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Behling AH, Wilson BC, Ho D, Cutfield WS, Vatanen T, O'Sullivan JM. Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity. MICROBIOME 2024; 12:26. [PMID: 38347627 PMCID: PMC10860221 DOI: 10.1186/s40168-024-01748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors. RESULTS Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention. CONCLUSION Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.
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Affiliation(s)
- Anna H Behling
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Brooke C Wilson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Daniel Ho
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Wayne S Cutfield
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
- Australian Parkinsons Mission, Garvan Institute of Medical Research, 384 Victoria Street, SydneyDarlinghurst, NSWNSW, 2010, Australia.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK.
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore.
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2
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Bedard DL, Van Slyke G, Nübel U, Bateson MM, Brumfield S, An YJ, Becraft ED, Wood JM, Thiel V, Ward DM. Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities. Microorganisms 2023; 11:2921. [PMID: 38138064 PMCID: PMC10746008 DOI: 10.3390/microorganisms11122921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.
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Affiliation(s)
- Donna L. Bedard
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Greta Van Slyke
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Ulrich Nübel
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - Mary M. Bateson
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
| | - Sue Brumfield
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA;
| | - Yong Jun An
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; (D.L.B.); (G.V.S.)
| | - Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Department of Biology, University of North Alabama, Florence, AL 35632, USA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
- Research Informatics Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Vera Thiel
- Leibniz-Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
| | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA; (U.N.); (M.M.B.); (E.D.B.); (J.M.W.)
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3
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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4
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Shepherd MJ, Pierce AP, Taylor TB. Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity. PLoS Biol 2023; 21:e3002348. [PMID: 37871011 PMCID: PMC10621929 DOI: 10.1371/journal.pbio.3002348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/02/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections-known as rewiring-that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. Here, using an experimental microbial model system with the soil bacterium Pseudomonas fluorescens, we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify 3 key properties-high activation, high expression, and preexisting low-level affinity for novel target genes-that facilitate transcription factor innovation. Ease of acquiring these properties is constrained by preexisting GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.
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Affiliation(s)
- Matthew J. Shepherd
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Aidan P. Pierce
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
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5
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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6
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Morawska LP, Kuipers OP. Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microb Biotechnol 2023; 16:784-798. [PMID: 36547214 PMCID: PMC10034627 DOI: 10.1111/1751-7915.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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7
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Beaugrand G. Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea. BIOLOGY 2023; 12:biology12030339. [PMID: 36979031 PMCID: PMC10044889 DOI: 10.3390/biology12030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change.
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Affiliation(s)
- Grégory Beaugrand
- CNRS, Univ. Littoral Côte d'Opale, Univ. Lille, UMR 8187 LOG, F-62930 Wimereux, France
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8
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García I, Chouaia B, Llabrés M, Simeoni M. Exploring the expressiveness of abstract metabolic networks. PLoS One 2023; 18:e0281047. [PMID: 36758030 PMCID: PMC9910719 DOI: 10.1371/journal.pone.0281047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Metabolism is characterised by chemical reactions linked to each other, creating a complex network structure. The whole metabolic network is divided into pathways of chemical reactions, such that every pathway is a metabolic function. A simplified representation of metabolism, which we call an abstract metabolic network, is a graph in which metabolic pathways are nodes and there is an edge between two nodes if their corresponding pathways share one or more compounds. The abstract metabolic network of a given organism results in a small network that requires low computational power to be analysed and makes it a suitable model to perform a large-scale comparison of organisms' metabolism. To explore the potentials and limits of such a basic representation, we considered a comprehensive set of KEGG organisms, represented through their abstract metabolic network. We performed pairwise comparisons using graph kernel methods and analyse the results through exploratory data analysis and machine learning techniques. The results show that abstract metabolic networks discriminate macro evolutionary events, indicating that they are expressive enough to capture key steps in metabolism evolution.
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Affiliation(s)
- Irene García
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Bessem Chouaia
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
| | - Mercè Llabrés
- Mathematics and Computer Science Department, University of the Balearic Islands, Palma, Spain
| | - Marta Simeoni
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, Venice, Italy
- European Centre for Living Technology (ECLT), Venice, Italy
- * E-mail:
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9
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Liu Q, Yang LL, Xin YH. Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers. Front Microbiol 2023; 14:1115168. [PMID: 37020720 PMCID: PMC10067761 DOI: 10.3389/fmicb.2023.1115168] [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: 12/03/2022] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T max) of ≤ 20°C and a T max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.
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10
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Abstract
The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.
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Lin YP, Tufts DM, Combs M, Dupuis AP, Marcinkiewicz AL, Hirsbrunner AD, Diaz AJ, Stout JL, Blom AM, Strle K, Davis AD, Kramer LD, Kolokotronis SO, Diuk-Wasser MA. Cellular and immunological mechanisms influence host-adapted phenotypes in a vector-borne microparasite. Proc Biol Sci 2022; 289:20212087. [PMID: 35193398 PMCID: PMC8864362 DOI: 10.1098/rspb.2021.2087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/18/2022] [Indexed: 01/15/2023] Open
Abstract
Predicting pathogen emergence and spillover risk requires understanding the determinants of a pathogens' host range and the traits involved in host competence. While host competence is often considered a fixed species-specific trait, it may be variable if pathogens diversify across hosts. Balancing selection can lead to maintenance of pathogen polymorphisms (multiple-niche-polymorphism; MNP). The causative agent of Lyme disease, Borrelia burgdorferi (Bb), provides a model to study the evolution of host adaptation, as some Bb strains defined by their outer surface protein C (ospC) genotype, are widespread in white-footed mice and others are associated with non-rodent vertebrates (e.g. birds). To identify the mechanisms underlying potential strain × host adaptation, we infected American robins and white-footed mice, with three Bb strains of different ospC genotypes. Bb burdens varied by strain in a host-dependent fashion, and strain persistence in hosts largely corresponded to Bb survival at early infection stages and with transmission to larvae (i.e. fitness). Early survival phenotypes are associated with cell adhesion, complement evasion and/or inflammatory and antibody-mediated removal of Bb, suggesting directional selective pressure for host adaptation and the potential role of MNP in maintaining OspC diversity. Our findings will guide future investigations to inform eco-evolutionary models of host adaptation for microparasites.
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Affiliation(s)
- Yi-Pin Lin
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
- Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - Danielle M. Tufts
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
- Infectious Diseases and Microbiology Department, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Combs
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Alan P. Dupuis
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | | | | | - Alexander J. Diaz
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Jessica L. Stout
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Anna M. Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Klemen Strle
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
- Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - April D. Davis
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Laura D. Kramer
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
- Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Institute for Genomic Health, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Division of Infectious Diseases, Department of Medicine, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Maria A. Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
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12
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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13
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Gomes-Neto JC, Pavlovikj N, Cano C, Abdalhamid B, Al-Ghalith GA, Loy JD, Knights D, Iwen PC, Chaves BD, Benson AK. Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.725791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide selective advantages in food production environments. Publicly available WGS data were obtained from NCBI database for three serovars of Salmonella enterica subsp. enterica lineage I (S. Typhimurium, S. Newport, and S. Infantis). Using the hierarchical genotypic classifications (Serovar, BAPS1, ST, cgMLST), datasets from each of the three serovars showed varying degrees of clonal structuring. When the accessory genome (PANGEA) was mapped onto these hierarchical structures, accessory loci could be linked with specific genotypes. A large heavy-metal resistance mobile element was found in the Monophasic ST34 lineage of S. Typhimurium, and laboratory testing showed that Monophasic isolates have on average a higher degree of copper resistance than the Biphasic ones. In S. Newport, an extra sugE gene copy was found among most isolates of the ST45 lineage, and laboratory testing of multiple isolates confirmed that isolates of S. Newport ST45 were on average less sensitive to the disinfectant cetylpyridimium chloride than non-ST45 isolates. Lastly, data-mining of the accessory genomic content of S. Infantis revealed two cryptic Ecotypes with distinct accessory genomic content and distinct ecological patterns. Poultry appears to be the major reservoir for Ecotype 1, and temporal analysis further suggested a recent ecological succession, with Ecotype 2 apparently being displaced by Ecotype 1. Altogether, the use of a heuristic hierarchical-based population structure analysis that includes bacterial pan-genomes (core and accessory genomes) can (1) improve genomic resolution for mapping populations and accessing epidemiological patterns; and (2) define lineage-specific informative loci that may be associated with survival in the food chain.
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14
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Fodelianakis S, Washburne AD, Bourquin M, Pramateftaki P, Kohler TJ, Styllas M, Tolosano M, De Staercke V, Schön M, Busi SB, Brandani J, Wilmes P, Peter H, Battin TJ. Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome. ISME JOURNAL 2021; 16:666-675. [PMID: 34522009 PMCID: PMC8857233 DOI: 10.1038/s41396-021-01106-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 02/01/2023]
Abstract
Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.
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Affiliation(s)
- Stilianos Fodelianakis
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| | | | - Massimo Bourquin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tyler J Kohler
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Michail Styllas
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Matteo Tolosano
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vincent De Staercke
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Martina Schön
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Susheel Bhanu Busi
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jade Brandani
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paul Wilmes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hannes Peter
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tom J Battin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
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15
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Likhitrattanapisal S, Siriarchawatana P, Seesang M, Chunhametha S, Boonsin W, Phithakrotchanakoon C, Kitikhun S, Eurwilaichitr L, Ingsriswang S. Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries. Sci Rep 2021; 11:582. [PMID: 33436774 PMCID: PMC7804445 DOI: 10.1038/s41598-020-79786-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.
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Affiliation(s)
- Somsak Likhitrattanapisal
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Paopit Siriarchawatana
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Mintra Seesang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Suwanee Chunhametha
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Worawongsin Boonsin
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Chitwadee Phithakrotchanakoon
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Supattra Kitikhun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Lily Eurwilaichitr
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
| | - Supawadee Ingsriswang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
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16
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Larkin AA, Moreno AR, Fagan AJ, Fowlds A, Ruiz A, Martiny AC. Persistent El Niño driven shifts in marine cyanobacteria populations. PLoS One 2020; 15:e0238405. [PMID: 32936809 PMCID: PMC7494125 DOI: 10.1371/journal.pone.0238405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/15/2020] [Indexed: 11/18/2022] Open
Abstract
In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014–2016, the North Pacific warm anomaly (a.k.a., the “blob”) and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this “marine heatwave” resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009–2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations.
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Affiliation(s)
- Alyse A. Larkin
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Allison R. Moreno
- Department of Ecology and Evolution, University of California at Irvine, Irvine, California, United States of America
| | - Adam J. Fagan
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Alyssa Fowlds
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Alani Ruiz
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
| | - Adam C. Martiny
- Department of Earth System Science, University of California at Irvine, Irvine, California, United States of America
- Department of Ecology and Evolution, University of California at Irvine, Irvine, California, United States of America
- * E-mail:
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17
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Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, Aury JM, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F, Garczarek L. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. Front Microbiol 2020; 11:567431. [PMID: 33042072 PMCID: PMC7522525 DOI: 10.3389/fmicb.2020.567431] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.
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Affiliation(s)
- Hugo Doré
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gregory K Farrant
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ulysse Guyet
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Florian Humily
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Morgane Ratin
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Frances D Pitt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Martin Ostrowski
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Christophe Six
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France.,Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Mark Hoebeke
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Antoine Bisch
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Erwan Corre
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Évry, France
| | - Dong Han Choi
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea.,Ocean Science and Technology School, Korea Maritime and Ocean University, Busan, South Korea
| | - Jae Hoon Noh
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea.,Department of Marine Biology, Korea University of Science and Technology, Daejeon, South Korea
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France.,Research Federation (FR2022) Tara Océans GO-SEE, Paris, France
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Frédéric Partensky
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France.,Research Federation (FR2022) Tara Océans GO-SEE, Paris, France
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18
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The multifunctional enzyme S-adenosylhomocysteine/methylthioadenosine nucleosidase is a key metabolic enzyme in the virulence of Salmonella enterica var Typhimurium. Biochem J 2020; 476:3435-3453. [PMID: 31675053 DOI: 10.1042/bcj20190297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 11/17/2022]
Abstract
Key physiological differences between bacterial and mammalian metabolism provide opportunities for the development of novel antimicrobials. We examined the role of the multifunctional enzyme S-adenosylhomocysteine/Methylthioadenosine (SAH/MTA) nucleosidase (Pfs) in the virulence of S. enterica var Typhimurium (S. Typhimurium) in mice, using a defined Pfs deletion mutant (i.e. Δpfs). Pfs was essential for growth of S. Typhimurium in M9 minimal medium, in tissue cultured cells, and in mice. Studies to resolve which of the three known functions of Pfs were key to murine virulence suggested that downstream production of autoinducer-2, spermidine and methylthioribose were non-essential for Salmonella virulence in a highly sensitive murine model. Mass spectrometry revealed the accumulation of SAH in S. Typhimurium Δpfs and complementation of the Pfs mutant with the specific SAH hydrolase from Legionella pneumophila reduced SAH levels, fully restored growth ex vivo and the virulence of S. Typhimurium Δpfs for mice. The data suggest that Pfs may be a legitimate target for antimicrobial development, and that the key role of Pfs in bacterial virulence may be in reducing the toxic accumulation of SAH which, in turn, suppresses an undefined methyltransferase.
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19
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Monteil CL, Grouzdev DS, Perrière G, Alonso B, Rouy Z, Cruveiller S, Ginet N, Pignol D, Lefevre CT. Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria. THE ISME JOURNAL 2020; 14:1783-1794. [PMID: 32296121 PMCID: PMC7305187 DOI: 10.1038/s41396-020-0647-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/27/2022]
Abstract
Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.
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Affiliation(s)
- Caroline L Monteil
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.
| | - Denis S Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Université Claude Bernard - Lyon 1, 69622, Villeurbanne, France
| | - Béatrice Alonso
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Zoé Rouy
- LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay, Evry, France
| | - Stéphane Cruveiller
- LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d'Evry, Universite Paris-Saclay, Evry, France
| | - Nicolas Ginet
- Aix Marseille University, CNRS, LCB, Marseille, France
| | - David Pignol
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Christopher T Lefevre
- Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.
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20
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VanInsberghe D, Arevalo P, Chien D, Polz MF. How can microbial population genomics inform community ecology? Philos Trans R Soc Lond B Biol Sci 2020; 375:20190253. [PMID: 32200748 PMCID: PMC7133533 DOI: 10.1098/rstb.2019.0253] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2019] [Indexed: 12/22/2022] Open
Abstract
Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- David VanInsberghe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Philip Arevalo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Diana Chien
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
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21
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Drewnowska J, Fiodor A, Barboza-Corona J, Swiecicka I. Chitinolytic activity of phylogenetically diverse Bacillus cereus sensu lato from natural environments. Syst Appl Microbiol 2020; 43:126075. [DOI: 10.1016/j.syapm.2020.126075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/29/2023]
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22
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Tromas N, Taranu ZE, Castelli M, Pimentel JSM, Pereira DA, Marcoz R, Shapiro BJ, Giani A. The evolution of realized niches within freshwater
Synechococcus. Environ Microbiol 2020; 22:1238-1250. [DOI: 10.1111/1462-2920.14930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Nicolas Tromas
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Zofia E. Taranu
- Environnement et Changement Climatique Canada 105 Rue McGill, Montréal QC H2Y 2E7 Canada
| | | | | | - Daniel A. Pereira
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
| | - Romane Marcoz
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - B. Jesse Shapiro
- Département de sciences biologiquesUniversité de Montréal Montréal QC H2V 2S9 Canada
| | - Alessandra Giani
- Federal University of Minas Gerais Belo Horizonte Minas Gerais Brazil
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23
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Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Herrera G, Ríos-Chaparro DI, Díaz-Arévalo D, Patarroyo MA, Lawley TD, Ramírez JD. Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. Virulence 2019; 10:657-676. [PMID: 31304854 PMCID: PMC6629180 DOI: 10.1080/21505594.2019.1637699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/23/2019] [Accepted: 06/25/2019] [Indexed: 01/23/2023] Open
Abstract
Some well-known Clostridiales species such as Clostridium difficile and C. perfringens are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertium and C. paraputrificum. Three fecal isolates were identified as Clostridium tertium (Gcol.A2 and Gcol.A43) and C. paraputrificum (Gcol.A11) during public health screening for C. difficile infections in Colombia. C. paraputrificum genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertium genomes than in the C. paraputrificum genomes. C. difficile tcdA and tcdB toxins encoding homologous sequences and other potential virulence factors were also identified. EndoA interferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertium genomes. toxA was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertium genomes compared with the C. paraputrificum genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Posgrado Interfacultades, Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
| | - Nitin Kumar
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Animal Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Trevor D. Lawley
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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24
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Srivastava A, Mohan S, Mauchline TH, Davies KG. Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in Pasteuria penetrans. FEMS Microbiol Ecol 2019; 95:5149496. [PMID: 30380051 PMCID: PMC6238073 DOI: 10.1093/femsec/fiy217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/29/2018] [Indexed: 11/16/2022] Open
Abstract
Pasteuria spp. belong to a group of genetically diverse endospore-forming bacteria (phylum: Firmicutes) that are known to parasitize plant-parasitic nematodes and water fleas (Daphnia spp.). Collagen-like fibres form the nap on the surface of endospores and the genes encoding these sequences have been hypothesised to be involved in the adhesion of the endospores of Pasteuria spp. to their hosts. We report a group of 17 unique collagen-like genes putatively encoded by Pasteuria penetrans (strain: Res148) that formed five different phylogenetic clusters and suggest that collagen-like proteins are an important source of genetic diversity in animal pathogenic Firmicutes including Pasteuria. Additionally, and unexpectedly, we identified a putative collagen-like sequence which had a very different sequence structure to the other collagen-like proteins but was similar to the protein sequences in Megaviruses that are involved in host-parasite interactions. We, therefore, suggest that these diverse endospore surface proteins in Pasteuria are involved in biological functions, such as cellular adhesion; however, they are not of monophyletic origin and were possibly obtained de novo by mutation or possibly through selection acting upon several historic horizontal gene transfer events.
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Affiliation(s)
- Arohi Srivastava
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Sharad Mohan
- Division of Nematology, Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Tim H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Keith G Davies
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Postboks 115, Ås-1431, Norway
- Corresponding author: Keith G Davies, Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK. E-mail:
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25
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Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR. The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome Biol Evol 2019; 11:1780-1796. [PMID: 31173069 PMCID: PMC6690169 DOI: 10.1093/gbe/evz119] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.
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Affiliation(s)
- Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine
| | - Ekpeno Nnah
- Lurie Children's Hospital, Chicago, Illinois
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Rachel J Whitaker
- Department of Microbiology and the Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana-Champaign
| | - Alan R Hauser
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine.,Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine
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26
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Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex. Genome Biol 2019; 20:3. [PMID: 30606234 PMCID: PMC6317194 DOI: 10.1186/s13059-018-1606-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/06/2018] [Indexed: 01/25/2023] Open
Abstract
Background Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 agricultural and environmental strains using whole-genome sequencing and evolutionary genomic analyses. Results We describe the phylogenetic distribution of all 77,728 orthologous gene families in the pan-genome, reconstruct the core genome phylogeny using the 2410 core genes, hierarchically cluster the accessory genome, identify the diversity and distribution of type III secretion systems and their effectors, predict ecologically and evolutionary relevant loci, and establish the molecular evolutionary processes operating on gene families. Phylogenetic and recombination analyses reveals that the species complex is subdivided into primary and secondary phylogroups, with the former primarily comprised of agricultural isolates, including all of the well-studied P. syringae strains. In contrast, the secondary phylogroups include numerous environmental isolates. These phylogroups also have levels of genetic diversity typically found among distinct species. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also find that “ecologically significant” virulence-associated loci and “evolutionarily significant” loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. Conclusions While inter-phylogroup recombination occurs relatively rarely, it is an important force maintaining the genetic cohesion of the species complex, particularly among primary phylogroup strains. This level of genetic cohesion, and the shared plant-associated niche, argues for considering the primary phylogroups as a single biological species. Electronic supplementary material The online version of this article (10.1186/s13059-018-1606-y) contains supplementary material, which is available to authorized users.
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27
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Stal LJ, Bolhuis H, Cretoiu MS. Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities. Environ Microbiol 2018; 21:1529-1551. [PMID: 30507057 DOI: 10.1111/1462-2920.14494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/02/2023]
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.
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Affiliation(s)
- Lucas J Stal
- IBED Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands.,Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Mariana S Cretoiu
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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28
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Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Guéguen L, Vial L, Muller D, Daubin V, Nesme X. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. Genome Biol Evol 2018; 9:3413-3431. [PMID: 29220487 PMCID: PMC5739047 DOI: 10.1093/gbe/evx255] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2017] [Indexed: 12/12/2022] Open
Abstract
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.
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Affiliation(s)
- Florent Lassalle
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France.,Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | - Rémi Planel
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Simon Penel
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - David Chapulliot
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France
| | - Audrey Dubost
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Alexandra Calteau
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - David Vallenet
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - Damien Mornico
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - Thomas Bigot
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Laurent Guéguen
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Ludovic Vial
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Daniel Muller
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Vincent Daubin
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Xavier Nesme
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
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29
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Viana MVC, Sahm A, Góes Neto A, Figueiredo HCP, Wattam AR, Azevedo V. Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis. PLoS One 2018; 13:e0207304. [PMID: 30419061 PMCID: PMC6231662 DOI: 10.1371/journal.pone.0207304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/28/2018] [Indexed: 02/01/2023] Open
Abstract
Phylogenomics and genome scale positive selection analyses were performed on 29 Corynebacterium pseudotuberculosis genomes that were isolated from different hosts, including representatives of the Ovis and Equi biovars. A total of 27 genes were identified as undergoing adaptive changes. An analysis of the clades within this species and these biovars, the genes specific to each branch, and the genes responding to selective pressure show clear differences, indicating that adaptation and specialization is occurring in different clades. These changes are often correlated with the isolation host but could indicate responses to some undetermined factor in the respective niches. The fact that some of these more-rapidly evolving genes have homology to known virulence factors, antimicrobial resistance genes and drug targets shows that this type of analysis could be used to identify novel targets, and that these could be used as a way to control this pathogen.
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Affiliation(s)
| | - Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Aristóteles Góes Neto
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique Cesar Pereira Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Vasco Azevedo
- Department of General Biology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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30
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Almagro G, Viale AM, Montero M, Muñoz FJ, Baroja-Fernández E, Mori H, Pozueta-Romero J. A cAMP/CRP-controlled mechanism for the incorporation of extracellular ADP-glucose in Escherichia coli involving NupC and NupG nucleoside transporters. Sci Rep 2018; 8:15509. [PMID: 30341391 PMCID: PMC6195507 DOI: 10.1038/s41598-018-33647-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/03/2018] [Indexed: 12/29/2022] Open
Abstract
ADP-glucose is the precursor of glycogen biosynthesis in bacteria, and a compound abundant in the starchy plant organs ingested by many mammals. Here we show that the enteric species Escherichia coli is capable of scavenging exogenous ADP-glucose for use as a glycosyl donor in glycogen biosynthesis and feed the adenine nucleotide pool. To unravel the molecular mechanisms involved in this process, we screened the E. coli single-gene deletion mutants of the Keio collection for glycogen content in ADP-glucose-containing culture medium. In comparison to wild-type (WT) cells, individual ∆nupC and ∆nupG mutants lacking the cAMP/CRP responsive inner-membrane nucleoside transporters NupC and NupG displayed reduced glycogen contents and slow ADP-glucose incorporation. In concordance, ∆cya and ∆crp mutants accumulated low levels of glycogen and slowly incorporated ADP-glucose. Two-thirds of the glycogen-excess mutants identified during screening lacked functions that underlie envelope biogenesis and integrity, including the RpoE specific RseA anti-sigma factor. These mutants exhibited higher ADP-glucose uptake than WT cells. The incorporation of either ∆crp, ∆nupG or ∆nupC null alleles sharply reduced the ADP-glucose incorporation and glycogen content initially witnessed in ∆rseA cells. Overall, the data showed that E. coli incorporates extracellular ADP-glucose through a cAMP/CRP-regulated process involving the NupC and NupG nucleoside transporters that is facilitated under envelope stress conditions.
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Affiliation(s)
- Goizeder Almagro
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Alejandro M Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 521, 2000, Rosario, Argentina
| | - Manuel Montero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Hirotada Mori
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101, Japan
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain.
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31
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Marcelletti S, Scortichini M. Some strains that have converged to infect Prunus spp. trees are members of distinct Pseudomonas syringae genomospecies and ecotypes as revealed by in silico genomic comparison. Arch Microbiol 2018; 201:67-80. [PMID: 30229267 DOI: 10.1007/s00203-018-1573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022]
Abstract
A complementary taxonomic and population genetic study was performed to delineate genetically and ecologically distinct species within the Pseudomonas syringae complex by assessing 16 strains including pathovar strains that have converged to infect Prunus spp. trees, and two outgroups. Both average nucleotide identity and genome-to-genome distance comparison methods revealed the occurrence of distinct genomospecies, namely 1, 2, 3 and 8 (sensu Gardan et al.), with the latter two being closely related. Strains classified as P. s. pv. morsprunorum clustered into two distinct genomospecies, namely 2 and 8. Both the AdaptML and hierarchical Bayesian analysis of population structure methods highlighted the presence of three ecotypes, and the taxonomically related genomospecies 3 and 8 strains were members of the same ecotype. The distribution of pathogenic and virulence-associated genetic traits among Pseudomonas strains did not reveal any distinct type III secretion system effector or phytotoxin distribution pattern that characterized single genomospecies and strains that infect Prunus spp. The complete WHOP (Woody HOst and Pseudomonas spp.) genomic region and the entire β-ketoadipate gene cluster, including the catBCA operon, were found only in the members of genomospecies 2 and in the two P. s. pv. morsprunorum strains of genomospecies 8. A reduced gene flow between the three ecotypes suggested that point mutations played a larger role during the evolution of the strains than recombination. Our data support the idea that Prunus trees can be infected by different strains of distinct Pseudomonas genomospecies/ecotypes through diverse mechanisms of host colonization and infection. Such strains may represent particular lineages that emerged from environments other than that of the infected plant upon acquiring genetic traits that gave them the ability to cause plant diseases. The complementary assessment of bacterial strains using both taxonomic approaches and methods that reveal ecologically homogeneous populations has proven useful in confirming the cohesion of bacterial clusters.
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Affiliation(s)
- Simone Marcelletti
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Via di Fioranello, 52, 00134, Rome, Italy
| | - Marco Scortichini
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Via di Fioranello, 52, 00134, Rome, Italy.
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32
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Abstract
Some bacteria can transfer to new host species, and this poses a risk to human health. Indeed, an estimated 60% of all human pathogens have originated from other animal species. Similarly, human-to-animal transitions are recognized as a major threat to sustainable livestock production, and emerging pathogens impose an increasing burden on crop yield and global food security. Recent advances in high-throughput sequencing technologies have enabled comparative genomic analyses of bacterial populations from multiple hosts. Such studies are providing new insights into the evolutionary processes that underpin the establishment of bacteria in new host niches. A better understanding of the genetic and mechanistic basis for bacterial host adaptation may reveal novel targets for controlling infection or inform the design of approaches to limit the emergence of new pathogens.
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Affiliation(s)
- Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
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33
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Sicard A, Zeilinger AR, Vanhove M, Schartel TE, Beal DJ, Daugherty MP, Almeida RPP. Xylella fastidiosa: Insights into an Emerging Plant Pathogen. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:181-202. [PMID: 29889627 DOI: 10.1146/annurev-phyto-080417-045849] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The bacterium Xylella fastidiosa re-emerged as a plant pathogen of global importance in 2013 when it was first associated with an olive tree disease epidemic in Italy. The current threat to Europe and the Mediterranean basin, as well as other world regions, has increased as multiple X. fastidiosa genotypes have now been detected in Italy, France, and Spain. Although X. fastidiosa has been studied in the Americas for more than a century, there are no therapeutic solutions to suppress disease development in infected plants. Furthermore, because X. fastidiosa is an obligatory plant and insect vector colonizer, the epidemiology and dynamics of each pathosystem are distinct. They depend on the ecological interplay of plant, pathogen, and vector and on how interactions are affected by biotic and abiotic factors, including anthropogenic activities and policy decisions. Our goal with this review is to stimulate discussion and novel research by contextualizing available knowledge on X. fastidiosa and how it may be applicable to emerging diseases.
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Affiliation(s)
- Anne Sicard
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
- Biologie et Génétique des Interactions Plant-Parasite, UMR 0385, Centre de Coopération Internationale en Recherche Agronomique pour le Développement-Institut National de la Recherche Agronomique-Montpellier SupAgro, Campus International de Baillarguet, 34398 Montpellier CEDEX 05, France
| | - Adam R Zeilinger
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
| | - Mathieu Vanhove
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
| | - Tyler E Schartel
- Department of Entomology, University of California, Riverside, California 92521, USA
| | - Dylan J Beal
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
| | - Matthew P Daugherty
- Department of Entomology, University of California, Riverside, California 92521, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
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Rutherford V, Yom K, Ozer EA, Pura O, Hughes A, Murphy KR, Cudzilo L, Mitchel D, Hauser AR. Environmental reservoirs for exoS+ and exoU+ strains of Pseudomonas aeruginosa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:485-492. [PMID: 29687624 PMCID: PMC6108916 DOI: 10.1111/1758-2229.12653] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas aeruginosa uses its type III secretion system to inject the effector proteins ExoS and ExoU into eukaryotic cells, which subverts these cells to the bacterium's advantage and contributes to severe infections. We studied the environmental reservoirs of exoS+ and exoU+ strains of P. aeruginosa by collecting water, soil, moist substrates and plant samples from environments in the Chicago region and neighbouring states. Whole-genome sequencing was used to determine the phylogeny and type III secretion system genotypes of 120 environmental isolates. No correlation existed between geographic separation of isolates and their genetic relatedness, which confirmed previous findings of both high genetic diversity within a single site and the widespread distribution of P. aeruginosa clonal complexes. After excluding clonal isolates cultured from the same samples, 74 exoS+ isolates and 16 exoU+ isolates remained. Of the exoS+ isolates, 41 (55%) were from natural environmental sites and 33 (45%) were from man-made sites. Of the exoU+ isolates, only 3 (19%) were from natural environmental sites and 13 (81%) were from man-made sites (p < 0.05). These findings suggest that man-made water systems may be a reservoir from which patients acquire exoU+ P. aeruginosa strains.
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Affiliation(s)
- Victoria Rutherford
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kelly Yom
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivia Pura
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ami Hughes
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Katherine R. Murphy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Laura Cudzilo
- Department of Biology, St. John’s University, Collegeville, Minnesota
| | - David Mitchel
- Department of Biology, St. John’s University, Collegeville, Minnesota
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Abstract
Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.
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Tromas N, Taranu ZE, Martin BD, Willis A, Fortin N, Greer CW, Shapiro BJ. Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria. Front Microbiol 2018; 9:438. [PMID: 29636727 PMCID: PMC5880894 DOI: 10.3389/fmicb.2018.00438] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/26/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering - in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering - such as competition between closely related taxa, or convergent trait evolution in distantly related taxa - in shaping particular traits in microbial communities.
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Affiliation(s)
- Nicolas Tromas
- Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
| | - Zofia E Taranu
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Bryan D Martin
- Department of Statistics, University of Washington, Seattle, WA, United States
| | - Amy Willis
- Department of Statistics, University of Washington, Seattle, WA, United States.,Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Nathalie Fortin
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada
| | - Charles W Greer
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
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Bernstein H, Bernstein C, Michod RE. Sex in microbial pathogens. INFECTION GENETICS AND EVOLUTION 2018; 57:8-25. [DOI: 10.1016/j.meegid.2017.10.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
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Fernandez-Lopez R, Redondo S, Garcillan-Barcia MP, de la Cruz F. Towards a taxonomy of conjugative plasmids. Curr Opin Microbiol 2017; 38:106-113. [PMID: 28586714 DOI: 10.1016/j.mib.2017.05.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 01/14/2023]
Abstract
Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies.
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Affiliation(s)
- Raul Fernandez-Lopez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain
| | - Santiago Redondo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain
| | - M Pilar Garcillan-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain.
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Larkin AA, Martiny AC. Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:55-70. [PMID: 28185400 DOI: 10.1111/1758-2229.12523] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood. Here, we present two theoretical models outlining the evolutionary mechanisms that drive the formation of microdiverse 'sub-taxa.' Additionally, we review recent literature and reveal that microdiversity influences a wide range of functional traits across diverse ecosystems and microbes. Moving to higher levels of organization, we use laboratory data from marine, soil, and host-associated bacteria to demonstrate that the aggregated trait-based response of microdiverse sub-taxa modifies the fundamental niche of microbes. The correspondence between microdiversity and niche space represents a critical tool for future studies of microbial ecology. By combining growth experiments on diverse isolates with examinations of environmental abundance patterns, researchers can better quantify the fundamental and realized niches of microbes and improve understanding of microbial biogeography and response to future environmental change.
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Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
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40
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Baltrus DA, McCann HC, Guttman DS. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:152-168. [PMID: 27798954 PMCID: PMC6638251 DOI: 10.1111/mpp.12506] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
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Affiliation(s)
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey UniversityAuckland 0632New Zealand
| | - David S. Guttman
- Department of Cell and Systems BiologyUniversity of TorontoTorontoON M5S 3B2Canada
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoON M5S 3B2Canada
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41
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Di Meglio L, Santos F, Gomariz M, Almansa C, López C, Antón J, Nercessian D. Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns. FEMS Microbiol Ecol 2016; 92:fiw184. [PMID: 27604253 DOI: 10.1093/femsec/fiw184] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 11/13/2022] Open
Abstract
Seasonal sampling was carried out at three Argentinian salterns, Salitral Negro (SN), Colorada Grande (CG) and Guatraché (G), to analyze abiotic parameters and microbial diversity and dynamics. Microbial assemblages were correlated to environmental factors by statistical analyses. Principal component analysis of the environmental data grouped SN and CG samples separately from G samples owing to G's higher pH values and sulfate concentration. Differences in microbial assemblages were also found. Many archaeal sequences belonged to uncultured members of Haloquadratum and Haloquadratum-related genera, with different environmental optima. Notably, nearly half of the archaeal sequences were affiliated to the recently described 'Candidatus Haloredividus' (phylum Nanohaloarchaeota), not previously detected in salt-saturated environments. Most bacterial sequences belonged to Salinibacter representatives, while sequences affiliated to the recently described genus Spiribacter were also found. Seasonal analysis showed at least 40% of the microbiota from the three salterns was prevalent through the year, indicating they are well adapted to environmental fluctuations. On the other hand, a minority of archaeal and bacterial sequences were found to be seasonally distributed. Five viral morphotypes and also eukaryal predators were detected, suggesting different mechanisms for controlling prokaryotic numbers. Notably, Guatraché was the saltern that harbored the highest virus-to-cell ratios reported to date for hypersaline environments.
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Affiliation(s)
- Leonardo Di Meglio
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, UNMDP - CONICET, Funes 3250 4° nivel, 7600 Mar del Plata, Argentina
| | - Fernando Santos
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - María Gomariz
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - Cristina Almansa
- Servicios Técnicos de Investigación (SSTTI), Unidad de Microscopía, Universidad de Alicante, Alicante, 03690 San Vicente del Raspeig, España
| | - Cristina López
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, UNMDP - CONICET, Funes 3250 4° nivel, 7600 Mar del Plata, Argentina
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Hambright WS, Deng J, Tiedje JM, Brettar I, Rodrigues JLM. Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions. mSphere 2016; 1:e00158-16. [PMID: 27777983 PMCID: PMC5071532 DOI: 10.1128/msphere.00158-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022] Open
Abstract
In bacterial populations, subtle expressional differences may promote ecological specialization through the formation of distinct ecotypes. In a barrier-free habitat, this process most likely precedes population divergence and may predict speciation events. To examine this, we used four sequenced strains of the bacterium Shewanella baltica, OS155, OS185, OS195, and OS223, as models to assess transcriptional variation and ecotype formation within a prokaryotic population. All strains were isolated from different depths throughout a water column of the Baltic Sea, occupying different ecological niches characterized by various abiotic parameters. Although the genome sequences are nearly 100% conserved, when grown in the laboratory under standardized conditions, all strains exhibited different growth rates, suggesting significant expressional variation. Using the Ecotype Simulation algorithm, all strains were considered to be discrete ecotypes when compared to 32 other S. baltica strains isolated from the same water column, suggesting ecological divergence. Next, we employed custom microarray slides containing oligonucleotide probes representing the core genome of OS155, OS185, OS195, and OS223 to detect natural transcriptional variation among strains grown under identical conditions. Significant transcriptional variation was noticed among all four strains. Differentially expressed gene profiles seemed to coincide with the metabolic signatures of the environment at the original isolation depth. Transcriptional pattern variations such as the ones highlighted here may be used as indicators of short-term evolution emerging from the formation of bacterial ecotypes. IMPORTANCE Eukaryotic studies have shown considerable transcriptional variation among individuals from the same population. It has been suggested that natural variation in eukaryotic gene expression may have significant evolutionary consequences and may explain large-scale phenotypic divergence of closely related species, such as humans and chimpanzees (M.-C. King and A. C. Wilson, Science 188:107-116, 1975, http://dx.doi.org/10.1126/science.1090005; M. F. Oleksiak, G. A. Churchill, and D. L. Crawford, Nat Genet 32:261-266, 2002, http://dx.doi.org/10.1038/ng983). However, natural variation in gene expression is much less well understood in prokaryotic organisms. In this study, we used four sequenced strains of the marine bacterium Shewanella baltica to better understand the natural transcriptional divergence of a stratified prokaryotic population. We found substantial low-magnitude expressional variation among the four S. baltica strains cultivated under identical laboratory conditions. Collectively, our results indicate that transcriptional variation is an important factor for ecological speciation.
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Affiliation(s)
- W. S. Hambright
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Jie Deng
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - Ingrid Brettar
- Department of Vaccinology and Applied Microbiology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Jorge L. M. Rodrigues
- Department of Land, Water and Air Resources, University of California, Davis, Davis, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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43
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Willis A, Chuang AW, Woodhouse JN, Neilan BA, Burford MA. Intraspecific variation in growth, morphology and toxin quotas for the cyanobacterium, Cylindrospermopsis raciborskii. Toxicon 2016; 119:307-10. [DOI: 10.1016/j.toxicon.2016.07.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/08/2023]
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Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly. ISME JOURNAL 2016; 11:201-211. [PMID: 27392085 DOI: 10.1038/ismej.2016.93] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 05/06/2016] [Accepted: 06/07/2016] [Indexed: 01/08/2023]
Abstract
A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273T. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273T synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.
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45
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Bull JW, Maron M. How humans drive speciation as well as extinction. Proc Biol Sci 2016; 283:20160600. [PMID: 27358365 PMCID: PMC4936035 DOI: 10.1098/rspb.2016.0600] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022] Open
Abstract
A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation-and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon 'no net loss' conservation literature-considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.
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Affiliation(s)
- J W Bull
- Department of Food and Resource Economics and Center for Macroecology, Evolution and Climate, University of Copenhagen, Rolighedsvej 23, 1958 Copenhagen, Denmark
| | - M Maron
- School of Geography, Planning and Environmental Management, The University of Queensland, Brisbane, Queensland 4072, Australia
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46
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Abstract
The H-NS (heat-stable nucleoid structuring) protein affects both nucleoid compaction and global gene regulation. H-NS appears to act primarily as a silencer of AT-rich genetic material acquired by horizontal gene transfer. As such, it is key in the regulation of most genes involved in virulence and in adaptation to new environmental niches. Here we review recent progress in understanding the biochemistry of H-NS and how xenogeneic silencing affects bacterial evolution. We highlight the strengths and weaknesses of some of the models proposed in H-NS-mediated nucleoprotein complex formation. Based on recent single-molecule studies, we also propose a novel mode of DNA compaction by H-NS termed intrabridging to explain over two decades of observations of the H-NS molecule.
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Affiliation(s)
- Kamna Singh
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada;
| | - Joshua N Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Ontario L5L 1C6, Canada.,Department of Physics, University of Toronto, Ontario M5S 1A7, Canada
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47
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Flexible genomic islands as drivers of genome evolution. Curr Opin Microbiol 2016; 31:154-160. [DOI: 10.1016/j.mib.2016.03.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 12/26/2022]
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48
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49
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Gómez-Lunar Z, Hernández-González I, Rodríguez-Torres MD, Souza V, Olmedo-Álvarez G. Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation. Front Microbiol 2016; 7:58. [PMID: 26903955 PMCID: PMC4744853 DOI: 10.3389/fmicb.2016.00058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/13/2016] [Indexed: 11/27/2022] Open
Abstract
Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that revealed that in addition to gene gain and loss, regulation adjustment of gene expression also has contributed to the intraspecific diversity of B. coahuilensis.
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Affiliation(s)
- Zulema Gómez-Lunar
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
| | - Ismael Hernández-González
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
| | - María-Dolores Rodríguez-Torres
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
| | - Valeria Souza
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México México City, Mexico
| | - Gabriela Olmedo-Álvarez
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
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Lokmer A, Kuenzel S, Baines JF, Wegner KM. The role of tissue-specific microbiota in initial establishment success of Pacific oysters. Environ Microbiol 2016; 18:970-87. [DOI: 10.1111/1462-2920.13163] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/27/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Ana Lokmer
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
| | - John F. Baines
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
- Institute for Experimental Medicine; Christian-Albrechts-University of Kiel; Arnold-Heller-Strasse 3 D-24105 Kiel Germany
| | - Karl Mathias Wegner
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
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