1
|
Rath KM, Fierer N, Murphy DV, Rousk J. Linking bacterial community composition to soil salinity along environmental gradients. ISME JOURNAL 2018; 13:836-846. [PMID: 30446737 PMCID: PMC6461869 DOI: 10.1038/s41396-018-0313-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/30/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022]
Abstract
Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose–response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities. Community salt tolerance was closely correlated with soil salinity, indicating a strong filtering effect of salinity on the bacterial communities. Accompanying the increases in salt tolerance were consistent shifts in bacterial community composition. We identified specific bacterial taxa that increased in relative abundances with community salt tolerance, which could be used as bioindicators for high community salt tolerance. A strong filtering effect was also observed for pH across the gradients, with pH tolerance of bacterial communities correlated to soil pH. We propose phenotypic trait distributions aggregated at the community level as a useful approach to study the role of environmental factors as filters of microbial community composition.
Collapse
Affiliation(s)
- Kristin M Rath
- Department of Biology, Section of Microbial Ecology, Lund University, Lund, Sweden.,Centre for Environmental and Climate Research (CEC), Lund University, Lund, Sweden
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Daniel V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Johannes Rousk
- Department of Biology, Section of Microbial Ecology, Lund University, Lund, Sweden.
| |
Collapse
|
2
|
Cheaib B, Le Boulch M, Mercier PL, Derome N. Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient. Front Microbiol 2018; 9:869. [PMID: 29774016 PMCID: PMC5943556 DOI: 10.3389/fmicb.2018.00869] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 04/16/2018] [Indexed: 11/29/2022] Open
Abstract
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.
Collapse
Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Malo Le Boulch
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada.,GenPhySE, Institut National de la Recherche Agronomique, Université de Toulouse, INPT, ENVT, Castanet-Tolosan, France
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| |
Collapse
|
3
|
Jacquiod S, Cyriaque V, Riber L, Al-Soud WA, Gillan DC, Wattiez R, Sørensen SJ. Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome. JOURNAL OF HAZARDOUS MATERIALS 2018; 344:299-307. [PMID: 29055834 DOI: 10.1016/j.jhazmat.2017.09.046] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/11/2017] [Accepted: 09/25/2017] [Indexed: 05/19/2023]
Abstract
Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.
Collapse
Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Leise Riber
- Section of Functional Genomics, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 Copenhagen N, Denmark.
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - David C Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| |
Collapse
|
4
|
Paulo SBM, Julio CD, Marcelo NVDO, Bruno CM, Arnaldo CB, Marcos RT, Julio CLN, Mauricio DC. Diversity and distribution of the endophytic fungal community in eucalyptus leaves. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajmr2016.8353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
5
|
Ling YC, Bush R, Grice K, Tulipani S, Berwick L, Moreau JW. Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation. Front Microbiol 2015; 6:624. [PMID: 26191042 PMCID: PMC4490247 DOI: 10.3389/fmicb.2015.00624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Coastal acid sulfate soils (CASS) constitute a serious and global environmental problem. Oxidation of iron sulfide minerals exposed to air generates sulfuric acid with consequently negative impacts on coastal and estuarine ecosystems. Tidal inundation represents one current treatment strategy for CASS, with the aim of neutralizing acidity by triggering microbial iron- and sulfate-reduction and inducing the precipitation of iron-sulfides. Although well-known functional guilds of bacteria drive these processes, their distributions within CASS environments, as well as their relationships to tidal cycling and the availability of nutrients and electron acceptors, are poorly understood. These factors will determine the long-term efficacy of "passive" CASS remediation strategies. Here we studied microbial community structure and functional guild distribution in sediment cores obtained from 10 depths ranging from 0 to 20 cm in three sites located in the supra-, inter- and sub-tidal segments, respectively, of a CASS-affected salt marsh (East Trinity, Cairns, Australia). Whole community 16S rRNA gene diversity within each site was assessed by 454 pyrotag sequencing and bioinformatic analyses in the context of local hydrological, geochemical, and lithological factors. The results illustrate spatial overlap, or close association, of iron-, and sulfate-reducing bacteria (SRB) in an environment rich in organic matter and controlled by parameters such as acidity, redox potential, degree of water saturation, and mineralization. The observed spatial distribution implies the need for empirical understanding of the timing, relative to tidal cycling, of various terminal electron-accepting processes that control acid generation and biogeochemical iron and sulfur cycling.
Collapse
Affiliation(s)
- Yu-Chen Ling
- School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| | - Richard Bush
- Southern Cross GeoScience, Southern Cross UniversityLismore, NSW, Australia
| | - Kliti Grice
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - Svenja Tulipani
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - Lyndon Berwick
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - John W. Moreau
- School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| |
Collapse
|
6
|
Sprocati AR, Alisi C, Tasso F, Fiore A, Marconi P, Langella F, Haferburg G, Nicoara A, Neagoe A, Kothe E. Bioprospecting at former mining sites across Europe: microbial and functional diversity in soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 21:6824-6835. [PMID: 23775004 DOI: 10.1007/s11356-013-1907-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
The planetary importance of microbial function requires urgently that our knowledge and our exploitation ability is extended, therefore every occasion of bioprospecting is welcome. In this work, bioprospecting is presented from the perspective of the UMBRELLA project, whose main goal was to develop an integral approach for remediation of soil influenced by mining activity, by using microorganisms in association with plants. Accordingly, this work relies on the cultivable fraction of microbial biodiversity, native to six mining sites across Europe, different for geographical, climatic and geochemical characteristics but similar for suffering from chronic stress. The comparative analysis of the soil functional diversity, resulting from the metabolic profiling at community level (BIOLOG ECOPlates) and confirmed by the multivariate analysis, separates the six soils in two clusters, identifying soils characterised by low functional diversity and low metabolic activity. The microbial biodiversity falls into four major bacterial phyla: Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes, including a total of 47 genera and 99 species. In each soil, despite harsh conditions, metabolic capacity of nitrogen fixation and plant growth promotion were quite widespread, and most of the strains showed multiple resistances to heavy metals. At species-level, Shannon's index (alpha diversity) and Sørensen's Similarity (beta diversity) indicates the sites are indeed diverse. Multivariate analysis of soil chemical factors and biodiversity identifies for each soil well-discriminating chemical factors and species, supporting the assumption that cultured biodiversity from the six mining sites presents, at phylum level, a convergence correlated to soil factors rather than to geographical factors while, at species level, reflects a remarkable local characterisation.
Collapse
Affiliation(s)
- Anna Rosa Sprocati
- Italian National Agency for New technologies, Energy and Sustainable Economic Development, via Anguillarese, 301-00123, Rome, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Laplante K, Sébastien B, Derome N. Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation. Evol Appl 2013; 6:643-59. [PMID: 23789031 PMCID: PMC3684745 DOI: 10.1111/eva.12050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 12/10/2012] [Accepted: 01/03/2013] [Indexed: 12/24/2022] Open
Abstract
Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities.
Collapse
Affiliation(s)
- Karine Laplante
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | | | | |
Collapse
|