Biology subjects

Dumont, M. G.

Publications and source records attributed to Dumont, M. G..

3 recordsLinked to original sources

bioRxiv2023

Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing and metagenomics

BackgroundIn this study, we aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil, by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced. ResultsAfter incubations, an increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) are highly abundant after two days of incubation with antibiotics. Several Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. On the other hand, only two ARGs from the unbinned-assembled light fractions were identified. ConclusionsThe results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil, and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.

microbiology↗

bioRxiv2020

Disproportionate CH4 sink strength from an endemic, sub-alpine Australian soil microbial community

Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil-vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil-vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5-cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49-93 mg CO2 m-2 h-1. Forest soils were strong net sinks for CH4 at rates up to -413 {micro}g CH4 m-2 h-1. Grassland soils varied with some soils acting as sources and some as sinks, but overall averaged -97 {micro}g CH4 m-2 h-1. Bog soils were net sources of CH4 (+340 {micro}g CH4 m-2 h-1). Methanotrophs were dominated by USC in forest and grassland soils, and Candidatus Methylomirabilis sp. in the bog soils. Methylocystis were also detected at relatively low abundance. The potential disproportionately large contribution of these ecosystems to global CH4 oxidation, and poorly understood microbial community regulating it, highlight our dependence on soil ecosystem services in remote locations can be driven by a unique population of soil microbes. Originality-Significance Statement(Identify the key aspects of originality and significance that place the work within the top 10% of current research in environmental microbiology) Novel methanotrophic bacteria have been discovered in recent years, but few studies have examined the total known diversity of methanotrophs together with the net flux of CH4 from soils. We used an ecosystem with a vegetation-soil gradient in the sub-alpine regions of Australia (with extremely strong consumption of atmospheric CH4) to examine microbial and abiotic drivers of CH4 fluxes across this gradient. Recently characterized methanotrophs, either USC in forest and grassland soils, or oxygenic Candidatus Methylomirabilis sp. in the bog soil were dominant. Methanotrophs belonging to the families Methylococcaceae and Methylocystaceae represented only a small minority of the methanotrophs in this ecosystem.

microbiology↗

bioRxiv2020

Rewiring of peatland plant-microbe networks outpaces species turnover

Enviro-climatological changes are thought to be causing alterations in ecosystem processes through shifts in plant and microbial communities; however, how links between plant and microbial communities change with enviro-climatological change is likely to be less straightforward but may be fundamental for many ecological processes. To address this, we assessed the composition of the plant community and the prokaryotic community -using amplicon-based sequencing- of three European peatlands that were distinct in enviro-climatological conditions. Bipartite networks were used to construct site-specific plant-prokaryote co-occurrence networks. Our data show that between sites, plant and prokaryotic communities differ and that turnover in interactions between the communities was complex. Essentially, turnover in plant-microbial interactions is much faster than turnover in the respective communities. Our findings suggest that network rewiring does largely result from novel associations between species that are common and shared across the networks. Turnover in network composition is largely driven by novel interactions between a core community of plants and microorganisms. Taken together our results indicate that plant-microbe associations are context dependent, and that changes in enviro-climatological conditions will likely lead to network rewiring. Integrating turnover in plant-microbe interactions into studies that assess the impact of enviro-climatological change on peatland ecosystems is essential to understand ecosystem dynamics and must be combined with studies on the impact of these changes on ecosystem processes.

ecology↗