1
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Zheng X, Li J, Ouyang Y, Wu G, He X, Wang D, Zhang XX. Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes. WATER RESEARCH 2024; 267:122491. [PMID: 39353343 DOI: 10.1016/j.watres.2024.122491] [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: 06/02/2024] [Revised: 08/15/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024]
Abstract
The inefficient biodegradation and incomplete mineralization of nitrogenous heterocyclic compounds (NHCs) have emerged as a pressing environmental concern. The top-down design offers potential solutions to this issue by targeting improvements in community function, but the ecological linkages between selection strength and the structure and function of desired microbiomes remain elusive. Herein, the integration of metagenomics, culture-based approach, non-targeted metabolite screening and enzymatic verification experiments revealed the effect of enrichment concentration on the top-down designed benzothiazole (BTH, a typical NHC)-degrading consortia. Significant differences were observed for the degradation efficiency and community structure under varying BTH selections. Notably, the enriched consortia at high concentrations of BTH were dominated by genus Rhodococcus, possessing higher degradation rates. Moreover, the isolate Rhodococcus pyridinivorans Rho48 displayed excellent efficiencies in BTH removal (98 %) and mineralization (∼ 60 %) through the hydroxylation and cleavage of thiazole and benzene rings, where cytochrome P450 enzyme was firstly reported to participate in BTH conversion. The functional annotation of 460 recovered genomes from the enriched consortia revealed diverse interspecific cooperation patterns that accounted for the BTH mineralization, particularly Nakamurella and Micropruina under low selection strength, and Rhodococcus and Marmoricola under high selection strength. This study highlights the significance of selection strength in top-down design of synthetic microbiomes for degrading refractory organic pollutants, providing valuable guidance for designing functionally optimized microbiomes used in environmental engineering.
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Affiliation(s)
- Xiulin Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Jie Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Yixin Ouyang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Gang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; School of Environment, Jiangsu Engineering Lab of Water and Soil Eco-Remediation, Nanjing Normal University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
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2
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Blake C, Barber JN, Connallon T, McDonald MJ. Evolutionary shift of a tipping point can precipitate, or forestall, collapse in a microbial community. Nat Ecol Evol 2024; 8:2325-2335. [PMID: 39294402 DOI: 10.1038/s41559-024-02543-0] [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: 02/19/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024]
Abstract
Global ecosystems are rapidly approaching tipping points, where minute shifts can lead to drastic ecological changes. Theory predicts that evolution can shape a system's tipping point behaviour, but direct experimental support is lacking. Here we investigate the power of evolutionary processes to alter these critical thresholds and protect an ecological community from collapse. To do this, we propagate a two-species microbial system composed of Escherichia coli and baker's yeast, Saccharomyces cerevisiae, for over 4,000 generations, and map ecological stability before and after coevolution. Our results reveal that tipping points-and other geometric properties of ecological communities-can evolve to alter the range of conditions under which our microbial community can flourish. We develop a mathematical model to illustrate how evolutionary changes in parameters such as growth rate, carrying capacity and resistance to environmental change affect ecological resilience. Our study shows that adaptation of key species can shift an ecological community's tipping point, potentially promoting ecological stability or accelerating collapse.
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Affiliation(s)
- Christopher Blake
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Jake N Barber
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
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3
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Larrouy JL, Ridgway HJ, Dhami MK, Jones EE. Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA. MICROBIAL ECOLOGY 2024; 87:124. [PMID: 39379709 PMCID: PMC11461681 DOI: 10.1007/s00248-024-02436-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 09/19/2024] [Indexed: 10/10/2024]
Abstract
Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.
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Affiliation(s)
- J L Larrouy
- Department of Pest-Management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Christchurch, 7647, New Zealand.
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, 7608, New Zealand.
| | - H J Ridgway
- Department of Pest-Management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Christchurch, 7647, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, 7608, New Zealand
| | - M K Dhami
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, 7608, New Zealand
| | - E E Jones
- Department of Pest-Management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Christchurch, 7647, New Zealand
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4
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Kostic T, Schloter M, Arruda P, Berg G, Charles TC, Cotter PD, Kiran GS, Lange L, Maguin E, Meisner A, van Overbeek L, Sanz Y, Sarand I, Selvin J, Tsakalidou E, Smidt H, Wagner M, Sessitsch A. Concepts and criteria defining emerging microbiome applications. Microb Biotechnol 2024; 17:e14550. [PMID: 39236296 PMCID: PMC11376781 DOI: 10.1111/1751-7915.14550] [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: 07/01/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024] Open
Abstract
In recent years, microbiomes and their potential applications for human, animal or plant health, food production and environmental management came into the spotlight of major national and international policies and strategies. This has been accompanied by substantial R&D investments in both public and private sectors, with an increasing number of products entering the market. Despite widespread agreement on the potential of microbiomes and their uses across disciplines, stakeholders and countries, there is no consensus on what defines a microbiome application. This often results in non-comprehensive communication or insufficient documentation making commercialisation and acceptance of the novel products challenging. To showcase the complexity of this issue we discuss two selected, well-established applications and propose criteria defining a microbiome application and their conditions of use for clear communication, facilitating suitable regulatory frameworks and building trust among stakeholders.
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Affiliation(s)
- Tanja Kostic
- AIT Austrian Institute of Technology GmbHViennaAustria
| | | | | | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, MooreparkAPC Microbiome Ireland and VistaMilkCorkIreland
| | | | - Lene Lange
- LL‐BioEconomy, Research and AdvisoryCopenhagenDenmark
| | - Emmanuelle Maguin
- Université Paris‐Saclay, INRAE, AgroParisTech, MICALIS UMR1319Jouy‐en‐JosasFrance
| | - Annelein Meisner
- Wageningen University & Research, Wageningen ResearchWageningenThe Netherlands
| | - Leo van Overbeek
- Wageningen University & Research, Wageningen ResearchWageningenThe Netherlands
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology – Spanish National Research Council (IATA‐CSIC)PaternaValenciaSpain
| | - Inga Sarand
- Tallinn University of TechnologyTallinnEstonia
| | | | | | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Martin Wagner
- FFoQSI GmbH – Austrian Competence Centre for Feed and Food Quality, Safety and InnovationTullnAustria
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5
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Silverstein MR, Bhatnagar JM, Segrè D. Metabolic complexity drives divergence in microbial communities. Nat Ecol Evol 2024; 8:1493-1504. [PMID: 38956426 DOI: 10.1038/s41559-024-02440-6] [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] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.
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Affiliation(s)
- Michael R Silverstein
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jennifer M Bhatnagar
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Daniel Segrè
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering and Department of Physics, Boston University, Boston, MA, USA.
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6
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Gestal MC, Oates AE, Akob DM, Criss AK. Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology. mSphere 2024; 9:e0025624. [PMID: 38920371 PMCID: PMC11288050 DOI: 10.1128/msphere.00256-24] [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] [Indexed: 06/27/2024] Open
Abstract
Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and 'omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.
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Affiliation(s)
- Monica C. Gestal
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | | | - Denise M. Akob
- U.S. Geological Survey, Geology, Energy and Minerals Science Center, Reston, Virginia, USA
| | - Alison K. Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Host-Microbe Retreat Planning CommitteeFidel, Jr.Paul L.1WatnickPaula I.2YoungVincent B.3ZackularJoseph4Department of Oral and Craniofacial Biology, Louisiana State University Health, New Orleans, Louisiana, USADivision of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts, USADepartment of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USAInstitute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
- American Society for Microbiology, Washington, DC, USA
- U.S. Geological Survey, Geology, Energy and Minerals Science Center, Reston, Virginia, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Host-Microbe Retreat SpeakersCasadevallArturo1GibbonsSean M.2HuffnagleGary B.3McFall-NgaiMargaret4NewmanDianne K.5NickersonCheryl A.6Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USAInstitute for Systems Biology, Seattle, Washington, USADepartment of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USAPacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USADivision of Biology and Biological Engineering, Caltech, Pasadena, California, USASchool of Life Sciences, Biodesign Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
- American Society for Microbiology, Washington, DC, USA
- U.S. Geological Survey, Geology, Energy and Minerals Science Center, Reston, Virginia, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
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7
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Matuszyńska A, Ebenhöh O, Zurbriggen MD, Ducat DC, Axmann IM. A new era of synthetic biology-microbial community design. Synth Biol (Oxf) 2024; 9:ysae011. [PMID: 39086602 PMCID: PMC11290361 DOI: 10.1093/synbio/ysae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/21/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Synthetic biology conceptualizes biological complexity as a network of biological parts, devices, and systems with predetermined functionalities and has had a revolutionary impact on fundamental and applied research. With the unprecedented ability to synthesize and transfer any DNA and RNA across organisms, the scope of synthetic biology is expanding and being recreated in previously unimaginable ways. The field has matured to a level where highly complex networks, such as artificial communities of synthetic organisms, can be constructed. In parallel, computational biology became an integral part of biological studies, with computational models aiding the unravelling of the escalating complexity and emerging properties of biological phenomena. However, there is still a vast untapped potential for the complete integration of modelling into the synthetic design process, presenting exciting opportunities for scientific advancements. Here, we first highlight the most recent advances in computer-aided design of microbial communities. Next, we propose that such a design can benefit from an organism-free modular modelling approach that places its emphasis on modules of organismal function towards the design of multispecies communities. We argue for a shift in perspective from single organism-centred approaches to emphasizing the functional contributions of organisms within the community. By assembling synthetic biological systems using modular computational models with mathematical descriptions of parts and circuits, we can tailor organisms to fulfil specific functional roles within the community. This approach aligns with synthetic biology strategies and presents exciting possibilities for the design of artificial communities. Graphical Abstract.
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Affiliation(s)
- Anna Matuszyńska
- Computational Life Science, Department of Biology, RWTH Aachen University, Aachen 52074, Germany
- Cluster of Excellence on Plant Sciences, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Oliver Ebenhöh
- Cluster of Excellence on Plant Sciences, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Matias D Zurbriggen
- Cluster of Excellence on Plant Sciences, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Synthetic Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Ilka M Axmann
- Cluster of Excellence on Plant Sciences, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
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8
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Thieffry S, Aubert J, Devers-Lamrani M, Martin-Laurent F, Romdhane S, Rouard N, Siol M, Spor A. Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134454. [PMID: 38688223 DOI: 10.1016/j.jhazmat.2024.134454] [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: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. Bioaugmentation i. e. the inoculation of degrading micro-organisms in polluted soil, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - between model predictions and measured pesticide degradation values. Multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.
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Affiliation(s)
- Sylvia Thieffry
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120 Palaiseau, France.
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120 Palaiseau, France
| | - Marion Devers-Lamrani
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Fabrice Martin-Laurent
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Sana Romdhane
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Nadine Rouard
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Mathieu Siol
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Aymé Spor
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France.
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9
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [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: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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10
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Wang C, Kuzyakov Y. Rhizosphere engineering for soil carbon sequestration. TRENDS IN PLANT SCIENCE 2024; 29:447-468. [PMID: 37867041 DOI: 10.1016/j.tplants.2023.09.015] [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: 05/06/2023] [Revised: 08/10/2023] [Accepted: 09/30/2023] [Indexed: 10/24/2023]
Abstract
The rhizosphere is the central hotspot of water and nutrient uptake by plants, rhizodeposition, microbial activities, and plant-soil-microbial interactions. The plasticity of plants offers possibilities to engineer the rhizosphere to mitigate climate change. We define rhizosphere engineering as targeted manipulation of plants, soil, microorganisms, and management to shift rhizosphere processes for specific aims [e.g., carbon (C) sequestration]. The rhizosphere components can be engineered by agronomic, physical, chemical, biological, and genomic approaches. These approaches increase plant productivity with a special focus on C inputs belowground, increase microbial necromass production, protect organic compounds and necromass by aggregation, and decrease C losses. Finally, we outline multifunctional options for rhizosphere engineering: how to boost C sequestration, increase soil health, and mitigate global change effects.
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Affiliation(s)
- Chaoqun Wang
- Biogeochemistry of Agroecosystems, University of Goettingen, 37077 Goettingen, Germany.
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Goettingen, 37077 Goettingen, Germany.
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11
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Pei TT, Luo H, Wang Y, Li H, Wang XY, Zhang YQ, An Y, Wu LL, Ma J, Liang X, Yan A, Yang L, Chen C, Dong T. Filamentous prophage Pf4 promotes genetic exchange in Pseudomonas aeruginosa. THE ISME JOURNAL 2024; 18:wrad025. [PMID: 38365255 PMCID: PMC10837833 DOI: 10.1093/ismejo/wrad025] [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: 11/24/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Filamentous prophages are widespread among bacteria and play crucial functions in virulence, antibiotic resistance, and biofilm structures. The filamentous Pf4 particles, extruded by an important pathogen Pseudomonas aeruginosa, can protect producing cells from adverse conditions. Contrary to the conventional belief that the Pf4-encoding cells resist reinfection, we herein report that the Pf4 prophage is reciprocally and commonly exchanged within P. aeruginosa colonies, which can repair defective Pf4 within the community. By labeling the Pf4 locus with antibiotic resistance and fluorescence markers, we demonstrate that the Pf4 locus is frequently exchanged within colony biofilms, in artificial sputum media, and in infected mouse lungs. We further show that Pf4 trafficking is a rapid process and capable of rescuing Pf4-defective mutants. The Pf4 phage is highly adaptable and can package additional DNA doubling its genome size. We also report that two clinical P. aeruginosa isolates are susceptible to the Pf4-mediated exchange, and the Pf5 prophage can be exchanged between cells as well. These findings suggest that the genetic exchanging interactions by filamentous prophages may facilitate defect rescue and the sharing of prophage-dependent benefits and costs within the P. aeruginosa community.
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Affiliation(s)
- Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Han Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Wang
- Unit of Pathogenic Fungal Infection and Host Immunity, Key Laboratory of Molecular Virology and Immunology, Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing-Yu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi-Qiu Zhang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying An
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Li-Li Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junhua Ma
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoye Liang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Changbin Chen
- Unit of Pathogenic Fungal Infection and Host Immunity, Key Laboratory of Molecular Virology and Immunology, Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Cantoran A, Maillard F, Baldrian P, Kennedy PG. Defining a core microbial necrobiome associated with decomposing fungal necromass. FEMS Microbiol Ecol 2023; 99:fiad098. [PMID: 37656873 DOI: 10.1093/femsec/fiad098] [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: 04/16/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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Affiliation(s)
- Anahi Cantoran
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Microbial Ecology Group, Department of Biology, Lund University, Naturvetarvägen 22362, Lund, Sweden
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídenská 1083, Prague 142 20, Czech Republic
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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Silverstein M, Bhatnagar JM, Segrè D. Metabolic complexity drives divergence in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551516. [PMID: 37577626 PMCID: PMC10418233 DOI: 10.1101/2023.08.03.551516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Microbial communities are shaped by the metabolites available in their environment, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. To this end, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the diverse assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively smaller ones, is necessary and sufficient to recapitulate all of our experimental observations. In addition to pointing to a fundamental principle of community assembly, the divergence-complexity effect has important implications for microbiome engineering applications, as it can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions.
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Affiliation(s)
- Michael Silverstein
- Bioinformatics Program, Boston University, Boston, MA
- Biological Design Center, Boston University, Boston, MA
| | - Jennifer M. Bhatnagar
- Bioinformatics Program, Boston University, Boston, MA
- Department of Biology, Boston University, Boston, MA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA
- Biological Design Center, Boston University, Boston, MA
- Department of Biology, Boston University, Boston, MA
- Department of Biomedical Engineering and Department of Physics, Boston University, Boston, MA
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14
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Jaiswal DK, Verma JP, Belwal T, Pereira APDA, Ade AB. Editorial: Microbial co-cultures: a new era of synthetic biology and metabolic engineering. Front Microbiol 2023; 14:1235565. [PMID: 37426012 PMCID: PMC10328387 DOI: 10.3389/fmicb.2023.1235565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Affiliation(s)
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Tarun Belwal
- Texas A&M University, College Station, TX, United States
| | | | - Avinash Bapurao Ade
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
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