C Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, Japan
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Djordje Bajić
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Section of Industrial Microbiology, Department of Biotechnology, Technical University Delft, Delft, The Netherlands
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