Biology subjects

Roy, H.

Publications and source records attributed to Roy, H..

4 recordsLinked to original sources

bioRxiv2026

Molecular Detection and Antibiogram Assay of Escherichia coli Isolated from Poultry Farm Environments

BackgroundEscherichia coli is a common environmental and zoonotic bacterium that serves as an important indicator of fecal contamination and antimicrobial resistance (AMR) in poultry production systems. The emergence of multidrug-resistant (MDR) E. coli in poultry farm environments poses a significant One Health threat to animal, human, and environmental health. ObjectiveThis study aimed to isolate, identify, determine the prevalence, assess the antibiotic susceptibility pattern, and molecularly confirm Escherichia coli isolated from poultry farm environments in Lalmonirhat district, Bangladesh. Materials and MethodsA cross-sectional study was conducted from January to June 2024 using 60 environmental samples comprising water (n = 20), soil (n = 20), and bird-dropping (n = 20) samples collected from poultry farms in five upazilas of Lalmonirhat district. Isolation and identification of E. coli were performed using standard cultural, morphological, and biochemical techniques. Antimicrobial susceptibility was determined by the Kirby-Bauer disc diffusion method following CLSI guidelines. Ten randomly selected isolates were confirmed by polymerase chain reaction (PCR) targeting the species-specific uidA gene. ResultsThe overall prevalence of E. coli was 50% (30/60). Source-wise prevalence was highest in bird-dropping samples (75%), followed by water (45%) and soil (30%). Area-wise prevalence ranged from 33.33% in Patgram to 66.67% in Hatibandha. The isolates exhibited the highest resistance to oxytetracycline (66.67%) and ciprofloxacin (60%), while the highest susceptibility was observed to erythromycin (63.33%), neomycin (56.67%), and amoxicillin (56.67%). All ten isolates subjected to PCR produced the expected 486 bp uidA gene amplicon, confirming their identity as E. coli. ConclusionThe findings demonstrate a considerable prevalence of antimicrobial-resistant E. coli in poultry farm environments of Lalmonirhat district. Strengthening farm biosecurity, improving hygiene and waste management, implementing antimicrobial stewardship, and maintaining continuous molecular surveillance are essential to minimize the dissemination of resistant E. coli within a One Health framework.

microbiology↗

bioRxiv2024

Drivers of methane-cycling archaeal abundances, community structure, and catabolic pathways in continental margin sediments

Marine sediments contain Earths largest reservoir of methane, with most of this methane being produced and consumed in situ by methane-cycling archaea. While numerous studies have investigated communities of methane-cycling archaea in hydrocarbon seeps and sulfate-methane transition zones, little is known about how these archaea change from the seafloor downward in the far more common diffusion-dominated marine sediments. Focusing on four continental margin sites of the North Sea-Baltic Sea transition, we here investigate the in situ drivers of methane-cycling archaeal community structure and metabolism based on geochemical and stable carbon-isotopic gradients, functional gene (mcrA) copy numbers and phylogenetic compositions, as well as thermodynamic calculations. We observe major vertical and lateral changes in community structure that largely follow changes in organic matter reactivity and content, sulfate concentration, and bioturbation activity. While methane-cycling archaeal communities in bioturbation and sulfate reduction zones are dominated by known methyl-dismutating taxa within the Methanosarcinaceae and putatively CO2-reducing Methanomicrobiaceae, the communities change toward dominance of known methane-oxidizing taxa (ANME-2a-b, ANME-2c, ANME-1a-b) in sulfate-methane transitions. Underlying methanogenesis zones were characterized by a change toward mainly physiologically uncharacterized groups, including ANME-1d and several new genus-level groups of putatively CO2-reducing Methanomicrobiaceae and methyl-reducing Methanomassiliicoccales. Notably, group-specific increases in mcrA copy numbers by 2 to 4 orders of magnitude from the sulfate reduction zone into the sulfate-methane transitions or methanogenesis zones indicate the thriving of several major methane-cycling archaeal taxa. Together our study provides insights into the community and pathway shifts vertically along the geochemical gradients and horizontally along the different sedimentary settings and their underlying drivers in continental margin sediments.

ecology↗

bioRxiv2019

Glacial runoff promotes deep burial of sulfur cycling-associated microorganisms in marine sediments

Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization, and will be increasingly important as climate warming causes more rapid glacial melt. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godth[a]bsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had young sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates, and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with sulfate reduction rates, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.\n\nContribution to the Field StatementIn most coastal marine sediments organic matter turnover and total energy flux are highest at the surface and decrease significantly with increasing sediment depth, causing depth-dependent changes in the microbial community composition. Glacial runoff in arctic and subarctic fjords alters the composition of the microbial community at the surface, mainly due to different availabilities of organic matter and metals. Here we show that glacial runoff also modifies microbial community assembly with sediment depth. Sediment age was a key driver of microbial community composition in six-meter-long marine sediment cores from the Godth[a]bsfjord region, south-western Greenland. High sedimentation rates at glacier-influenced sediment stations enabled a complex community of sulfur-cycling-associated microorganisms to continuously thrive at high relative abundances from the surface into the sediment subsurface. These communities consisted of putative fermenters, sulfate reducers and sulfur oxidizers, which likely depended on high metal concentrations in the relatively young, glacier-influenced sediments. In non-glacier-influenced sediments with lower sedimentation rates, these sulfur-cycling-associated microorganisms were only present near the surface. With increasing sediment depth these surface microorganisms were largely replaced by other surface microorganisms that positively correlated with sediment age and belong to known taxa of the energy-limited, marine deep biosphere.

microbiology↗

bioRxiv2019

Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay

Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g. Chloroflexi & Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.

microbiology↗