Aquatic Bacterial Communities Research Articles

Aquatic Bacterial Community Connectivity: The Effect of Hydrological Flow on Community Diversity and Composition

Microbial communities are vital components of freshwater ecosystems due to their role in nutrient cycling and energy flow; however, the mechanisms driving their variation are still being explored. In aquatic systems, water flow (hydrology) can impact microbial community composition through community connectivity; however, the details of hydrology’s effects on microbial connectivity remain unclear. To address this question, we used 16S rRNA metabarcoding to determine bacterial community composition and connectivity across flow transects in three connected Great Lakes waterbodies with very different water-flow regimes: the Little River (high flow), the Detroit River (moderate flow), and Lake Erie (low flow). Bacterial alpha diversity (Chao1) did not differ among the three locations or sample sites along the transects. Analyses of beta diversity using community dissimilarity matrices identified significant differences among the three locations and among sample sites within locations. Bacterial community connectivity varied among the three locations, with a significant distance–decay relationship observed only in the low-flow location, which is indicative of connectivity driven by spatial proximity. Directional analyses showed that the water-flow direction affected bacterial similarity, consistent with the expected hydrological effects on community connectivity and previous published work. Our results indicate that (1) microbial community composition varies within and among even geographically close sampling locations and (2) the specific water-flow regime appears to affect bacterial community connectivity. Including hydrology in models of bacterial community composition will improve our understanding of the relative roles of selection versus stochastic effects on bacterial community diversity and composition in freshwater ecosystems.

Application of Biolog Ecoplate™ Technique for Assessing the Effects of Macrophyte Harvesting on Aquatic Bacterial Communities

Macrophyte overgrowth in freshwater ecosystems is a worldwide problem, and a common management practice for these ecosystems is to remove the aquatic vegetation. In the study, the short-term effects of macrophyte harvesting in a mountain lake (Trevnoto Lake, Bulgaria) on both bacterial metabolic activity and fingerprints were assessed using Biolog Ecoplate™ assay. Bacterial responses to human activity were manifested by: 1) increased bacterial metabolic activity by 15%, and 2) shifts in bacterial metabolic fingerprints. The most affected carbon sources were those with low availability for aquatic bacteria – 85% of them were influenced and the rates of their utilizations changed from a decrease of 96% to an increase of 681%. In general, a clear trend was formed that the greater the bioavailability of the carbon sources, the less susceptible is their utilization to the environmental change. This preliminary study indicates an immediate impact of macrophyte harvesting on lake bacteria. In this aspect, Biolog Ecoplate™ assay could be useful in lake monitoring programmes in order to develop better sustainable management practices for restoration.

Temperature Adaptation of Aquatic Bacterial Community Growth Is Faster in Response to Rising than to Falling Temperature

Bacteria are key organisms in energy and nutrient cycles, and predicting the effects of temperature change on bacterial activity is important in assessing global change effects. A changing in situ temperature will affect the temperature adaptation of bacterial growth in lake water, both long term in response to global change, and short term in response to seasonal variations. The rate of adaptation may, however, depend on whether temperature is increasing or decreasing, since bacterial growth and turnover scale with temperature. Temperature adaptation was studied for winter (in situ temperature 2.5 °C) and summer communities (16.5 °C) from a temperate lake in Southern Sweden by exposing them to a temperature treatment gradient between 0 and 30 °C in ~ 5 °C increments. This resulted mainly in a temperature increase for the winter and a decrease for the summer community. Temperature adaptation of bacterial community growth was estimated as leucine incorporation using a temperature Sensitivity Index (SI, log growth at 35 °C/4 °C), where higher values indicate adaptation to higher temperatures. High treatment temperatures resulted in higher SI within days for the winter community, resulting in an expected level of community adaptation within 2 weeks. Adaptation for the summer community was also correlated to treatment temperature, but the rate of adaption was slower. Even after 5 weeks, the bacterial community had not fully adapted to the lowest temperature conditions. Thus, during periods of increasing temperature, the bacterial community will rapidly adapt to function optimally, while decreasing temperature may result in long periods of non-optimal functioning.

Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence.

When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.

Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem

Aquatic ecosystems in anthropogenically impacted areas are important reservoirs of antibiotic resistance genes (ARGs) of allochthonous origin. However, the dynamics of the different ARGs within the bacterial communities of lakes and rivers, as well as the factors that drive their selection, are not completely understood. In this study, we analysed the fate of the bacterial resistome (total content of ARGs and of metal resistance genes, MRGs) for a period of six months (summer-winter) in a continuum lake-river-lake system (Lake Varese, River Bardello, Lake Maggiore) in Northern Italy, by shotgun metagenomics. The metagenomic data were then compared with chemical, physical and microbiological data, to infer the role of anthropogenic pressure in the different sampling stations. ARGs and MRGs were more abundant and diverse in the River Bardello, characterised by the highest anthropogenic pollution. The date of sampling influenced ARGs and MRGs, with higher abundances in summer (August) than in fall or in winter, when the impact of the treated wastewater discharge in the river was limited by a higher water flow from Lake Varese. ARG and MRG abundances were significantly correlated and they co-occurred in the main network analysis modules with potential pathogenic bacteria. Different levels of anthropogenic impact selectively promoted specific ARGs while others, generally abundant in waters, were not affected by anthropogenic pressure. Reducing the level of anthropogenic pressure resulted in a rapid decrease of most ARGs. From our results, the role of anthropogenic pressure in promoting the spread of specific antibiotic resistances and of potential pathogens in aquatic ecosystem becomes clear. Finally we highlight the strict correlation between ARGs and MRGs suggesting their potential co-selection in stressed aquatic bacterial communities.

Linking pharmaceutical residues to dissolved organic matter and aquatic bacterial communities in a highly urbanized bay

Pharmaceuticals are causing environmental concerns associated with their widespread distribution in aquatic ecosystems. The environmental fate and behavior of pharmaceutical residues are related to dissolved organic matter and bacterial communities, both of which are strongly influenced by human activities. However, the relationships among pharmaceutical pollution, dissolved organic matter pool, and bacterial community structure under the pressure of human activities are still unclear, especially in highly urbanized bay areas. In this study, we investigated the occurrence and distribution of 35 pharmaceuticals in a typical urbanized bay (Hangzhou Bay) in Eastern China, and analyzed their relationships with dissolved organic matter and aquatic bacterial community structure. The target pharmaceuticals were ubiquitously detected in surface water samples, with their concentrations ranging from undetectable to 263 ng/L. The detected pharmaceuticals were mostly sulfonamides, macrolides, antidepressants, and metabolites of stimulants. Significant positive correlations were observed between the concentrations of pharmaceuticals and the intensity of human activities. Strong correlations also emerged between the concentration of antidepressants and the speed of urban expansion, as well as between the concentration of cardiovascular drugs and the population density or nightlight index. Three fluorescent components (protein-like C1, terrestrial humic-like C2, protein tryptophan-like C3) were significantly positively correlated with the total concentration of pharmaceuticals. Pharmaceutical pollution reshaped aquatic bacterial communities, based on the close correlation observed between pharmaceutical concentration and bacterial community structure. The results elucidate the potential dynamics of dissolved organic matter pool and aquatic bacterial communities in response to pharmaceutical pollution in urbanized bay ecosystems.

Seasonal succession of microbial community co-occurrence patterns and community assembly mechanism in coal mining subsidence lakes.

Coal mining subsidence lakes are classic hydrologic characteristics created by underground coal mining and represent severe anthropogenic disturbances and environmental challenges. However, the assembly mechanisms and diversity of microbial communities shaped by such environments are poorly understood yet. In this study, we explored aquatic bacterial community diversity and ecological assembly processes in subsidence lakes during winter and summer using 16S rRNA gene sequencing. We observed that clear bacterial community structure was driven by seasonality more than by habitat, and the α-diversity and functional diversity of the bacterial community in summer were significantly higher than in winter (p < 0.001). Canonical correspondence analysis indicated that temperature and chlorophyll-a were the most crucial contributing factors influencing the community season variations in subsidence lakes. Specifically, temperature and chlorophyll-a explained 18.26 and 14.69% of the community season variation, respectively. The bacterial community variation was driven by deterministic processes in winter but dominated by stochastic processes in summer. Compared to winter, the network of bacterial communities in summer exhibited a higher average degree, modularity, and keystone taxa (hubs and connectors in a network), thereby forming a highly complex and stable community structure. These results illustrate the clear season heterogeneity of bacterial communities in subsidence lakes and provide new insights into revealing the effects of seasonal succession on microbial assembly processes in coal mining subsidence lake ecosystems.

Compositional responses of aquatic bacterial communities and their network interactions to phytoplankton-derived dissolved organic matter from freshwater ponds

Bacteria play a central role in the degradation of phytoplankton-derived dissolved organic matter (P-DOM) particularly in algal-blooming aquatic systems; yet our understanding of the interaction between bacteria and P-DOM is still poor. We supplied differential P-DOM that varied in concentration and molecular weight (released from distinct phytoplankton collected from blue-green algal-blooming grass carp Ctenopharyngodon idellus farming ponds) to similar aquatic bacterial communities (isolated from non-blooming grass carp ponds), to explore how P-DOM affects bacterial community dynamics and to identify the most responsive degrading taxa using UV-visible absorption spectroscopy and high-throughput sequencing. Bacterial cultures all had similar degradation effects upon P-DOM, causing decreases in its concentration but increases in its molecular weight and aromaticity. In contrast, bacterial compositional changes varied primarily depending on P-DOM molecular weight, and Bacteroidia taxa were mostly affected, appearing more adapted to metabolize high-molecular-weight P-DOM. Nevertheless, most of the degrading taxa were recurrent and typically members within Gammaproteobacteria and Bacilli, indicating substrate-controlled bacterial responses induced by P-DOM. Network analysis revealed that bacterial communities harbored relatively low-abundant degrading members rather than dominant ones as keystone taxa, which presented simultaneously crucial microbial connections within communities and strong associations with environments and therefore played an over proportional role in maintaining community stability and functioning. Moreover, the keystone taxa may be generalists, and their ecological attributes can be described by oligotrophs that correspond to the K-strategists. Generally, this study implied a pivotal role of Gammaproteobacteria, particularly Pseudomonas, in P-DOM biodegradation, most probably in algal-blooming aquatic environments.

Increased similarity of aquatic bacterial communities of different origin after antibiotic disturbance

Stochastic or deterministic processes control the bacterial community assembly in waters and their understanding is a fundamental question to correctly manage aquatic environments exposed to the release of antibiotics from anthropogenic sources. It has been suggested that microdiversity (i.e. the rare biosphere) convers freshwater communities with stability, meaning that previously rare taxa bloom when the community is disturbed. Since there might be a seed bank of similar, but not abundant, bacterial taxa in different waters, we tested whether a disturbance by an antibiotic cocktail would increase similarity in bacterial communities from different freshwater systems (a wastewater effluent and two lakes). In a continuous culture set-up in chemostats, we show that disturbance with antibiotics causes communities from different environments to become more similar. Once the antibiotic pressure is released the communities tend to become more dissimilar again. This shows that there is a similar shift in community composition even in waters from very different origins when they are disturbed by antibiotics, even at low concentrations. Antibiotics impact the bacterial communities at the cell and the community level, independently by the original degree of anthropogenic stress they are adapted to, altering the original phenotypes, genotypes, and the relations between bacteria.

Suspended particulates mediate bacterial community coalescence in different habitats of a large sediment-laden river

Many studies have reported the influence of dispersal processes on aquatic bacterial communities, but the role of community coalescence is still unknown in sediment-laden rivers. Here, we examined the assembly of distinctive bacterial communities (free-living [FL], particle-attached [PA], and surface-sediment [SS]) with differing habitat preferences across different regions of the Yellow River (China) in the spring and autumn of 2019. We demonstrated that in both seasons SS bacteria featured the highest diversity, followed by PA bacteria, and then FL bacteria. Nonetheless, both FL and PA groups showed remarkable seasonal variation in water samples, while the SS group in sediment samples showed significant spatial variation. Furthermore, species sorting and dispersal limitation respectively governed the biogeographic patterns (strong distance–decay relationships) of water and sediment bacterial communities. With respect to community coalescence, not only the same habitats (i.e., water–water, particle–particle, and sediment–sediment) but also similar habitats (i.e., water–particle) had higher proportions of overlapped amplicon sequence variants (ASVs) compared with different habitats (i.e., water–sediment and particle–sediment). Moreover, the proportions of overlapped ASVs between PA and SS groups were higher than those between FL and SS groups. Network analysis revealed that the SS group harbored the highest network complexity, followed by PA and FL groups. Most connectors in the networks were identified as FL–PA–SS ASVs irrespective of the river reaches sampled. These findings demonstrate the biogeographic patterns of distinctive bacterial communities driven by species sorting and dispersal limitation, and provide evidence for bacterial community coalescence in the Yellow River’s water and sediment. Bacteria attached to suspended particles may play a paramount role in the microbial ecology of different habitats in large sediment-laden rivers.

Spatial Variations of Aquatic Bacterial Community Structure and Co-Occurrence Patterns in a Coal Mining Subsidence Lake

Land subsidence caused by underground coal mining critically influences the structure and function of ecosystems in mining areas. However, knowledge on the aquatic bacterial community structure and interspecies interactions in subsidence lakes are still limited. To address this issue, we collected water samples from a coal mining subsidence lake and its connected river and investigated the spatial distribution and co-occurrence patterns of the bacterial community using 16S rRNA amplicon sequencing. The results revealed that the bacterial α-diversity in the subsidence lake was higher than that in the river. The bacterial community composition was also significantly different between the subsidence lake and its connected river. Total nitrogen explained 21.4% of the bacterial community composition variation, while sulfate explained 38.4% of the bacterial functional composition variation. Co-occurrence network analysis indicated that the modularity indices and stability of the microbial network in the subsidence lake were significantly higher than those in rivers, which presented more resistance to environmental disturbance. Keystone bacterial taxa in the subsidence lake and river included the Clostridiaceae 1 family, and the Shewanella, Flavobacterium, and Limnohabitans genera, which play vital roles in the carbon, sulfur, and nitrogen cycles. Moreover, functional analysis showed that assimilatory sulfate reduction processes had a major role in the sulfur cycle of the subsidence lake and its connected river ecosystem. Overall, our findings provide new insights into the microbial community structure and assembly in subsidence lakes and its connected river ecosystems, with significant implications for the responsible utilization of water resources and the promotion of sustainable development in mining areas.

Enhanced microbial nitrification-denitrification processes in a subtropical metropolitan river network

Urban rivers are hotspots of regional nitrogen (N) pollution and N transformations. Previous studies have reported that the microbial community of urban rivers was different from that of natural rivers. However, how microbial community affects N transformations in the urban rivers is still unclear. In this study, we employed N nutrients-related isotope technology (includes natural-abundance isotopes survey and isotope-labeling method) and bioinformatics methods (includes 16S rRNA high-throughput sequencing and quantitative PCR analysis) to investigate the major N transformations, microbial communities as well as functional gene abundances in a metropolitan river network. Our results suggested that the bacterial community structure in the highly urbanized rivers was characterized by higher richness, less complexity and increased abundances of nitrification and denitrifying bacterium compared to those in the suburban rivers. These differences were mainly caused by high sewage discharge and N loadings. In addition, the abundances of nitrifier gene (amoA) and denitrifier genes (nirK and nirS) were significantly higher in the highly urbanized rivers (2.36 × 103, 7.43 × 107 and 2.28 × 107 copies·mL−1) than that in the suburban rivers (0.43 × 103, 2.18 × 107 and 0.99 × 107 copies·mL−1). These changes in microbes have accelerated nitrification-denitrification processes in the highly urbanized rivers as compared to those in the suburban rivers, which was evidenced by environmental isotopes and the rates of nitrification (10.52 vs. 0.03 nmol·L−1·h−1) and denitrification (83.31 vs. 22.49 nmol·g−1·h−1). Overall, this study concluded that the excess exogenous N has significantly shaped the specific aquatic bacterial communities, which had a potential for enhancing nitrification-denitrification processes in the highly urbanized river network. This study provides a further understanding of microbial N cycling in urban river ecosystems and expands the combined application of isotopic technology and bioinformatics methods in studying biogeochemical cycling.

Effects of alder- and salmon-derived nutrients on aquatic bacterial community structure and microbial community metabolism in subarctic lakes.

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r2 = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r2 = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity.

Recent Differentiation of Aquatic Bacterial Communities in a Hydrological System in the Cuatro Ciénegas Basin, After a Natural Perturbation

Pozas Rojas is a hydrological system comprising nine isolated shallow ponds and a deep lagoon, which were temporally merged in 2010 by increased rainfall due to a tropical cyclone. In this work, we assess which components, biotic interactions, or environment filtering effects, drive the assembly of microbial communities after a natural perturbation. Arsenic, pH, and temperature are among the most significant environmental variables between each pond, clustering the samples in two main groups, whereas microbial composition is diverse and unique to each site, with no core at the operational taxonomic unit level and only 150 core genera when studied at the genus level. Los Hundidos lagoon has the most differentiated community, which is highly similar to the epipelagic Mediterranean Sea communities. On the other hand, the shallow ponds at the Pozas Rojas system resemble more to epicontinental hydrological systems, such as some cold rivers of the world and the phreatic mantle from Iowa. Overall, despite being a sole of water body 2 years prior to the sampling, interspecific interactions, rather than environmental selection, seem to play a more important role in Pozas Rojas, bolstered by founder effects on each poza and subsequent isolation of each water body.

A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities.

ABSTRACTAgrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, the herbicide glyphosate has the potential to indirectly select for antibiotic-resistant bacteria. Such cross-selection could occur if the same genes (encoding efflux pumps, for example) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added a glyphosate-based herbicide (GBH) to 1,000-liter mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs can cross-select for antibiotic resistance in natural freshwater bacteria.IMPORTANCE Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here, we performed a freshwater mesocosm experiment showing that a GBH strongly selects for ARGs, particularly multidrug efflux pumps. These selective effects were evident after just a few days, and the ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes and, to a lesser extent, by mutations in EPSPS. Intensive GBH application may therefore have the unintended consequence of selecting for ARGs in natural freshwater communities.

Comprehensive assessment of bacterial communities and their functional profiles in the Huang Gang Creek in the Tatun Volcano Group basin, Taiwan using 16S rRNA amplicon sequencing

The microbial characteristics of water bodies located in the outflow of hot springs may affect the water quality parameters of the associated river ecosystem. Using 16S rRNA amplicon sequencing, we investigated the bacterial diversity and functional profiles of the Huang Gang (HG) Creek, located in the trace metal-rich, acid-sulfate thermal springs zone of the Tatun Volcano Group (TVG). Biofilms and water samples were collected from the upstream, midstream, and geothermal valleys and downstream of the creek. The results showed that the biofilm and water samples had distinct bacterial diversity and abundance profiles. Acidophilic sulfur-oxidizing bacteria were found to be more abundant in water samples, whereas aquatic photosynthetic bacterial communities were dominant in biofilms. The water samples were contaminated with Legionella and Chlamydiae, which could contaminate the nearby river and cause clinical infections in humans. The upstream samples were highly unique and displayed higher diversity than the other sites. Moderate thermo-acidophiles were dominant in the upstream and midstream regions, whereas the geothermal valley and downstream samples were abundant in thermo-acidophiles. In addition, functional profiling revealed higher expression of sulfur, arsenic, and iron-related functions in water and lead-related functions in the biofilms of the creek. As described in previous studies, the hydrochemical properties of the HG Creek were influenced by the TVG hot springs. Our findings indicated that the hydrochemical properties of the HG Creek were highly correlated with the bacterial diversity and functional potential of running water as compared to biofilms.

Machine learning predicts the impact of antibiotic properties on the composition and functioning of bacterial community in aquatic habitats

In the past decades, hundreds of antibiotics have been isolated from microbial metabolites or have been artificially synthesized for protecting humans, animals and crops from microbial infections. Their everlasting usage results in impacts on the microbial community composition and causes well-known collateral damage to the functioning of microbial communities. Nevertheless, the impact of different antibiotic properties on aquatic microbial communities have so far only poorly been disentangled. Here we characterized the environmental risk of 50 main kinds of antibiotics from 9 classes at a concentration of 10 μg/L for aquatic bacterial communities via metadata analysis combined with machine learning. Metadata analysis showed that the alpha diversity of the bacterial community increased only after treatment with aminoglycoside and β-lactam antibiotics, while its structure was changed by almost all tested antibiotics. The antibiotic treatment also disturbed the functions of the bacterial community, especially with regard to metabolic pathways, including amino acids, cofactors, vitamins, xenobiotics and carbohydrate metabolism. The critical characteristics (atom stereocenter count, number of hydrogen atoms in the antibiotic, and the adipose water coefficient) of antibiotics affecting the composition of the bacterial community in aquatic habitats were screened by machine learning. The key characteristics of antibiotics affecting the function bacterial communities were the number of hydrogen atoms, molecular weight and complexity. In summary, by developing machine learning models and by performing metadata analysis, this study provides the relationship between the properties of antibiotics and their adverse impacts on aquatic microbial communities from a macro perspective. The study also provides guidance for the rational design of antibiotics.

Effects of wind-wave disturbance and nutrient addition on aquatic bacterial diversity, community composition, and co-occurrence patterns: A mesocosm study

Wind-wave disturbance and nutrient input are the major environmental factors that shape bacterial diversity and community composition in lakes. However, knowledge of bacteria as bio-indicators' synergistic response to disturbance patterns and nutrient addition is still poor. To address this knowledge gap, we conducted a mesocosm experiment over 21 days, and collected 90 water samples from tanks under six different patterns of disturbance and nutrient addition; we explored the bacterial communities using high-throughput 16S rRNA gene sequencing. We found significantly increased bacterial diversity in continuously disturbed conditions and in intermittently disturbed conditions, and significantly decreased bacterial diversity under the synergistic effect of disturbances and nutrients. Bacterial community composition (BCC) under conditions of disturbance and nutrient addition exhibited different variations. However, there were no significant differences in BCC between continuously and intermittently disturbed mesocosms. Co-occurrence networks analysis showed that the proportion of positive correlations among edges in nutrient addition conditions were significantly higher than that in disturbed condition, indicating that nutrient input may increase the proportion of niche overlap, and enhance positive interactions among bacteria. Meanwhile, the co-occurrence patterns between algal and bacterial communities suggested shared environmental preferences or potential interactions among these two groups. Our study provides a new insight into the restoration of shallow eutrophic lake ecosystems. Moreover, the different distribution patterns of bacterial community act as ecological indicators of response to disturbances and nutrient input.

Spatial Variations of Aquatic Bacterial Community Structure and Co-Occurrence Patterns in Coal Mining Subsidence Lake

Spatial Variations of Aquatic Bacterial Community Structure and Co-Occurrence Patterns in Coal Mining Subsidence Lake

Substrate diversity affects carbon utilization rate and threshold concentration for uptake by natural bacterioplankton communities

Persistence of dissolved organic matter (DOM) in aquatic environments may in part be explained by high diversity and low concentrations of carbon substrates. However, changes in dissolved substrate quality can modify aquatic bacterial community composition and rate of carbon uptake. The aim of this study was to test if the presence of multiple simple substrates affects the turnover of organic carbon. Natural bacterial communities were grown in continuous cultures supplied with either individual carbon substrates—salicylic acid (SA), tryptophan (Trp) or tyrosine (Tyr)—or a combination of the 3 substrates. Concentrations were tracked using fluorescence spectroscopy, and steady-state concentrations of a few nanomolar were reached. Bacterial growth efficiency was dependent on which carbon sources were present and reached an intermediate level in the combined treatment. The bacterial community maintained steady-state concentrations of Trp that were lower in the combined treatment than in the individual substrate treatment. In addition, steady-state concentrations were reached faster during growth on combined carbon substrates, although the maximum utilization rate of each individual compound was lower. However, the steady-state concentration of total carbon (sum of carbon content of SA, Trp and Tyr) was higher in the combined culture than in the individual substrate treatments, and seemed to be determined by the carbon substate for which the bacteria had the lowest affinity. The results from this study indicate that persistence of dissolved organic carbon can in part be explained by vast substrate diversity, which raises the threshold concentration for utilization by natural bacterial communities.