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Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO3- contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests. [ABSTRACT FROM AUTHOR]

Simple Summary: The humic lake represents a special kind of aquatic ecosystem with high humic substances, low irradiance, and a high potential for greenhouse gas emissions. Despite the special environment and biogeochemical processes in humic lake water, knowledge about the underlying microbial-driven functions remains elusive. Here, we studied the compositions and functional gene structures of microbial communities in a humic lake (HL) and a reference weakly alkaline lake (RAL). We found that the high organic matter content in the HL supported higher gene diversity; and, specifically, the carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction might be enhanced more in the HL than in the RAL. By contrast, the humic fractions in the HL might reduce microbial metabolic potential for sulfur oxidation and phosphorus degradation. The potential interactions between different functional microorganisms might be down-regulated provided that there were more easily acquired nutrients in the HL. Overall, our results showed the functional gene "landscape" of microbial communities in the surface water of a humic lake, which helps understand the biogeochemical processes and the remediation of organic matter pollution in lacustrine ecosystems. Humic lakes (HLs) are special water bodies (high organic matter content, low pH, and low transparency) that are important sources of major greenhouse gases. The knowledge about microbial functional potentials and the interactions among different genes in HL water has been scarcely understood. In this study, we used 16S rRNA gene sequencing and the GeoChip 5.0 to investigate microbial community compositions and functional gene structures in an HL and a reference weakly alkaline lake (RAL). The HL microbial communities showed distinct compositions and functional gene structures than those in the RAL. The functional gene diversity was significantly higher in the HL than in the RAL. Specifically, higher gene relative intensities in carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction were observed in the HL samples. By contrast, the metabolic potentials of microorganisms involved in dissimilatory N reduction, phosphorus degradation, and sulfur oxidation were weaker in the HL than in the RAL. Despite higher functional gene diversity, the interaction efficiency among genes (reflected by network geodesic distance and clustering coefficient) might be reduced in the HL. Different functional microbes may develop less interdependent relationships in acquiring nutrients given the high resource availability in the HL. Overall, the enhanced microbial metabolic potentials and less efficient functional interactions might have great consequences on nutrient cycling and greenhouse gas emissions in the HL ecosystem. [ABSTRACT FROM AUTHOR]

Elevation has a strong influence on microbial community composition, but its influence on microbial functional genes remains unclear in the aquatic ecosystem. In this study, the functional gene structure of microbes in two lakes at low elevation (ca. 530 m) and two lakes at high elevation (ca. 4,600 m) was examined using a comprehensive functional gene array GeoChip 5.0. Microbial functional composition, but not functional gene richness, was significantly different between the low- and high-elevation lakes. The greatest difference was that microbial communities from high-elevation lakes were enriched in functional genes of stress responses, including cold shock, oxygen limitation, osmotic stress, nitrogen limitation, phosphate limitation, glucose limitation, radiation stress, heat shock, protein stress, and sigma factor genes compared with microbial communities from the low-elevation lakes. Higher metabolic potentials were also observed in the degradation of aromatic compounds, chitin, cellulose, and hemicellulose at higher elevations. Only one phytate degradation gene and one nitrate reduction gene were enriched in the high-elevation lakes. Furthermore, the enhanced interactions and complexity among the co-occurring functional genes in microbial communities of lakes at high elevations were revealed in terms of network size, links, connectivity, and clustering coefficients, and there were more functional genes of stress responses mediating the module hub of this network. The findings of this study highlight the well-developed functional strategies utilized by aquatic microbial communities to withstand the harsh conditions at high elevations. [ABSTRACT FROM AUTHOR]

Abstract: Acidic coal mining lakes (AMLs) are characterized by low pH, low biodiversity, and high concentrations of sulfate and metals. However, to date, knowledge is inadequate on the involvement of the aquatic microbial functions in biogeochemical processes of an AML. Here, we use a natural weakly alkaline lake (WAL) as a reference to investigate the functional gene structure of microbial communities in the aerobic surface waters of an AML by using a metagenomic approach with GeoChip‐based functional gene arrays (GeoChip 5.0). We found significant differences in the compositions of the microbial functional genes between the two lake types. The AML had significantly lower gene diversity than the WAL, and the functional genes detected in the AML were almost a subset of those in the WAL. We also found significant differences in the microbial metabolic potentials between the two lake types. In the AML, the microbial communities had higher functional capacities in phosphorus‐utilization, sulfur oxidation, and metal‐detoxification and had lower metabolic potentials of carbon and nitrogen fixation, and the degradation of starch, hemicellulose, cellulose, chitin, and lignin than those in the WAL. By performing null model and network analyses, we observed stronger deterministic effects of the functional gene assemblages and greater clustering among the co‐occurring functional genes in the AML than those in the WAL. Altogether, we demonstrated contrasting patterns of freshwater microbial metabolic potentials and functional gene interactions between an AML and a WAL, which may advance the understanding of microbial functional response to acidification in freshwater lakes. [ABSTRACT FROM AUTHOR]