Biology subjects

Dechesne, A.

Publications and source records attributed to Dechesne, A..

8 recordsLinked to original sources

bioRxiv2026

Viscoelastic flow-integrated Raman spectroscopy platform

We demonstrate the first viscoelastic-based flow-integrated Raman spectroscopy (FIRS) platform using spontaneous Raman spectroscopy with a simplified fluidic design that precisely controls particle transit speed and predicts arrival time to the Raman interrogation region, together with time synchronized triggered acquisition. Using viscoelastic flow focusing and optical detection of velocity for hardware triggering, the setup enables high-throughput, real-time Raman analysis of particles in continuous flow. The system operates with a single pressure pump, two sets of fiber-coupled lasers and detectors, and a microcapillary precisely aligned in a projection micro-stereolithography 3D-printed mount, and ensures detection stability across various flow rates. The demonstrated platform is modular and scalable. Detection rates of up to 80 cells per minute were achieved and dinoflagellate Alexandrium ostenfeldii cultures were analyzed. The integrated optical trigger mechanism supports future extensions such as cell sorting or additional analyses. A user-friendly graphical interface provides full control of fluidics, spectroscopy, and real-time monitoring, making this compact, low-cost FIRS platform accessible across a wide range of laboratory environments.

molecular biology↗

bioRxiv2025

An integrated meta-omics approach for identifying candidate organic micropollutant degraders in complex microbial communities

Biotransformation is a significant determinant of the fate of organic micropollutants (OMPs) in natural and engineered environments; yet identifying OMP-transforming microorganisms remains challenging. Integrating metagenomics and metatranscriptomics, we searched for correlations between the biotransformation of ammonia and atenolol and the transcriptional activity of metagenome-assembled genomes (MAGs) across five nitrifier-rich cultures in batch experiments. The biotransformation of ammonia correlated with the activity of ammonia-oxidizing bacterium Nitrosomonas europaea but not with the activity of other bacteria, including several ammonia oxidizers. Additionally, the biotransformation of ammonia correlated with the transcript abundance of the ammonia monooxygenase (AMO) expressed by N. europaea but not with the transcript abundance of AMO at the community level. Atenolol biotransformation correlated with the activity of four MAGs representing three heterotrophic genera: Terrimonas, Flavobacterium, and Zeimonas. It did not correlate with the total transcript abundance of any member of a comprehensive set of amidohydrolases, which are predicted to transform this drug. By contrast, it correlated with the expression of the amidohydrolase asparagine synthase (AsnB) identified in the Terrimonas and Flavobacterium MAGs. In summary, we present a novel association-based method for elucidating biotransformation processes robust to variability in enzyme reaction kinetics with implications for OMP control. SynopsisThe fate of organic micropollutants in natural and engineered systems depends greatly on biotransformation by microbes. This study proposes an approach for identifying these microbes with implications for the study and control of organic micropollutant removal. ABSTRACT GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/639455v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@17c7f1org.highwire.dtl.DTLVardef@147b9eforg.highwire.dtl.DTLVardef@1fffc9eorg.highwire.dtl.DTLVardef@121fd96_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Plasmid Permissiveness of Wastewater Microbiomes can be Predicted from 16S rDNA sequences by Machine Learning

Wastewater Treatment Plants (WWTPs) contain a diverse microbial community with high cell density. They constantly receive antimicrobial residues and resistant strains and, therefore, may offer conditions for the Horizontal Gene Transfer (HGT) of antimicrobial resistance determinants, transmitting clinically important genes between, e.g., enteric and environmental bacteria and vice versa. Despite the clinical importance, tools for predicting HGT are still under-developed. In this study, we examined to which extent microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e., the ability of cells to receive a plasmid through conjugation, for microbial communities in the water cycle, using data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, translating to the range of hosts a plasmid is able to transfer to, for three broad host-range resistance plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.45 for pB10 (95% CI: 0.42-0.52), 0.42 for pKJK5 (0.95% CI: 0.38-0.45) and 0.52 for RP4 (0.95% CI:0.45-0.55) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite these being broad host-range plasmids. Our results provide a framework that contributes to assessing the risk of AMR pollution in wastewater systems. The predictive tool is available as a an application under https://github.com/DaneshMoradigaravand/PlasmidPerm.

bioinformatics↗

bioRxiv2020

Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage

Integrated and quantitative observations of antibiotic resistance genes (ARGs) in urban water systems (UWSs) are lacking. We sampled three UWSs for clinically important extended spectrum {beta}-lactamase (ESBL) and carbapenemase (CP) genes, mobile genetic elements and microbial communities. Sewage - especially from hospitals - carried substantial loads of ESBL and CP genes (106 - 107 per person equivalent), but those loads progressively declined along the UWS, resulting in minimal emissions (101 - 104 copies per person equivalent). Removal was primarily during sewage conveyance (65% {+/-} 36%) rather than within sewage treatment (34% {+/-} 23%). The ARGs clustered in groups based on their persistence; less persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while more persistent groups appear horizontally transferred as they correlated with mobile genetic elements. This first documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based ARG surveillance.

ecology↗

bioRxiv2020

Evolutionary ecology of natural comammox Nitrospira populations

Microbes commonly exists in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interactions and evolution has increased in the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. They showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interactions and evolution in complex microbial communities, and sheds light on the environmental dependency of evolutionary processes.

microbiology↗

bioRxiv2019

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Pseudomonas and Enterobacteriaceae, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in a high-throughput way without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognized potential to maintain plasmids for long-term community-wide access.

ecology↗

bioRxiv2019

Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira

Nitrification was long thought to consist in the stepwise oxidation of ammonia to nitrite and of nitrite to nitrate by ammonia oxidizing and nitrite oxidizing microorganisms, respectively. Recently, single microorganisms capable of complete ammonia to nitrate oxidation (comammox) were identified in the Nitrospira genus. This genus, previously considered to only contain canonical nitrite oxidizers is diverse and has a broad environmental distribution. Yet, a global insight into the abundance, niche preference, and genomic diversity of Nitrospira is missing. Here, we established the largest Nitrospira genome database to date, revealing 68 putative species, most without cultivated representatives. We performed a global survey through read recruitment of metagenomic data from various environments against this database that identified that environmental filtering structures species distribution, without large scale biogeographical signal. The ecological success of comammox Nitrospira is evident as they outnumber and are more diverse than canonical Nitrospira in communities from all environments but wastewater treatment plants. We detect a phylogenetic signal in Nitrospira species habitat preference, that is strongest for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex with subclades achieving rapid niche divergence via horizontal transfer of genes, including that encoding the hydroxylamine oxidoreductase, one of the key enzymes involved in nitrification.

microbiology↗

bioRxiv2017

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of Comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria ({beta}-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.\n\nComammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to {beta}-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to {beta}-AOB.\n\n{beta}-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from {beta}-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from {beta}-AOB to comammox Nitrospira is predicted - followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.\n\nSignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

microbiology↗