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Piñeiro J, Dang C, Walkup JGV, Kuzniar T, Winslett R, Blazewicz SJ, Freedman ZB, Brzostek E, Morrissey EM. Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees. GLOBAL CHANGE BIOLOGY 2024; 30:e17030. [PMID: 38010627 DOI: 10.1111/gcb.17030] [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: 07/19/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023]
Abstract
Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. Our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.
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Affiliation(s)
- Juan Piñeiro
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
- School of Forest Engineering and Natural Resources, Polytechnic University of Madrid, Madrid, Spain
| | - Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Jeth G V Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Teagan Kuzniar
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Rachel Winslett
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | | | - Zachary B Freedman
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward Brzostek
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
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2
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Wang T, Weiss A, Aqeel A, Wu F, Lopatkin AJ, David LA, You L. Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Nat Chem Biol 2022; 18:1245-1252. [PMID: 36050493 PMCID: PMC10018779 DOI: 10.1038/s41589-022-01114-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/15/2022] [Indexed: 11/09/2022]
Abstract
The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, we proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. We combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the stability of gene abundance in microbial communities. We further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the reanalysis of data from the literature. Our results demonstrate a generalizable strategy to program the gene stability of microbial communities.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ammara Aqeel
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Allison J Lopatkin
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
| | - Lawrence A David
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
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3
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Melle Säve‐Söderbergh
- Science Division Swedish Food Agency Uppsala Sweden
- Institute of Environmental Medicine, Karolinska Institutet Stockholm Sweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public Health Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
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4
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Tran T, French E, Iyer-Pascuzzi AS. In vitro functional characterization predicts the impact of bacterial root endophytes on plant growth. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5758-5772. [PMID: 35596672 DOI: 10.1093/jxb/erac228] [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: 12/15/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Utilizing beneficial microbes for crop improvement is one strategy to achieve sustainable agriculture. However, identifying microbial isolates that promote crop growth is challenging, in part because using bacterial taxonomy to predict an isolate's effect on plant growth may not be reliable. The overall aim of this work was to determine whether in vitro functional traits of bacteria were predictive of their in planta impact. We isolated 183 bacterial endophytes from field-grown roots of two tomato species, Solanum lycopersicum and S. pimpinellifolium. Sixty isolates were screened for six in vitro functional traits: auxin production, siderophore production, phosphate solubilization, antagonism to a soilborne pathogen, and the presence of two antimicrobial metabolite synthesis genes. Hierarchical clustering of the isolates based on the in vitro functional traits identified several groups of isolates sharing similar traits. We called these groups 'functional groups'. To understand how in vitro functional traits of bacteria relate to their impact on plants, we inoculated three isolates from each of the functional groups on tomato seedlings. Isolates within the same functional group promoted plant growth at similar levels, regardless of their host origin or taxonomy. Together, our results demonstrate the importance of examining root endophyte functions for improving crop production.
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Affiliation(s)
- Tri Tran
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Elizabeth French
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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Obieze CC, Wani GA, Shah MA, Reshi ZA, Comeau AM, Khasa DP. Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154292. [PMID: 35248630 DOI: 10.1016/j.scitotenv.2022.154292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Freshwater lakes are important reservoirs and sources of drinking water globally. However, the microbiota, which supports the functionality of these ecosystems is threatened by the influx of nutrients, heavy metals and other toxic chemical substances from anthropogenic activities. The influence of these factors on the diversity, assembly mechanisms and co-occurrence patterns of bacterial communities in freshwater lakes is not clearly understood. Hence, samples were collected from six different impacted lakes in Canada and India and examined by 454-pyrosequencing technology. The trophic status of these lakes was determined using specific chemical parameters. Our results revealed that bacterial diversity and community composition was altered by both the lake water chemistry and geographic distance. Anthropogenic activities pervasively influenced species distribution. Dispersal limitation (32.3%), homogenous selection (31.8%) and drift (20%) accounted for the largest proportions of the bacterial community assembly mechanisms. Homogenous selection increased in lakes with higher nutrient concentration, while stochasticity reduced. Community functional profiles revealed that deterministic processes dominated the assembly mechanisms of phylotypes with higher potential for biodegradation, while stochasticity dominated the assembly of phylotypes with potential for antimicrobial resistance. Bacteroidota (44%) and Proteobacteria (34%) were the most abundant phyla. Co-occurrence network analysis revealed that complexity increased in more impacted lakes, while competition and the nature of anthropogenic activity contributed to species sorting. Overall, this study demonstrates that bacterial community changes in freshwater lakes are linked to anthropogenic activities, with corresponding consequences on the distribution of phylotypes of environmental and human health interest.
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Affiliation(s)
- Chinedu C Obieze
- Centre for Forest Research, Institute of Integrative Biology and Systems, Université Laval, Quebec, QC G1V0A6, Canada.
| | - Gowher A Wani
- Centre for Forest Research, Institute of Integrative Biology and Systems, Université Laval, Quebec, QC G1V0A6, Canada; Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - André M Comeau
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada
| | - Damase P Khasa
- Centre for Forest Research, Institute of Integrative Biology and Systems and Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC G1V0A6, Canada
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da Costa Silva TA, de Paula M, Silva WS, Lacorte GA. Can moderate heavy metal soil contaminations due to cement production influence the surrounding soil bacterial communities? ECOTOXICOLOGY (LONDON, ENGLAND) 2022; 31:134-148. [PMID: 34748159 DOI: 10.1007/s10646-021-02494-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Events of soil contamination by heavy metals are mostly related to human activities that release these metals into the environment as emissions or effluents. Among the industrial activities related to heavy metal pollution, cement production plants are considered one of the most common sources. In this work we applied the High-throughput sequencing approach called 16 S rDNA metabarcoding to perform the taxonomic characterization of the prokaryotic communities of the soil surrounding three cement plants as well as two areas outside the influence of the cement plants that represented agricultural production environments free of heavy metal contamination (control areas). We applied the environmental genomics approaches known as "structural community metrics" (α- and β-diversity metrics) and "functional community metrics" (PICRUSt2 approach) to verify whether or not the effects of heavy metal contamination in the study area generated impacts on soil bacterial communities. We found that the impact related to the elevation of heavy metal concentration due to the operation of cement plants in the surrounding soil can be considered smooth according to globally recognized indices such as Igeo. However, we identified that both the taxonomic and functional structures of the communities surrounding cement plants were different from those found in the control areas. We consider that our findings contribute significantly to the general understanding of the effects of heavy metals on the soil ecosystem by showing that light contamination can disturb the dynamics of ecosystem services provided by soil, specifically those associated with microbial metabolism.
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Affiliation(s)
- Thiago Augusto da Costa Silva
- Molecular Biology Lab, Department of Science and Languages, Federal Institute of Minas Gerais - Bambuí Campus, Bambuí, Minas Gerais State, Brazil
| | - Marcos de Paula
- Molecular Biology Lab, Department of Science and Languages, Federal Institute of Minas Gerais - Bambuí Campus, Bambuí, Minas Gerais State, Brazil
| | | | - Gustavo Augusto Lacorte
- Molecular Biology Lab, Department of Science and Languages, Federal Institute of Minas Gerais - Bambuí Campus, Bambuí, Minas Gerais State, Brazil.
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7
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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [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: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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Scavizzi F, Bassi C, Lupini L, Guerriero P, Raspa M, Sabbioni S. A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing. Anim Microbiome 2021; 3:53. [PMID: 34325744 PMCID: PMC8323313 DOI: 10.1186/s42523-021-00113-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Background Health surveillance of murine colonies employed for scientific purposes aim at detecting unwanted infection that can affect the well-being of animals and personnel, and potentially undermine scientific results. In this study, we investigated the use of a next-generation sequencing (NGS) metagenomic approach for monitoring the microbiota composition and uncovering the possible presence of pathogens in mice housed in specific pathogen-free (SPF) or conventional (non-SPF) facilities.
Results Analysis of metagenomic NGS assay through public and free algorithms and databases allowed to precisely assess the composition of mouse gut microbiome and quantify the contribution of the different microorganisms at the species level. Sequence analysis allowed the uncovering of pathogens or the presence of imbalances in the microbiota composition. In several cases, fecal pellets taken from conventional facilities were found to carry gene sequences from bacterial pathogens (Helicobacter hepaticus, Helicobacter typhlonius, Chlamydia muridarum, Streptococcus pyogenes, Rodentibacter pneumotropicus, Citrobacter rodentium, Staphylococcus aureus), intestinal protozoa (Entamoeba muris, Tritrichomonas muris, Spironucleus muris) nematoda (Aspiculuris tetraptera, Syphacia obvelata), eukaryotic parasites (Myocoptes musculinus) and RNA virus (Norwalk virus). Thus, the use of NGS metagenomics can reduce the number of tests required for the detection of pathogens and avoid the use of sentinel mice. Conclusions In summary, in comparison with standard approaches, which require multiple types of test, NGS assay can detect bacteria, fungi, DNA and RNA viruses, and eukaryotic parasites from fecal pellets in a single test. Considering the need to protect animal well-being and to improve the success and reproducibility of preclinical studies, this work provides the proof-of-concept that the use of NGS metagenomics for health monitoring of laboratory mice is a feasible and dependable approach, that is able to broaden the current concept of health monitoring of laboratory mice from “pathogen surveillance” to a more inclusive “microbiota surveillance”. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00113-4.
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Affiliation(s)
- Ferdinando Scavizzi
- National Research Council (IBBC), CNR-Campus International Development, (EMMA-INFRAFRONTIER- IMPC), Monterotondo Scalo, Italy
| | - Cristian Bassi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121, Ferrara, Italy.,Laboratorio Per Le Tecnologie Delle Terapie Avanzate (LTTA), University of Ferrara, 44121, Ferrara, Italy
| | - Laura Lupini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Paola Guerriero
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121, Ferrara, Italy
| | - Marcello Raspa
- National Research Council (IBBC), CNR-Campus International Development, (EMMA-INFRAFRONTIER- IMPC), Monterotondo Scalo, Italy
| | - Silvia Sabbioni
- Laboratorio Per Le Tecnologie Delle Terapie Avanzate (LTTA), University of Ferrara, 44121, Ferrara, Italy. .,Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121, Ferrara, Italy.
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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10
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Cheaib B, Seghouani H, Llewellyn M, Vandal-Lenghan K, Mercier PL, Derome N. The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance. Anim Microbiome 2021; 3:3. [PMID: 33499999 PMCID: PMC7934398 DOI: 10.1186/s42523-020-00063-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022] Open
Abstract
Background Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial habitats, free-living (water), and host-associated (skin and gut) were experimentally exposed to either a constant or gradual selection regime exerted by two sublethal cadmium chloride dosages (CdCl2). Yellow Perch (Perca flavescens) was used as a piscivorous ecotoxicological model. Using 16S rDNA gene based metataxonomics, quantitative diversity metrics of water, skin and gut microbial communities were characterized along with development and across experimental conditions. Results After 30 days, constant and gradual selection regimes drove a significant alpha diversity increase for both skin and gut microbiota. In the skin, pervasive negative correlations between taxa in both selection regimes in addition to the taxonomic convergence with the environmental bacterial community, suggest a loss of colonisation resistance resulting in the dysbiosis of yellow perch microbiota. Furthermore, the network connectivity in gut microbiome was exclusively maintained by rare (low abundance) OTUs, while most abundant OTUs were mainly composed of opportunistic invaders such as Mycoplasma and other genera related to fish pathogens such as Flavobacterium. Finally, the mathematical modelling of community assembly using both non-linear least squares models (NLS) based estimates of migration rates and normalized stochasticity ratios (NST) based beta-diversity distances suggested neutral processes drove by taxonomic drift in host and water communities for almost all treatments. The NLS models predicted higher demographic stochasticity in the cadmium-free host and water microbiomes, however, NST models suggested higher ecological stochasticity under perturbations. Conclusions Neutral models agree that water and host-microbiota assembly promoted by rare taxa have evolved predominantly under neutral processes with potential involvement of deterministic forces sourced from host filtering and cadmium selection. The early signals of perturbations in the skin microbiome revealed antagonistic interactions by a preponderance of negative correlations in the co-abundance networks. Our findings enhance our understanding of community assembly host-associated and free-living under anthropogenic selective pressure.
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Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada. .,Institute of Biodiversity, Animal Health and Comparative Medicine (BACHM), Glasgow, University of Glasgow, Glasgow, UK. .,School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Hamza Seghouani
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Martin Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine (BACHM), Glasgow, University of Glasgow, Glasgow, UK
| | - Katherine Vandal-Lenghan
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC, G1V 0A6, Canada
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Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
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Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
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Cheaib B, Seghouani H, Ijaz UZ, Derome N. Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations. MICROBIOME 2020; 8:14. [PMID: 32041654 PMCID: PMC7011381 DOI: 10.1186/s40168-020-0789-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/19/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq). RESULTS Our data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery. CONCLUSIONS The short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes. Video Abtract.
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Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6 Canada
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ Scotland
| | - Hamza Seghouani
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ Scotland
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6 Canada
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Escalas A, Hale L, Voordeckers JW, Yang Y, Firestone MK, Alvarez‐Cohen L, Zhou J. Microbial functional diversity: From concepts to applications. Ecol Evol 2019; 9:12000-12016. [PMID: 31695904 PMCID: PMC6822047 DOI: 10.1002/ece3.5670] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/21/2022] Open
Abstract
Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.
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Affiliation(s)
- Arthur Escalas
- MARBECCNRSIfremerIRDUniversity of MontpellierMontpellier Cedex 5France
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Lauren Hale
- Water Management Research UnitSJVASCUSDA‐ARSParlierCAUSA
| | | | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua UniversityBeijingChina
| | - Mary K. Firestone
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCAUSA
| | - Lisa Alvarez‐Cohen
- Department of Civil and Environmental EngineeringUniversity of CaliforniaBerkeleyCAUSA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua UniversityBeijingChina
- Earth and Environmental SciencesLawrence Berkeley National LaboratoryBerkeleyCAUSA
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Sylvain F, Holland A, Audet‐Gilbert É, Luis Val A, Derome N. Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients. Mol Ecol 2019; 28:3612-3626. [DOI: 10.1111/mec.15184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Aleicia Holland
- Department of Ecology, Environment and Evolution School of Life Science La Trobe University Bundoora Vic. Australia
| | - Émie Audet‐Gilbert
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec City QC Canada
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec City QC Canada
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