Biology subjects

Jacquemin, N.

Publications and source records attributed to Jacquemin, N..

4 recordsLinked to original sources

bioRxiv2025

High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules

Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most microbial taxa remain uncultured, hindering research and biotechnological applications. Isolating environmental anaerobes using traditional methods is particularly cumbersome and low throughput. Here, we present a novel, high-throughput approach for the cultivation and isolation of anaerobes, which involves trapping and growing single microbes within selectively permeable hydrogel capsules followed by fluorescence-activated cell sorting to distribute compartmentalized isolates into liquid medium for further growth. We show that diverse anaerobes can grow within capsules and that slower-growing ones (e.g. methanogens) can be enriched with this platform. We also applied this approach to isolate anaerobes from soil, including strains of the sulfate-reducing bacteria Desulfovibrio desulfuricans and Nitratidesulfovibrio vulgaris. Overall, this work introduces a robust, high-throughput alternative to traditional techniques for isolating environmental anaerobes and expands the emerging set of microfluidics-based tools for the cultivation of novel taxa.

microbiology↗

bioRxiv2024

Impact of redox fluctuations on the spatial distribution of the microbial community in a forest soil: A lysimeter experiment

Climate change is expected to affect precipitation intensity and soil temperature and indirectly impact the release of leached dissolved organic carbon (LDOC) from leaf litter during the early stages of its decomposition, which could affect the health and function of forest soil ecosystem. Here, we experimentally investigate the spatially-explicit impact of LDOC on the forest soil microbiome and the associated biogeochemical processes. Homogenized soil columns were subjected to realistic artificial precipitation for 3 months with the initial level of LDOC adjusted by the number of times the leaf litter was flushed in preparation for the experiment. Hydrological and geochemical parameters (redox potential, pH, dissolved oxygen, soil moisture, matric potential, chemical speciation) were measured continuously as a function of time and depth. The same initial microbial community developed into distinct communities under different LDOC and above and below the water table. The LDOC from leaf litter increased the availability of carbon (C) and nitrogen (N) in porewater four-fold and two-fold respectively in the first two weeks. This resulted in the expansion of the anoxic zone above the water table and a decrease in the soil microbial metabolic potential for cellulolysis and N2 fixation in unsaturated soil along with an increase of soil microbial metabolic potential for fermentation at all depths. Finally, increased LDOC decreased the stability, phylogenetic diversity, and complexity of the soil microbiome, limiting its functional diversity. Thus, management of leaf litter should receive more attention due to its indirect role in the impact of climate change on the soil microbiome. HighlightsO_LIDecreased microbiome diversity and stability due to enhanced leaf litter leaching C_LIO_LIExpansion of the anoxic zone into the unsaturated zone due to increased organic carbon supply C_LIO_LIDecreased soil microbiome metabolic potential for cellulolysis and N2 fixation in unsaturated soil C_LIO_LIDepth-dependent response of microbial community to increased organic carbon availability C_LIO_LIImplications for soil response to climate change C_LI

microbiology↗

bioRxiv2023

The Effect of Growth Substrate Availability on Anaerobic Arsenic Methylation by Paraclostridium bifermentans strain EML

Microbial arsenic methylation is established as a detoxification process under aerobic conditions (converting arsenite to monomethylated arsenate) but proposed to be a microbial warfare strategy under anoxic conditions due to the toxicity of its main product monomethylarsonous acid (MMAs(III)). Here, we leveraged a paddy soil-derived anaerobic arsenic methylator, Paraclostridium bifermentans strain EML, to gain insights into this process. Strain EML was inoculated into a series of media involving systematic dilutions of Reinforced Clostridial Broth (RCB) with 25 M arsenite to assess the impact of growth substrate concentration on arsenic methylation. Growth curves evidenced the sensitivity of strain EML to arsenite, and As speciation analysis revealed the production of MMAs(III). Concentrations of MMAs(III) and arsenic methylation gene (arsM) transcription were found to be positively correlated with the RCB dilution, suggesting that substrate limitation enhances arsM gene expression and associated anaerobic arsenic methylation. We propose that growth substrate competition between microorganisms may also lead to an increase in anaerobic As methylation. This hypothesis was further evaluated in an anaerobic co-couture mode of strain EML with either wild-type Escherichia coli K-12 MG1655 (WT) or E. coli expressing the MMAs(III)-resistance gene (arsP), (ArsP E. coli). We found increased MMAs(III) production in the presence of E. coli than its absence and growth inhibition of WT E. coli to a greater extent than ArsP E. coli, presumably due to MMAs(III) produced by strain EML. Taken together, our findings point to an ecological role for anaerobic arsenic methylation, highlighting the role of microbe-microbe competition/interaction in this process. IMPORTANCEAnaerobic arsenic methylation is enhanced in rice paddy soils under flooding conditions than that under drying conditions, leading to increased methylated arsenic accumulation in rice grains. Unlike the known detoxification role for aerobic arsenic methylation, the ecological role of anaerobic arsenic methylation remains elusive and is proposed to be an antibiotic-producing process involving in microbial warfare. In this study, we interrogated a rice paddy soil-derived anaerobic arsenic-methylating bacterium (Paraclostridium bifermentans strain EML) to investigate the effect of growth substrate limitation on arsenic methylation by strain EML in the context of the microbial warfare hypothesis. We provide direct evidence for the role of growth substrate competition in anaerobic arsenic methylation by strain EML. Furthermore, we evidence a feedback loop, by which a bacterium resistant to MMAs(III) enhances its production, presumably through enhanced arsM expression resulting from substrate limitation. Our work uncovers complex interactions between an anaerobic arsenic methylator and potential competitors.

microbiology↗

bioRxiv2022

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harboring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

microbiology↗