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Article: Trait-trait relationships and tradeoffs vary with genome size in prokaryotes.

Beier, Sara / Werner, Johannes / Bouvier, Thierry / Mouquet, Nicolas / Violle, Cyrille

2022 Volume 13, Page(s) 985216

Abstract: We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we ...

Abstract	We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted
Language	English
Publishing date	2022-10-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.985216
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Article: Niche breadth affects bacterial transcription patterns along a salinity gradient

Rain‐Franco, Angel / Mouquet, Nicolas / Gougat‐Barbera, Claire / Bouvier, Thierry / Beier, Sara

Molecular ecology. 2022 Feb., v. 31, no. 4

2022

Abstract: Understanding the molecular mechanisms that determine a species' life history is important for predicting their susceptibility to environmental change. While specialist species with a narrow niche breadth (NB) maximize their fitness in their optimum ... ...

Abstract	Understanding the molecular mechanisms that determine a species' life history is important for predicting their susceptibility to environmental change. While specialist species with a narrow niche breadth (NB) maximize their fitness in their optimum habitat, generalists with broad NB adapt to multiple environments. The main objective of this study was to identify general transcriptional patterns that would distinguish bacterial strains characterized by contrasted NBs along a salinity gradient. More specifically, we hypothesized that genes encoding fitness‐related traits, such as biomass production, have a higher degree of transcriptional regulation in specialists than in generalists, because the fitness of specialists is more variable under environmental change. By contrast, we expected that generalists would exhibit enhanced transcriptional regulation of genes encoding traits that protect them against cellular damage. To test these hypotheses, we assessed the transcriptional regulation of fitness‐related and adaptation‐related genes of 11 bacterial strains in relation to their NB and stress exposure under changing salinity conditions. The results suggested that transcriptional regulation levels of fitness‐ and adaptation‐related genes correlated with the NB and/or the stress exposure of the inspected strains. We further identified a shortlist of candidate stress marker genes that could be used in future studies to monitor the susceptibility of bacterial populations or communities to environmental changes.
Keywords	biomass production ; habitats ; life history ; salinity ; transcription (genetics)
Language	English
Dates of publication	2022-02
Size	p. 1216-1233.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16316
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Article ; Online: Metagenomic data of bacterial communities associated with

Nguyen, Duong Huy / Chu, Nhat Huy / Bettarel, Yvan / Auguet, Jean-Christophe / Bouvier, Thierry / Chu, Ha Hoang / Bui, Van Ngoc

Data in brief

2023 Volume 47, Page(s) 108977

Abstract: ... ...

Abstract	Acropora
Language	English
Publishing date	2023-02-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2023.108977
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Article ; Online: Microplastics in the insular marine environment of the Southwest Indian Ocean carry a microbiome including antimicrobial resistant (AMR) bacteria: A case study from Reunion Island.

Sababadichetty, Loik / Miltgen, Guillaume / Vincent, Bryan / Guilhaumon, François / Lenoble, Veronique / Thibault, Margot / Bureau, Sophie / Tortosa, Pablo / Bouvier, Thierry / Jourand, Philippe

Marine pollution bulletin

2023 Volume 198, Page(s) 115911

Abstract: The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by ... ...

Abstract	The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by plastics. We characterized the plastic pollution on the island's coastal waters, described the associated microbiome, explored viable bacterial flora and the presence of antimicrobial resistant (AMR) bacteria. Reunion Island faces plastic pollution with up to 10,000 items/km
MeSH term(s)	Humans ; Indian Ocean ; Microplastics ; Plastics ; Reunion ; Bacteria ; Microbiota ; Environmental Monitoring ; Water Pollutants, Chemical/analysis
Chemical Substances	Microplastics ; Plastics ; Water Pollutants, Chemical
Language	English
Publishing date	2023-12-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2023.115911
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Article ; Online: Identifying macroplastic pathobiomes and antibiotic resistance in a subtropical fish farm

Naudet, Jeanne / d'Orbcastel, Emmanuelle Roque / Bouvier, Thierry / Godreuil, Sylvain / Dyall, Sabrina / Bouvy, Simon / Rieuvilleneuve, Fabien / Restrepo-Ortiz, Claudia / Bettarel, Yvan / Auguet, Jean-Christophe

Marine Pollution Bulletin. 2023, p.115267-

2023 , Page(s) 115267–

Abstract: Macroplastics are ubiquitous in aquaculture ecosystems. However, to date the potential role of plastics as a support for bacterial biofilm that can include potential human pathogenic bacteria (PHPB) and antibiotic-resistant bacteria (ARB) has been ... ...

Abstract	Macroplastics are ubiquitous in aquaculture ecosystems. However, to date the potential role of plastics as a support for bacterial biofilm that can include potential human pathogenic bacteria (PHPB) and antibiotic-resistant bacteria (ARB) has been largely overlooked. In this study, we used a combination of metabarcoding and standard antibiotic susceptibility testing to study the pathobiome and resistome of macroplastics, fish guts and the environment in a marine aquaculture farm in Mauritius. Aquaculture macroplastics were found to be higher in PHPB, dominated by the Vibrionaceae family (0.34 % of the total community), compared with environmental samples. Moreover, isolates from aquaculture plastics showed higher significant multiple antibiotic resistance (MAR) compared to non-plastic samples of seawater, sediment and fish guts. These results suggest that plastics act as a reservoir and fomite of PHPB and ARB in aquaculture, potentially threatening the health of farmed fish and human consumers.
Keywords	DNA barcoding ; Vibrionaceae ; antibiotic resistance ; antibiotic resistance genes ; biofilm ; farmed fish ; fish farms ; fomites ; humans ; mariculture ; marine pollution ; multiple drug resistance ; pathogens ; seawater ; sediments ; Mauritius ; Plastisphere ; Aquaculture ; Pathogen
Language	English
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2023.115267
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Article ; Online: Niche breadth affects bacterial transcription patterns along a salinity gradient.

Rain-Franco, Angel / Mouquet, Nicolas / Gougat-Barbera, Claire / Bouvier, Thierry / Beier, Sara

Molecular ecology

2021 Volume 31, Issue 4, Page(s) 1216–1233

Abstract	Understanding the molecular mechanisms that determine a species' life history is important for predicting their susceptibility to environmental change. While specialist species with a narrow niche breadth (NB) maximize their fitness in their optimum habitat, generalists with broad NB adapt to multiple environments. The main objective of this study was to identify general transcriptional patterns that would distinguish bacterial strains characterized by contrasted NBs along a salinity gradient. More specifically, we hypothesized that genes encoding fitness-related traits, such as biomass production, have a higher degree of transcriptional regulation in specialists than in generalists, because the fitness of specialists is more variable under environmental change. By contrast, we expected that generalists would exhibit enhanced transcriptional regulation of genes encoding traits that protect them against cellular damage. To test these hypotheses, we assessed the transcriptional regulation of fitness-related and adaptation-related genes of 11 bacterial strains in relation to their NB and stress exposure under changing salinity conditions. The results suggested that transcriptional regulation levels of fitness- and adaptation-related genes correlated with the NB and/or the stress exposure of the inspected strains. We further identified a shortlist of candidate stress marker genes that could be used in future studies to monitor the susceptibility of bacterial populations or communities to environmental changes.
MeSH term(s)	Acclimatization ; Adaptation, Physiological ; Bacteria/genetics ; Ecosystem ; Salinity
Language	English
Publishing date	2021-12-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16316
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Article: Fishing for the Virome of Tropical Tuna

Gadoin, Elsa / Desnues, Christelle / Monteil-Bouchard, Sonia / Bouvier, Thierry / Auguet, Jean-Christophe / Roque d’Orbcastel, Emmanuelle / Bettarel, Yvan

Viruses. 2021 July 02, v. 13, no. 7

2021

Abstract: While planktonic viruses have received much attention in recent decades, knowledge of the virome of marine organisms, especially fish, still remains rudimentary. This is notably the case with tuna, which are among the most consumed fish worldwide and ... ...

Abstract	While planktonic viruses have received much attention in recent decades, knowledge of the virome of marine organisms, especially fish, still remains rudimentary. This is notably the case with tuna, which are among the most consumed fish worldwide and represent considerable economic, social and nutritional value. Yet the composition of the tuna virome and its biological and environmental determinants remain unknown. To begin to address this gap, we investigated the taxonomic diversity of viral communities inhabiting the skin mucus, gut and liver of two major tropical tuna species (skipjack and yellowfin) in individuals fished in the Atlantic and Indian Oceans. While we found significant differences in the virome composition between the organs, this was totally independent of the tuna species or sex. The tuna virome was mainly dominated by eukaryotic viruses in the digestive organs (gut and liver), while bacteriophages were predominant in the mucus. We observed the presence of specific viral families in each organ, some previously identified as fish or human pathogens (e.g., Iridoviridae, Parvoviridae, Alloherpesviridae, Papillomaviridae). Interestingly, we also detected a ‘core virome’ that was shared by all the organs and was mainly composed of Caudovirales, Microviridae and Circoviridae. These results show that tuna host a mosaic of viral niches, whose establishment, role and circulation remain to be elucidated.
Keywords	Alloherpesviridae ; Caudovirales ; Circoviridae ; Iridoviridae ; Microviridae ; Papillomaviridae ; Parvoviridae ; humans ; liver ; mucus ; nutritive value ; plankton ; species diversity ; tuna
Language	English
Dates of publication	2021-0702
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13071291
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Article ; Online: Tracking spoilage bacteria in the tuna microbiome.

Gadoin, Elsa / Desnues, Christelle / Bouvier, Thierry / Roque D'orbcastel, Emmanuelle / Auguet, Jean-Christophe / Crochemore, Sandrine / Adingra, Antoinette / Bettarel, Yvan

FEMS microbiology ecology

2022 Volume 98, Issue 10

Abstract: Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. ...

Abstract	Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120 h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50 ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.
MeSH term(s)	Animals ; Bacteria/genetics ; Food Microbiology ; Histamine/analysis ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Salts ; Tuna/genetics ; Tuna/microbiology
Chemical Substances	RNA, Ribosomal, 16S ; Salts ; brine ; Histamine (820484N8I3)
Language	English
Publishing date	2022-10-03
Publishing country	England
Document type	Journal Article
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiac110
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Article: An invasive herbivorous fish (Siganus rivulatus) influences both benthic and planktonic microbes through defecation and nutrient excretion

Escalas, Arthur / Avouac, Amandine / Belmaker, Jonathan / Bouvier, Thierry / Clédassou, Valentin / Ferraton, Frank / Rieuvilleneuve, Fabien / Rilov, Gil / Mulet, Anna Rovirosa / Shapiro-Goldberg, Daphna / Villéger, Sébastien

Science of the total environment. 2022 May 20,

2022

Abstract: Direct and indirect impacts by invasive animals on plants and other animals through predation and competition have been evidenced in many ecosystems. For instance, the rabbitfish Siganus rivulatus, originating from the Red Sea, is now the most abundant ... ...

Abstract	Direct and indirect impacts by invasive animals on plants and other animals through predation and competition have been evidenced in many ecosystems. For instance, the rabbitfish Siganus rivulatus, originating from the Red Sea, is now the most abundant species in costal habitats of South-Eastern Mediterranean Sea where it overgrazes algae. However, little is known about its impacts on microbes through release of metabolic wastes and feces. We used a mesocosm experiment to test the effect of S. rivulatus on planktonic and benthic microbial communities. Excretion of dissolved nutrients by fish resulted in higher concentrations of dissolved inorganic nitrogen (NH₄, NO₂/NO₃). This increase in availability of N was associated with higher N content in macroalgae, higher biomass of phytoplankton, higher abundance of bacterioplankton and shift in the structure of planktonic bacterial communities. The feces released mostly under the shelters where the fish rest at night, led to significant increases in diversity of sediment bacterial communities and shifts in their structure. The impact of S. rivulatus on planktonic microbes was related to the indirect bottom-up effect induced by excreted dissolved nutrients while its effect on benthic microbes was due to the direct release of both organic matter and microbes present in feces. Overall, this first evidence of the impacts of invasive species on planktonic and benthic microbes highlights that ongoing changes in fish biodiversity could have ecosystem-wide consequences.
Keywords	Siganus rivulatus ; bacterioplankton ; biodiversity ; biomass ; defecation ; dissolved inorganic nitrogen ; environment ; excretion ; feces ; herbivorous fish ; invasive species ; macroalgae ; organic matter ; phytoplankton ; predation ; sediments ; Mediterranean Sea ; Red Sea
Language	English
Dates of publication	2022-0520
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.156207
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Article: Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity.

Troussellier, Marc / Escalas, Arthur / Bouvier, Thierry / Mouillot, David

Frontiers in microbiology

2017 Volume 8, Page(s) 947

Abstract: Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. ... ...

Abstract	Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely
Language	English
Publishing date	2017-05-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2017.00947
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