Biology subjects

Graham, D. W.

Publications and source records attributed to Graham, D. W..

4 recordsLinked to original sources

bioRxiv2026

Rapid Antimicrobial Resistance Decline Coupled with Microbial Community Shifts in Sewage Polluted River Mesocosms

Antimicrobial resistance poses a global health threat, yet the fate of antimicrobial resistance genes (ARGs) and microbial communities from wastewaters in receiving rivers is rarely quantified. This study investigated the degradation kinetics of ARGs in sewage-polluted river water mesocosms and under sulfamethoxazole and copper stress, separately and in combination. Seven clinically relevant ARGs (blaCTX-M, blaNDM, qnrS, sul2, tetW, ermF, and aph(3'')-Ib), a mobile genetic element marker (intI1) and bacterial marker genes (uidA, 16S rDNA) were quantified by qPCR. Bacterial community changes were monitored using 16S rDNA amplicon sequencing. All target genes decayed with approximately first-order kinetics in all conditions, with qnrS (half-life: 8.0 h) and blaCTX-M (8.4 h) declining most rapidly and intI1 (32.5 h) and sul2 (46.5 h) declining most slowly. Ordination showed that ARG composition shifted primarily over time rather than by antibiotic/metal treatment. Bacterial communities shifted from initially Campylobacterota dominated ([≥] 90%) to Pseudomonadota, Bacillota, and Actinomycetota dominated communities over 168 h. Quantitative microbiome profiling showed a 95% reduction in ASV richness. PICRUSt2 analysis suggested progressive enrichment of aerobic and several metabolic pathways, as the mesocosms transitioned from highly polluted anoxic conditions to oxygenated conditions. Shifts in microbial community composition were coupled with changes in the resistome as identified by Procrustes analyses (r = 0.841, p = 0.001) and other analyses. Together, results show that river self-purification can rapidly reduce ARG loads, at least in warmer climates. This study provides approximate kinetic parameters for mathematical models to predict the fate of ARGs in rivers.

microbiology↗

bioRxiv2025

Aridity drives global convergence of desert microbiomes and biogeochemical activities

Deserts cover a third of the worlds surface, supporting unique biomes and ecosystem services. Yet, we lack a comprehensive assessment of what defines and drives the microbial communities that dominate life in these regions. Here, we conducted a standardized field survey in contrasting cold, hot, and polar deserts across the seven continents, and observed geographically distant deserts share similar structure, function, and activities. Desert communities are dominated by genomically streamlined Actinobacteriota and Chloroflexota, and compared with non-desert soils, are significantly enriched with stress tolerance genes, mobile genetic elements, and antiviral strategies, revealing previously unknown ecological and evolutionary dynamics. Metabolically, these communities exhibit reduced capacity for carbohydrate and protein degradation, and instead are enriched for chemosynthetic carbon fixation, continuous energy harvesting using atmospheric trace gases and sunlight, and energy reserve biosynthesis. All sampled soils mediated respiration, trace gas oxidation, and carbon fixation, with detectable activity even in hyper-arid Atacama and Antarctic soils at the margins of life. Driver analyses identified aridity as the primary overriding driver of the microbial communities and biogeochemical activities. Collectively, these findings suggest that aridity selects for metabolically self-sufficient taxa capable of continuously meeting energy and carbon needs independently of vegetation-derived inputs, while enduring physicochemical stressors and potentially elevated viral pressure. These new insights are integral to forecast the future of soils amid increasing desertification. Significance statementDesert soils occupy a vast and expanding portion of Earth, yet what defines and governs their dominant microbial life remains incompletely defined. By assessing the composition, capabilities, and activities of microbial communities across deserts on all seven continents, we identify unifying signatures of life under extreme water limitation. We show microbial communities are highly self-sufficient, capable of acquiring energy and carbon even where plant inputs are minimal. This planetary-scale understanding of the desert microbiome has important ramifications for forecasting potential shifts of microbial communities and the services they provide as desertification intensifies.

microbiology↗

bioRxiv2024

Field monitoring and hydraulic modelling quantify untreated wastewater as dominant source of AMR in a small river running through a big city

Quantifying sources of antimicrobial resistance (AMR) in rivers receiving various waste streams is essential for targeting mitigation strategies yet rarely performed. This study combined field monitoring with hydraulic modelling and mass balance calculations to attribute sources of AMR in the Musi River running through Hyderabad, India, a city renowned for pharmaceutical manufacturing. We quantified antibiotic resistance genes (ARGs), resistant bacteria (ARBs), and physicochemical parameters in water and sediment samples in the dry and wet season. Absolute ARG and ARB abundances spiked in the city, declining again downstream. Changes were more gradual in the wet season. Pollution levels were significantly different between upstream, city and downstream stretches and seasons. Hydraulic modelling revealed that 60-80% or 20-40% of the river water in the city derived from untreated sewage during the dry or wet seasons, respectively. This established municipal waste, not pharmaceutical sources, as the dominant driver of AMR in the Musi. Linear discriminant analysis identified dissolved oxygen and total nitrogen as reliable proxies for distinguishing AMR-polluted from less-polluted sites. The Musi, with insufficient wastewater treatment and limited dilution of point-source loadings, is typical for many urban rivers in resource-limited countries highlighting the urgent need for improved wastewater management to reduce AMR exposures.

microbiology↗

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↗