Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.

Chemical pollution mixtures enter aquatic environments and interact with microorganisms in eclectic ways with disparate consequences for microbial ecosystem services. Can using a thermodynamic framework help to determine the net influence of a chemical mixture on the functional capacity of benthic microbial communities? We examined this question by comparing benthic stream microbial communities exposed to a gradient of neutral-alkaline coalmine effluent. Using a combination of approaches (metagenomics, quantitative polymerase chain reaction [qPCR], and functional assays), we show that functional genes and pathways of microbial communities growing in mine effluent differed in composition, but not diversity. The majority of functional genes and pathways that changed decreased at sites exposed to mine effluent, resulting in lower abundances of nitrogenase and methanogen genes and fermentation pathways. However, selenate reductase gene abundance increased with water and sediment concentration of an ecologically important contaminant at mined sites: selenium. Denitrification genes nosZ and nirK differed between sites: metagenome-based nosZ increased with dissolved nitrate concentration and qPCR-based nirK had a hump-shaped pattern across the mining gradient. Osmoprotectant gene abundance did not change. Extracellular enzyme assays and alkaline phosphatase gene relative abundance suggested that mined stream microbial communities may be constrained by phosphorus bioavailability. Subsidies and stressors related to changes in a set of functional genes and pathways, but differences were not consistently predictable using thermodynamic expectations. This suggests that pairing hypotheses for expected subsidies and stressors with post hoc explorations can yield valuable directions for future study of how microbial functional capacity responds to pollutant mixtures.

Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.

Biofilms can develop on nearly any surface, and in aquatic ecosystems they are essential components of biogeochemical cycles and food webs. Plastic waste in waterways is a new type of surface for biofilm colonisation. To analyse the influence of plastic pollution on the development and diversity of microbial freshwater biofilms that colonised them, we incubated 388 cm ² veneers of high‐density polyethylene (HDPE) with two veneer textures, smooth and rough, and tulip tree wood ( Liriodendron tulipifera ), in three rural headwater streams at the Savannah River Site (Aiken, SC, USA). We collected biofilms from veneers after 14, 28 and 56 days of incubation and analysed 16S rRNA genes and biofilm properties. We found that plastic negatively affected species richness of biofilms compared with wood, but that evenness was greatest on rough textured HDPE. Beta diversity was primarily influenced by stream site. Beta diversity differed more between wood and plastic veneers than with plastic surface texture and became more different over time. Wood had nine times more biomass than rough HDPE and 40 times more biomass than smooth HDPE. Given the projected increase of macroplastic pollution in aquatic ecosystems, our findings emphasise the need to further understand its effects on biofilm characteristics.