Biology subjects

Villemur, R.

Publications and source records attributed to Villemur, R..

8 recordsLinked to original sources

bioRxiv2025

The profiles of mammals, birds and fish in twelve water bodies on the Island of Montreal by mitochondrial DNA: detection of invasive animals and meat and fish waste

The Island of Montreal is composed of a variety of environments, such as undeveloped natural areas, urban parks, and dense residential areas. These environments are home to several types of surface waters, such as ponds, marshes, lakes, streams, and rivers, where some wild animals have adapted. Among them are exotic and invasive animals, which could displace natural animals or endanger people through unwanted interactions. The Montreal Urban Community (MUC) wishes to assess the extent of the presence of exotic or invasive animals in waterbodies on the Island of Montreal to coordinate mitigation measures. Here, I present animal profiles, primarily mammals, birds, and fish, from twelve waterbodies on the Island of Montreal using amplicon sequencing of mitochondrial DNA from environmental DNA. Water samples were collected, and total DNA was extracted. PCR amplifications of a portion of the mitochondrial 16S ribosomal RNA genome were performed with primers designed to primarily target mammals, fish, and birds. After sequencing, the animal lineages and their proportions were determined. Our results showed that invasive animals, primarily fish such as pumpkinseed, common carp or brown bullhead, were detected in high proportions in five water bodies. However, I did not detect any exotic animals. I also detect significant proportions of sequences affiliated with bovine, porcine and several marine fish species, which was unexpected as these animals are not living on the Island of Montreal. Given the commercial or industrial activities surrounding the water bodies, sequences of these unexpected animals are likely related to the release of meat or seafood waste into the water bodies. Our molecular approach is effective for assessing the animal profiles of water bodies. However, caution should be exercised when interpreting the presence of animal waste.

ecology↗

bioRxiv2025

Monitoring mammals, birds and fish during summer 2022 at the outlet of an agricultural stream by mtDNA

Fecal contamination of surface waters poses a potential risk to public and environmental health but can also impact the local economy and recreational activities. Determining its source could facilitate mitigation of the contamination. Fecal contamination can originate from several animals, particularly in areas where urban and agricultural activities overlap. In previous work, we developed a molecular approach to detect the presence of mammals, fish, and birds by sequencing mitochondrial DNA (mtDNA) amplicons derived from environmental DNA. In this report, we monitored the outlet of a stream located in an agricultural area for 16 weeks to detect the presence of mammals, including humans, livestock, domestic and wild mammals, birds and fish. We were able to detect mtDNA sequences affiliated to at least 73 animal lineages. Sequences affiliated to fish were proportionally the most abundant, followed by those affiliated to mammals. We observed increases in bovine and human mtDNA sequences after episodes of high flow in the watershed, suggesting that soil runoff to surface waters carried organic matter (e.g., manure, feces, wastewater) from these animals. Our approach could provide crucial information for farmers to mitigate fecal pollution generated by agricultural activities.

ecology↗

bioRxiv2025

Influence of carbon-to-nitrogen ratio on the denitrifying activities of a methanol-fed, marine recirculating denitrification reactor, and the evolution of the bacteria community during the operating process.

BackgroundCarbon-to-nitrogen ratio (C/N) is an essential parameter known to influence both the function and the activity of microbial communities in bioprocesses. The right balance between the contribution of each of these resources are essential for sustainable and cost-efficiency bioprocess. Here we aimed to assess the influence of C/N (here methanol and nitrate) on the performance of a recirculating denitrifying reactor for 31 weeks under marine conditions. We also monitored the evolution of its microbial community during the operating conditions. MethodologyA 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N over 31 weeks under anoxic conditions. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO2 production) throughout the operating conditions. Evolution of the bacterial community in the biofilm during the operating conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes of representative conditions were performed to derive (1) the relative gene expression profiles of Methylophaga nitratireducenticrescens strain GP59, the main denitrifier, and (2) the functional diversity of the biofilm. ResultsChanges in C/N did not impact the denitrifying activities of the recirculating reactor but did impact the carbon dynamics. Throughout the operating time, nitrite and N2 O appeared transiently, and ammonium was not observed. The bacterial community in the reactor increased in diversity as the biofilm aged, especially in heterotrophic bacteria, at the expense of methylotrophic bacteria. The functional diversity suggests that heterotrophs could use formaldehyde, which may have been released by methylotrophs in the biofilm, as energy and carbon source. The relative expression profiles of strain GP59 in the biofilm is distinct of those of GP59 planktonic pure cultures, and that the expression of several riboswitches and xoxF would be involved in such differences. ConclusionsWhen the biofilm community is well established in the reactor, it can sustain changes in C/N with limited impact on the denitrification performance. Increase in the proportion of heterotrophs would allow the reactor to be more flexible for carbon sources. Such knowledge can be useful in the optimisation of denitrification process.

microbiology↗

bioRxiv2021

Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions

Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 were the principal bacteria involved in the denitrifying activities of a methanol-fed, fluidized marine denitrification reactor. We believe that a tight relationship has developed between these two strains to achieve denitrification in the reactor under marine conditions. To characterize the potential synergy between strain JAM1 and strain NL23, we compared some of their physiological traits, and performed co-cultures. Pure cultures of strain JAM1 had a readiness to reduce nitrate (NO3-) with no lag phase for growth contrary to pure cultures of strain NL23, which has a 2-3 days lag phase before NO3- starts to be consumed and growth to occur. Compared to strain NL23, strain JAM1 has a higher max for growth and higher specific NO3- reduction rates. Antagonist assays showed no sign of exclusion by both strains. Planktonic co-cultures could only be performed on low NaCl concentrations for strain NL23 to survive. Denitrification rates were twice higher in the planktonic co-cultures than those measured in strain NL23 pure cultures. Biofilm co-cultures were performed for several months in a 500-mL bioreactor filled with Bioflow supports, and operated under fed-batch mode with increasing concentrations of NaCl for strain NL23 to acclimate to marine conditions. Under these conditions, the biofilm co-cultures showed sustained denitrifying activities and surface colonization by both strains. Increase in ectoine concentrations produced by strain JAM1 was observed in the biofilm with increasing NaCl concentrations. These results illustrate the capacity of both strains to act together in performing denitrification under marine environments. Although strain JAM1 did not contribute in better specific denitrifying activities in the biofilm co-cultures, its presence was essential for strain NL23 to survive in a medium with NaCl concentrations > 1.0%. We believe that ectoine is an important factor for the survival of strain NL23 in these environments.

microbiology↗

bioRxiv2019

Liquid biopsies for omics-based analysis in sentinel mussels.

Liquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in sentinel mussels to assess the quality of marine ecosystems.

ecology↗

bioRxiv2019

Impact of NaCl, nitrate and temperature on the microbial community of a methanol-fed, denitrifying marine biofilm

BackgroundThe biofilm of a continuous, methanol-fed, fluidized denitrification system that treated a marine effluent at the Montreal Biodome is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans NL23 and Methylophaga nitratireducenticrescens JAM1 are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm taken from the denitrification system was cultured at laboratory scale in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific physico-chemical parameters. We previously showed that the seawater formulation and the NaCl concentrations had a strong impact on the H. nitrativorans NL23 population, with its displacement by a new denitrifier, M. nitratireducenticrescens GP59. Here, we report the impact of these cultures conditions on the dynamics of the overall microbial community of the denitrifying biofilm.\n\nMethodsThe original biofilm (OB) taken from the denitrification system was acclimated for five weeks in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate concentrations and temperatures. The OB was also acclimated to the commercial Instant Ocean seawater medium (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA amplicon metagenome sequencing. Culture-dependent approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of some of the biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans NL23 and M. nitratireducentricrescens GP59 cultivated under denitrifying conditions.\n\nResultsThe 16S metagenomic data revealed very high proportions of M. nitratireducenticrescens in the biofilm cultures. H. nitrativorans NL23 was found in high proportion in the OB, both was absent in the biofilm cultures with 2.75% NaCl in the ASW medium. It was found however in low proportions in the biofilm cultures with 0 to 1% NaCl in the ASW medium and in the IO biofilm cultures. Emergence of Marinicella spp. occurred in these biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes in strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures.\n\nConclusionsThese results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes in strain GP59 and strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm compared to the planktonic pure cultures. Other denitrifying heterotrophic bacteria are present in low proportions in the biofilm, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments.

microbiology↗

bioRxiv2019

Impact of physico-chemical parameters on the denitrification and the co-occurrence of Methylophaga nitratireducenticrescens and Hyphomicrobium nitrativorans in a methanol-fed marine denitrifying biofilm

BackgroundThe biofilm of a continuous, methanol-fed, fluidized denitrification system that treated a marine effluent is composed of multi-species microorganisms, among which Hyphomicrobium nitrativorans NL23 and Methylophaga nitratireducenticrescens JAM1 are the principal bacteria involved in the denitrifying activities. This biofilm can be cultured at laboratory-scale under batch mode conditions without losing the denitrifying activities. Here, we report the capacity of the denitrifying biofilm to sustain changes to specific physico-chemical parameters, and the impact of these changes on the denitrification performance and the co-occurrence of H. nitrativorans and M. nitratireducenticrescens.\n\nMethodsThe original biofilm (OB) taken from the denitrification system was acclimated to an artificial seawater (ASW) medium under anoxic conditions to generate the Reference biofilm cultures (300 mg-NO3--N/L, 23{degrees}C). In the first set of assays, the Reference biofilm cultures were subjected to short exposures (1-3 days) of a range of NaCl, methanol, nitrate (NO3-) and nitrite (NO2-) concentrations, and to different pHs and temperatures. In the second set of assays, the OB was acclimated in an ASW-modified medium for five weeks i) to a range of NaCl concentrations (0% to 8%), ii) to four combinations of NO3- concentrations and temperatures, iii) to NO2-, and iv) under oxic conditions. Finally, the OB was acclimated to the commercial Instant Ocean (IO) medium. The growth of the biofilm and the dynamics of NO3- and NO2- were determined. The levels of M. nitratireducenticrescens and H. nitrativorans were measured by qPCR in these cultures.\n\nResultsThe denitrifying capacities of the OB was preserved in the Reference biofilm cultures. In these cultures, however, H. nitrativorans NL23 decreased by three orders of magnitude in concentration with the occurrence of the same magnitude of a new denitrifying bacterial strain (M. nitratireducenticrescens GP59). Results from the first set of assays showed that the Reference biofilm cultures can sustain denitrifying activities in most of the tested conditions. Inhibition occurred when these biofilm cultures were exposed at pH 10 or with 1.5% methanol. Results from the second set of assays showed the persistence of H. nitrativorans NL23 in the biofilm cultures acclimated to low NaCl concentrations (0% to 1.0%). Poor biofilm development occurred in biofilm cultures acclimated to 5% and 8% NaCl. Finally, high proportion of H. nitrativorans NL23 was found in the IO biofilm cultures.\n\nConclusionsThese results confirm the plasticity of the marine methylotrophic denitrifying biofilm in adapting to different conditions. The NaCl concentration is a crucial factor in the dynamics of H. nitrativorans NL23, for which growth was impaired above 1% NaCl in the ASW-based biofilm cultures in favor of M. nitratireducenticrescens GP59. This study contributes to the understanding on the population dynamics of co-occurring bacteria performing denitrifying activities in biofilm under seawater environment. This could benefit in the development of optimal denitrifying bioprocess under marine conditions.

microbiology↗

bioRxiv2017

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate (NO3-) to nitrite (NO2-), which accumulates in the medium. These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (NarGHJI). M. nitratireducenticrescens strain JAM1 also contains gene clusters encoding two putative nitric oxide reductase (NO) reductases and one putative nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. In this study, we show that strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory copper-(NirK) or cytochrome cd1-type (NirS) NO2- reductase, NO3--amended strain JAM1 cultures produce N2O, representing up to 6% of the N-input. NO2- was shown to be the key intermediate of this production process. In NO3-amended cultures, we analyzed denitrification genes in succession of net N2O-production and -consumption phases at the gene expression level. These phases were found to correlate with changes in the expression levels of the NO reductase gene cnorB1 and nnrS, which indicated NO production in the cultures.\n\nImportanceBy showing that all the three denitrification reductases are active, this demonstrates that Methylophaga nitratireducenticrescens JAM1 is one of many bacteria species that maintain genes associated primarily with denitrification, but not necessarily related to the maintenance of the entire pathway. The reason to maintain such incomplete pathway could be related to the specific role of strain JAM1 in the denitrifying biofilm of a denitrification reactor from which it originates. The small production of N2O via NO in strain JAM1 did not involve Nar contrary to what was demonstrated in Escherichia coli. M. nitratireducenticrescens JAM1 is the only reported Methylophaga species that has the capacity to grow under anoxic conditions by using NO3- and N2O as sole electron acceptors for its growth. It is also one of a few marine methylotrophs that is studied at the physiological and genetic levels in relation to its capacity to perform denitrifying activities.

microbiology↗