pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments

Decoupling of diversity and network complexity of bacterial communities during water quality deterioration

Numerous studies have examined the impact of water quality degradation on bacterial community structure, yet insights into its effects on the bacterial ecological networks remain scarce. In this study, we investigated the diversity, composition, assembly patterns, ecological networks, and environmental determinants of bacterial communities across 20 ponds to understand the impact of water quality degradation. Our findings revealed that water quality degradation significantly reduces the α-diversity of bacterial communities in water samples, while sediment samples remain unaffected. Additionally, water quality deterioration increases the complexity of bacterial networks in water samples but reduces it in sediment samples. These shifts in bacterial communities were primarily governed by deterministic processes, with heterogeneous selection being particularly influential. Through redundancy analysis (RDA), multiple regression on matrices (MRM), and Mantel tests, we identified dissolved oxygen (DO), ammonium nitrogen (NH4+-N), and C/N ratio as key factors affecting the composition and network complexity of bacterial communities in both water and sediment. Overall, this study contributes a novel perspective on the effect of water quality deterioration on microbial ecosystems and provides valuable insights for improving ecological evaluations and biomonitoring practices related to water quality management.

Environmental DNA: Preliminary Characterization of Microbiota in Three Sicilian Lakes

Freshwater ecosystems play a key role in biogeochemical cycles and face various anthropogenic impacts. Understanding microbial communities within these ecosystems is crucial for ecosystem management and conservation. This study conducted a metabarcoding analysis of the bacterial 16S rDNA of environmental DNA (eDNA) to investigate the microbial diversity and composition in three Sicilian lakes (Poma, Piana, and Scanzano). The results revealed a common core microbiota in all the lakes, with Poma and Piana showing similar compositions, followed by Scanzano. Key bacterial phyla identified as core members across the sampled sites included Actinobacteriota, Proteobacteria, Bacteroidota, Verrucomicrobiota, Planctomycetota, and Cyanobacteria. Additionally, specific bacterial families such as Comamonadaceae, Burkholderiaceae, Ilumatobacteraceae, and Sporichthyaceae uniquely contributed to the microbial community structures. eDNA demonstrates potential as a quicker and less invasive tool to investigate biodiversity studies for these sites. The findings illuminate the intricate microbial dynamics within Sicilian freshwater ecosystems and emphasize the importance of considering microbial diversity in freshwater conservation and management strategies.

Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins

Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.

IMPORTANCE

Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.

Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments

BACKGROUND

the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks.

OBJECTIVES

this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023.

METHODS

the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system.

RESULTS

the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water.

CONCLUSIONS

these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.

The role of microorganisms in phosphorus cycling at river-lake confluences: Insights from a study on microbial community dynamics

River-lake confluences are key zones in the river-lake network, essential for managing contaminant transport and transformation. However, the role of biogeochemical transformations, particularly in phosphorus (P) dynamics, has been underexplored. As a result, this study looks into the dynamics of microbial communities and how important microbes are to the cycling of P. It was revealed that microorganisms contribute differently to phosphorus cycling in different hydraulic regions. Regions with higher-velocity and finer sediment showed increased microbial diversity and enhanced capabilities for organic phosphorus (OP) mineralization and inorganic phosphorus (IP) solubilization due to lower bio-available P (bio-P) concentrations. In areas characterized by flow deflection (FD), flow stagnation (FST), and flow separation (FSE), distinct P fraction distributions were observed: Total phosphorus (TP) and bio-P were found to be more abundant in the FST and FD regions, but residual phosphorus (Res-P) and calcium phosphorus (Ca-P) were more prevalent in the FSE region. Sediment characteristics, including P species like aluminum-phosphorus (Al-P), OP, iron-associate phosphorus (BD-P), and sediment mid-diameter (D50), significantly influence microbial community composition. These results improve our comprehension of the distribution of microbial community distribution and its role in the phosphorus cycle at river-lake confluence, providing useful provide valuable information for managing river-lake confluences and protecting aquatic ecosystems.

Bacterial Diversity in Sediments from Lianhuan Lake, Northeast China

Lake microbiota play a crucial role in geochemical cycles, influencing both energy flow and material production. However, the distribution patterns of bacterial communities in lake sediments remain largely unclear. In this study, we used 16S rRNA high-throughput sequencing technology to investigate the bacterial structure and diversity in sediments across different locations (six independent lakes) within Lianhuan Lake and analyzed their relationship with environmental factors. Our findings revealed that both the alpha and beta diversity of sediment bacterial communities varied significantly among the six independent lakes. Furthermore, changes between lakes had a significant impact on the relative abundance of bacterial phyla, such as Pseudomonadota and Chloroflexota. The relative abundance of Pseudomonadota was highest in Habuta Lake and lowest in Xihulu Lake, while Chloroflexota abundance was lowest in Habuta Lake and highest in Tiehala Lake. At the genus level, the relative abundance of Luteitalea was highest in Xihulu Lake compared to the other five lakes, whereas the relative abundances of Clostridium, Thiobacillus, and Ilumatobacter were highest in Habuta Lake. Mantel tests and heatmaps revealed that the relative abundance of Pseudomonadota was significantly negatively correlated with pH, while the abundance of Chloroflexota was significantly positively correlated with total phosphorus and total nitrogen in water, and negatively correlated with electrical conductivity. In conclusion, this study significantly enhances our understanding of bacterial communities in the different lakes within the Lianhuan Lake watershed.

Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers

Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities.

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.