Enhanced Metabolic Potentials and Functional Gene Interactions of Microbial Stress Responses to a 4,100-m Elevational Increase in Freshwater Lakes

Abstract

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.

Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China

“…A 5-l Schindler sampler was used to collect water samples at a depth of 0.5 m at each sampling site. After removing large plankton and other particles with 5-μm pore-sized polycarbonate filters, 0.2-μm polycarbonate filters were used to collect the free-living microbes in the water samples (Li et al 2021 ). These microbial samples were stored at −80°C until further analyses were undertaken of the FMFG diversity.…”

“…The genomic DNA of the free-living microbial samples was extracted and purified using previous methods (Wu et al 2007 , Li et al. 2021 ). The purified DNA samples were then analyzed using a functional gene chip.…”

“…Such variations affect free-living microbial community composition, and function (Xu et al 2014 , Ren et al 2018 , Li et al. 2021 , Wang et al 2021 ), and may also affect FMFG composition and richness. However, it is unclear how Microcystis blooms affect FMFG composition and richness, partly due to the lack of techniques for detecting the extremely diverse functions of micro-organisms.…”

“…GeoChip is a high-throughput microarray-based genomic technology that contains hundreds to thousands of different gene families involved in various biogeochemical processes, including cycling of carbon, nitrogen, sulfur, and phosphorus, heavy metal resistance, antibiotic resistance, pathogenicity, secondary metabolism, organic pollutant degradation, electron transport, stress responses, virulence and viruses (He et al 2010 , Wang et al 2014 ). GeoChip has been demonstrated to be a powerful method for surveying the composition, richness, and interactions of FMFG in various aquatic ecosystems, such as freshwater lakes (Wang et al 2019 , Li et al 2021 ), acidic mining lakes (Ren et al 2018 ), and groundwater (He et al 2018 ). This method will help investigations into the responses of FMFG richness, composition and interactions to Microcystis blooms.…”

Difference and Network Analysis of Functional Genes Revealed the Hot Area of Carbon Degradation, Nitrogen, Phosphorus, and Sulfur Cycling in Blending Systems with Pyrite and Poly(3-hydroxybutyrate-hydroxyvalerate) for Nitrogen and Phosphorus Removal

“…Therefore, the HT-qPCR technology would provide the detailed underlying molecular mechanism that governs nitrogen transformation and the distribution of microbial genes involving C, N, and P cycles in the blend system of pyrite and PHBV. Furthermore, according to the abundance of functional gens, there is a powerful method for examining complex interactions among genes/microbes in different ecosystems through building microbial network analysis to explore these genes/microbe interactions and how some species occur together in niches and how they interact with functional gens . Moreover, it can identify the “keystone” genes as biomarkers with low abundance but have a large influence in communities …”