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1.
Environ Microbiol ; 25(12): 3753-3770, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38031968

RESUMO

Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.


Assuntos
Microbiota , Vitamina B 12 , Vitamina B 12/metabolismo , Estações do Ano , Archaea/genética , Archaea/metabolismo , Vitaminas/metabolismo
2.
PLoS Biol ; 17(9): e3000483, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31545807

RESUMO

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.


Assuntos
Antozoários/microbiologia , Recifes de Corais , Expedições , Microbiota , Animais , Metabolômica , Metagenômica , Oceano Pacífico , Simbiose
3.
Environ Microbiol ; 23(5): 2592-2604, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33760330

RESUMO

Marine picoplankton contribute to global carbon sequestration and nutrient recycling. These processes are directly related to the composition of communities, which in turn depends on microbial interactions and environmental forcing. Under regular seasonal cycles, marine communities show strong predictable patterns of annual re-occurrences, but little is known about the effect of environmental perturbation on their organization. The aim of our study was to investigate the co-occurrence patterns of planktonic picoeukaryote, bacteria and archaea under contrasting environmental conditions. The study was designed to have high sampling frequency that could match both the biological rhythm of marine microbes and the short time scale of extreme weather events. Our results show that microbial networks changed from year to year depending on conditions. In addition, individual taxa became less interconnected and changed neighbours, which revealed an unfaithful relationship between marine microorganisms. This unexpected pattern suggests possible switches between organisms that have similar specific functions, or hints at the presence of organisms that share similar environmental niches without interacting. Despite the observed annual changes, the time series showed re-occurring communities that appear to recover from perturbations. Changing co-occurrence patterns between marine microorganisms may allow the long-term stability of ecosystems exposed to contrasting meteorological events.


Assuntos
Archaea , Ecossistema , Archaea/genética , Bactérias/genética , Plâncton , Estações do Ano
4.
Proc Biol Sci ; 288(1965): 20212117, 2021 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-34905712

RESUMO

Cold-water corals are threatened by global warming, especially in the Mediterranean Sea where they live close to their upper known thermal limit (i.e. 13°C), yet their response to rising temperatures is not well known. Here, temperature effects on Lophelia pertusa and Madrepora oculata holobionts (i.e. the host and its associated microbiome) were investigated. We found that at warmer seawater temperature (+2°C), L. pertusa showed a modification of its microbiome prior to a change in behaviour, leading to lower energy reserves and skeletal growth, whereas M. oculata was more resilient. At extreme temperature (+4°C), both species quickly lost their specific bacterial signature followed by lower physiological activity prior to death. In addition, our results showing the holobionts' negative response to colder temperatures (-3°C), suggest that Mediterranean corals live close to their thermal optimum. The species-specific response to temperature change highlights that global warming may affect dramatically the main deep-sea reef-builders, which would alter the associated biodiversity and related ecosystem services.


Assuntos
Antozoários , Microbiota , Animais , Antozoários/fisiologia , Recifes de Corais , Mar Mediterrâneo , Água do Mar , Água
5.
Environ Microbiol ; 22(1): 354-368, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31696646

RESUMO

Different cold-water coral (CWC) species harbour distinct microbial communities and the community composition is thought to be linked to the ecological strategies of the host. Here we test whether diet shapes the composition of bacterial communities associated with CWC. We compared the microbiomes of two common CWC species in aquaria, Lophelia pertusa and Madrepora oculata, when they were either starved, or fed respectively with a carnivorous diet, two different herbivorous diets, or a mix of the 3. We targeted both the standing stock (16S rDNA) and the active fraction (16S rRNA) of the bacterial communities and showed that in both species, the corals' microbiome was specific to the given diet. A part of the microbiome remained, however, species-specific, which indicates that the microbiome's plasticity is framed by the identity of the host. In addition, the storage lipid content of the coral tissue showed that different diets had different effects on the corals' metabolisms. The combined results suggest that L. pertusa may be preying preferentially on zooplankton while M. oculata may in addition use phytoplankton and detritus. The results cast a new light on coral microbiomes as they indicate that a portion of the CWC's bacterial community could represent a food influenced microbiome.


Assuntos
Antozoários/microbiologia , Bactérias/metabolismo , Metabolismo dos Lipídeos/fisiologia , Lipídeos/análise , Microbiota/fisiologia , Animais , Bactérias/genética , Temperatura Baixa , DNA Ribossômico/genética , Dieta , Microbiota/genética , RNA Ribossômico 16S/genética , Especificidade da Espécie , Zooplâncton
6.
Mol Ecol ; 29(23): 4605-4617, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33001506

RESUMO

A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.


Assuntos
Bacteriófagos , Microbiota , Bacteriófagos/genética , Lagos , Metagenoma , Metagenômica
7.
Environ Microbiol ; 20(7): 2422-2437, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29687572

RESUMO

Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (105 to 109 copies g-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.


Assuntos
Archaea/efeitos dos fármacos , Lagos/microbiologia , Metais/toxicidade , Microbiologia da Água , Poluentes Químicos da Água/toxicidade , Archaea/genética , Ciclo do Carbono , DNA Arqueal , Ecossistema , Sedimentos Geológicos/microbiologia , Filogenia , RNA Ribossômico 16S
8.
Mol Ecol ; 27(6): 1494-1504, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29412497

RESUMO

The description of a rare biosphere within microbial communities has created great interest because microbes play a fundamental role in the functioning of all ecosystems on earth. Despite recent progress in understanding the ecology of the rare biosphere, the concept itself is still discussed, and fundamental questions remain. Here, we target the seed bank compartment of the rare biosphere, assess the level of rarity at which micro-organisms are still able to colonize an ecosystem and investigate whether rare species are functionally redundant. Using an original experimental design where wood in aquaria was inoculated with increasingly diluted coastal seawater, we show that bacteria that represented as few as 0.00000002% of the cells in the environment (or 1 cell in 10 L of seawater) were still able to grow and play key roles within the ecosystem. Our experiment further showed that some bacteria can be replaced by others that have the potential to fulfil the same metabolic tasks. This finding suggests some functional redundancy within bacterial species. However, when ultrarare bacteria were progressively removed, productivity was reduced, and below a certain threshold some processes were lost, and the function of the ecosystem was altered. Overall the study shows that bacteria that are not detected by high-throughput sequencing approaches are nevertheless viable and able to colonize new ecosystems, suggesting the need to consider ultrarare microbes in the marine environment.


Assuntos
Bactérias/genética , Biodiversidade , Ecossistema , Filogenia , Bactérias/classificação , Bactérias/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Água do Mar/microbiologia , Enxofre/metabolismo
9.
Antonie Van Leeuwenhoek ; 111(8): 1421-1432, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29626330

RESUMO

Northern Chile harbors different bioclimatic zones including hyper-arid and arid ecosystems and hotspots of microbial life, such as high altitude wetlands, which may contribute differentially to greenhouse gases (GHG) such as carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). In this study, we explored ground level GHG distribution and the potential role of a wetland situated at 3800 m.a.s.l, and characterized by high solar radiation < 1600 W m-2, extreme temperature ranges (-12 to 24 °C) and wind stress (< 17 m s-1). The water source of the wetland is mainly groundwater springs, which generates streams and ponds surrounded by peatlands. These sites support a rich microbial aquatic life including diverse bacteria and archaea communities, which transiently form more complex structures, such as microbial mats. In this study, GHG were measured in the water and above ground level air at the wetland site and along an elevation gradient in different bioclimatic areas from arid to hyper-arid zones. The microbiome from the water and sediments was described by high-throughput sequencing 16S rRNA and rDNA genes. The results indicate that GHG at ground level were variable along the elevation gradient potentially associated with different bioclimatic zones, reaching high values at the high Andean steppe and variable but lower values in the Atacama Desert and at the wetland. The water areas of the wetland presented high concentrations of CH4 and CO2, particularly at the spring areas and in air bubbles below microbial mats. The microbial community was rich (> 40 phyla), including archaea and bacteria potentially active in the different matrices studied (water, sediments and mats). Functional microbial groups associated with GHG recycling were detected at low frequency, i.e., < 2.5% of total sequences. Our results indicate that hyper-arid and arid areas of northern Chile are sites of GHG exchange associated with various bioclimatic zones and particularly in aquatic areas of the wetland where this ecosystem could represent a net sink of N2O and a source for CH4 and CO2.


Assuntos
Altitude , Clima Desértico , Ecossistema , Gases de Efeito Estufa/análise , Microbiota/fisiologia , Áreas Alagadas , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Dióxido de Carbono/análise , Dióxido de Carbono/metabolismo , Chile , DNA Arqueal/genética , DNA Bacteriano/genética , Sedimentos Geológicos/microbiologia , Gases de Efeito Estufa/metabolismo , Metano/análise , Metano/metabolismo , Óxido Nitroso/análise , Óxido Nitroso/metabolismo , RNA Ribossômico/genética , Raios Ultravioleta
10.
Environ Microbiol ; 18(12): 4537-4548, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27555520

RESUMO

Growing evidence indicates that dense water formation and flow over the continental shelf is a globally relevant oceanographic process, potentially affecting microbial assemblages down to the deep ocean. However, the extent and consequences of this influence have yet to be investigated. Here it is shown that dense water propagation to the deep ocean increases the abundance of prokaryotic plankton, and stimulates carbon production and organic matter degradation rates. Dense waters spilling off the shelf modifies community composition of deep sea microbial assemblages, leading to the increased relevance of taxa likely originating from the sea surface and the seafloor. This phenomenon can be explained by a combination of factors that interplay during the dense waters propagation, such as the transport of surface microbes to the ocean floor (delivering in our site 0.1 megatons of C), the stimulation of microbial metabolism due to increased ventilation and nutrients availability, the sediment re-suspension, and the mixing with ambient waters along the path. Thus, these results highlight a hitherto unidentified role for dense currents flowing over continental shelves in influencing deep sea microbes. In light of climate projections, this process will affect significantly the microbial functioning and biogeochemical cycling of large sectors of the ocean interior.


Assuntos
Bactérias/metabolismo , Plâncton/metabolismo , Plâncton/microbiologia , Microbiologia da Água , Movimentos da Água , Carbono/metabolismo , Clima , Ecossistema , Oceanos e Mares , Água do Mar
11.
Proc Natl Acad Sci U S A ; 110(15): 6004-9, 2013 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-23536290

RESUMO

Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.


Assuntos
Archaea/fisiologia , Ecótipo , Estações do Ano , Água do Mar , Archaea/genética , Biologia Computacional , DNA Ribossômico/genética , Ecologia , Mar Mediterrâneo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de RNA , Microbiologia da Água
12.
Environ Microbiol ; 17(10): 3882-97, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25856307

RESUMO

Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.


Assuntos
Archaea/classificação , Bactérias/classificação , Água Doce/microbiologia , Fungos/classificação , Camada de Gelo/microbiologia , Microbiota/genética , Sequência de Bases , Chile , Mudança Climática , Ecossistema , Estuários , Dados de Sequência Molecular , Proteobactérias , RNA Ribossômico 16S/genética , Estações do Ano , Análise de Sequência de DNA
13.
Mol Ecol ; 24(23): 5785-95, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26289961

RESUMO

Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro-organisms, but similar links for marine micro-organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity-productivity relationship was independent of community diversity calculated as the Shannon index. From our long-term (7-year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning.


Assuntos
Bactérias/classificação , Biodiversidade , Ecossistema , Filogenia , Água do Mar/microbiologia , DNA Bacteriano/genética , Mar Mediterrâneo , Modelos Genéticos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Microbiologia da Água
14.
Microb Ecol ; 70(2): 473-83, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25851445

RESUMO

To test if different niches for potential nitrifiers exist in estuarine systems, we assessed by pyrosequencing the diversity of archaeal gene transcript markers for taxonomy (16S ribosomal RNA (rRNA)) during an entire year along a salinity gradient in surface waters of the Charente estuary (Atlantic coast, France). We further investigated the potential for estuarine prokaryotes to oxidize ammonia and hydrolyze urea by quantifying thaumarchaeal amoA and ureC and bacterial amoA transcripts. Our results showed a succession of different nitrifiers from river to sea with bacterial amoA transcripts dominating in the freshwater station while archaeal transcripts were predominant in the marine station. The 16S rRNA sequence analysis revealed that Thaumarchaeota marine group I (MGI) were the most abundant overall but other archaeal groups like Methanosaeta were also potentially active in winter (December-March) and Euryarchaeota marine group II (MGII) were dominant in seawater in summer (April-August). Each station also contained different Thaumarchaeota MGI phylogenetic clusters, and the clusters' microdiversity was associated to specific environmental conditions suggesting the presence of ecotypes adapted to distinct ecological niches. The amoA and ureC transcript dynamics further indicated that some of the Thaumarchaeota MGI subclusters were involved in ammonia oxidation through the hydrolysis of urea. Our findings show that ammonia-oxidizing Archaea and Bacteria were adapted to contrasted conditions and that the Thaumarchaeota MGI diversity probably corresponds to distinct metabolisms or life strategies.


Assuntos
Archaea/genética , Archaea/classificação , Bactérias/classificação , Bactérias/genética , DNA Ribossômico , Estuários , Água Doce/microbiologia , Filogenia , Rios/microbiologia , Água do Mar/microbiologia
15.
Proc Natl Acad Sci U S A ; 109(43): 17633-8, 2012 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-23045668

RESUMO

The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.


Assuntos
Bactérias/isolamento & purificação , Geografia , Biologia Marinha , Microbiologia da Água , Regiões Antárticas , Regiões Árticas , Bactérias/classificação , Bactérias/genética , Filogenia , RNA Ribossômico/genética
16.
Mol Ecol Resour ; 24(3): e13923, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38189173

RESUMO

The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.


Assuntos
Bactérias , Lagos , Ferro/metabolismo , Sulfetos/metabolismo , Enxofre/metabolismo , Genômica
17.
Environ Microbiol ; 15(11): 3008-19, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-24118834

RESUMO

In this study, we pursue unravelling the bacterial communities of 26 sponges, belonging to several taxonomical orders, and comprising low microbial abundance (LMA) and high microbial abundance (HMA) representatives. Particularly, we searched for species-specific bacteria, which could be considered as symbionts. To reduce temporal and spatial environmentally caused differences between host species, we sampled all the sponge species present in an isolated small rocky area in a single dive. The bacterial communities identified by pyrosequencing the 16S rRNA gene showed that all HMA species clustered separated from LMA sponges and seawater. HMA sponges often had highest diversity, but some LMA sponges had also very diverse bacterial communities. Network analyses indicated that no core bacterial community seemed to exist for the studied sponges, not even for such a space and time-restricted sampling. Most sequences, particularly the most abundant ones in each species, were species-specific for both HMA and LMA sponges. The bacterial sequences retrieved from LMA sponges, despite being phylogenetically more similar to seawater, did not represent transient seawater bacteria. We conclude that sponge bacterial communities depend more on the host affiliation to the HMA or LMA groups than on host phylogeny.


Assuntos
Bactérias/classificação , Bactérias/genética , Poríferos/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Animais , Sequência de Bases , Biodiversidade , Chloroflexi/classificação , Chloroflexi/genética , Chloroflexi/isolamento & purificação , DNA Bacteriano/genética , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Consórcios Microbianos , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Análise de Sequência de DNA , Especificidade da Espécie , Simbiose
18.
Anim Microbiome ; 5(1): 30, 2023 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-37264469

RESUMO

BACKGROUND: High latitude seeps are dominated by Oligobrachia siboglinid worms. Since these worms are often the sole chemosymbiotrophic taxon present (they host chemosynthetic bacteria within the trophosome organ in their trunk region), a key question in the study of high latitude seep ecology has been whether they harbor methanotrophic symbionts. This debate has manifested due to the mismatch between stable carbon isotope signatures of the worms (lower than -50‰ and usually indicative of methanotrophic symbioses) and the lack of molecular or microscopic evidence for methanotrophic symbionts. Two hypotheses have circulated to explain this paradox: (1) the uptake of sediment carbon compounds with depleted δC13 values from the seep environment, and (2) a small, but significant and difficult to detect population of methanotrophic symbionts. We conducted 16S rRNA amplicon sequencing of the V3-V4 regions on two species of northern seep Oligobrachia (Oligobrachia webbi and Oligobrachia sp. CPL-clade), from four different high latitude sites, to investigate the latter hypothesis. We also visually checked the worms' symbiotic bacteria within the symbiont-hosting organ, the trophosome, through transmission electron microscopy. RESULTS: The vast majority of the obtained reads corresponded to sulfide-oxidizers and only a very small proportion of the reads pertained to methane-oxidizers, which suggests a lack of methanotrophic symbionts. A number of sulfur oxidizing bacterial strains were recovered from the different worms, however, host individuals tended to possess a single strain, or sometimes two closely-related strains. However, strains did not correspond specifically with either of the two Oligobrachia species we investigated. Water depth could play a role in determining local sediment bacterial communities that were opportunistically taken up by the worms. Bacteria were abundant in non-trophosome (and thereby symbiont-free) tissue and are likely epibiotic or tube bacterial communities. CONCLUSIONS: The absence of methanotrophic bacterial sequences in the trophosome of Arctic and north Atlantic seep Oligobrachia likely indicates a lack of methanotrophic symbionts in these worms, which suggests that nutrition is sulfur-based. This is turn implies that sediment carbon uptake is responsible for the low δ13C values of these animals. Furthermore, endosymbiotic partners could be locally determined, and possibly only represent a fraction of all bacterial sequences obtained from tissues of these (and other) species of frenulates.

20.
Sci Rep ; 13(1): 11589, 2023 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-37463961

RESUMO

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.


Assuntos
Antozoários , Calcinose , Animais , Antozoários/fisiologia , Recifes de Corais , Regulação para Cima , Concentração de Íons de Hidrogênio , Carbonatos/metabolismo , Carbonato de Cálcio/metabolismo , Calcificação Fisiológica/fisiologia , Água do Mar
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