Biology subjects

Vuillemin, A.

Publications and source records attributed to Vuillemin, A..

7 recordsLinked to original sources

bioRxiv2025

Microbial Diversity and Community Shifts in a Petroleum Reservoir under Production: Effects of Water Breakthrough and Anthropogenic Alterations

Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production processes like water injection, which introduces external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough in the Edvard Grieg oil reservoir offshore Norway using 16S rRNA gene and metagenomic sequencing. We found clear regional heterogeneity in community composition, with low diversity dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while well A07 showed a distinct microbial signature. The dominant genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not due to widespread replacement by injected microbes, but via the increase of sulfate-reducing bacteria. Metagenomic data supported these observations and suggested rapid microbial transport between injection water and the water separator. These findings support the use of microbial signatures as cost-effective tools for monitoring oil reservoir processes and integrity.

microbiology↗

bioRxiv2025

Microbial Worlds Apart: Distinct Communities in Crude Oil and Production Waters

Genomic analyses of microbial community composition are used to improve oil reservoir engineering and monitor reservoir dynamics. Given the challenges of extracting nucleic acids from oil, production water samples are often used as proxies from which to infer microbial community information from oil reservoirs. We employed 16S rRNA gene amplicon and metagenomic sequencing on samples of crude oil and production water from four North Sea oil fields. Taxonomic profiling revealed differences in microbial compositions and functions between production water and crude oil. Production water was more homogeneous, less diverse, harboured taxa associated with conditions non-native to the reservoir (e.g., seawater), and exhibited evidence of contact with atmospheric oxygen, most likely from passing through the water separators. Conversely, crude oil samples harboured microbial taxa typically associated with oil reservoirs. Despite long-term production and, in some cases, re-injection of production waters, the putative native microbial communities were still present in the oil. These findings demonstrate that crude oil samples are much more representative of oil reservoir microbiomes than their production water proxies.

microbiology↗

bioRxiv2022

Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia

Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes and stable-isotope probing incubations from the water column and subseafloor of the Benguela Upwelling System. Taxonomic assemblages and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity towards mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification prevails over canonical denitrification when Namibian coastal waters are ventilated during austral winter.

microbiology↗

bioRxiv2020

Genome evolution in bacteria isolated from million-year-old subseafloor sediments

Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes has been unknown. Here we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve by point mutation, with a relatively low rate of homologous recombination and a high frequency of pseudogenes. Ratios of synonymous to non-synonymous mutation rates correlate with the accumulation of pseudogenes, consistent with a dominant role for genetic drift in the subseafloor strains, but not in type strains of Thalassospira isolated from the surface world. Our findings demonstrate that the long term physical isolation of these bacteria, in the absence of recombination, has resulted in clonal populations that evolve consistent with Mullers Ratchet, whereby reduced access to novel genetic material from neighbors has resulted in fixation of new mutations that accumulate in genomes over millions of years. Significance statementThe nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor is unknown. Subseafloor populations have ultra-slow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting the genome evolution of these bacteria has been dominated by genetic drift, whereby under long-term physical isolation in small population sizes, and in the absence of homologous recombination, newly acquired mutations accumulate in the genomes of clonal populations over millions of years.

microbiology↗

bioRxiv2020

Chloroflexi persisting for millions of years in oxic and anoxic deep-sea clay

Chloroflexi are widespread in energy-limited subseafloor sediments, but how Chloroflexi respond to subseafloor energy limitation under oxic and anoxic conditions is poorly understood. Here, we characterize the diversity, abundance, activity, and metabolic potential of Chloroflexi in oxic and anoxic abyssal clay from three deep-sea cores covering up to 15 million years of sediment deposition, where Chloroflexi are a major component of the community throughout the entire cored sequence at all sites. In oxic red clay at two different sites, Chloroflexi communities exhibit net death over both 10-15 million year cored sequences, and gene expression was below detection despite the availability of oxygen as a high energy electron acceptor, indicating a reduced level of activity. In contrast at the anoxic site, Chloroflexi abundance and gene expression increase below the seafloor and peak in 2 to 3 million year old sediment. The anaerobic subseafloor Chloroflexi exhibited a homoacetogenic metabolism and potential for energetically efficient intracellular H2 recycling that have been proposed to confer a fitness advantage in energy-limited subseafloor habitats. Our findings indicate that the expression of this energy efficient metabolism in Chloroflexi coincides with net growth over million year timescales in deep-sea anoxic clay. Significance statementChloroflexi are widespread in energy-limited subseafloor sediments, both in oxic subseafloor sediments that are energetically limited by the availability of electron donors (organic matter) and in anoxic sediments that are energetically limited by the availability of high energy terminal electron acceptors. How Chloroflexi respond to these different forms of energy limitation over long time scales is poorly understood. We present new data that demonstrates how key differences in metabolism are manifested in different communities of aerobic and anaerobic Chloroflexi subsisting over millions of years in oxic and anoxic deep-sea clay. These data provide new insights into how certain Chloroflexi respond to different types of long-term energy limitation.

microbiology↗

bioRxiv2020

Anaerobic metabolism of Foraminifera thriving below the seafloor

Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. The relative abundance of Foraminifera gene expression in anoxic sediment depths increased an order of magnitude, which was confirmed in a ten-day incubation experiment where the development of anoxia coincided with a 27-fold increase in the relative abundance of Foraminifera protein encoding transcripts. This indicates that many Foraminifera were not only surviving, but thriving under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, dissimilatory nitrate reduction, fumarate reduction, and dephosphorylation of creatine phosphate. This was co-expressed alongside genes involved in production of reticulopodia, phagocytosis, calcification, and clathrin-mediated-endocytosis (CME). Thus, Foraminifera may use CME under anoxic conditions to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These mechanisms help explain how some Foraminifera can thrive under anoxia, which would help to explain their ecological success documented in the fossil record since the Cambrian period more than 500 million years ago.

microbiology↗

bioRxiv2019

Lokiarchaeon exhibits homoacetogenesis

The proposed Asgard superphylum of Archaea comprises the closest archaeal relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Genomes of the Asgard candidate Phylum Candidatus Lokiarchaeota [Lokiarchaeon] suggest an acetogenic H2 -dependent lifestyle5 and mixotrophic capabilities6. However, data on the activity of Lokiarchaeon are currently lacking, and the ecology of the host cell that acquired the mitochondrion is debated4,7. Here, we show that in anoxic marine sediments underlying highly productive waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth below the seafloor, and was significantly different across a redox gradient spanning hypoxic to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was consistent with the expression of Lokiarchaeon genes involved in transport and fermentation of sugars and amino acids. Remarkably, several Asgard populations were more enriched with 13C-dEPS compared to the community average, indicating a preference for dEPS as a growth substrate. The qSIP and gene expression data indicate a metabolism of \"Candidatus Lokiarchaeota\" similar to that of sugar fermenting homoacetogenic bacteria8, namely that Lokiarchaeon can couple fermentative H2 production from organic substrates with electron bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access a wide range of substrates and relatively high ATP gain during acetogenic sugar fermentation8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy limited settings.

microbiology↗