Lakes

BackgroundTibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.ResultsHere, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.ConclusionsAltogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.

Eutrophication is an emerging global issue that is becoming increasingly severe due to the rising nutrient inputs and limited availability of electron donors for nitrogen removal. In sediments where redox conditions fluctuate dramatically, extracellular electron transfer (EET) critically supports microbial metabolism. However, the biogeochemical significance of EET-coupled denitrification and its EET mechanisms remain unclear. Here, through field investigations and laboratory 15N isotope experiments, we reveal that humic substance (HS)-mediated electron shuttling significantly enhances denitrification primarily by stimulating bacterial outer membrane c-type cytochrome. Specifically, EET mitigates the emission of greenhouse gas nitrous oxide by enriching nosZII-type reducers. Notably, the efficacy of exogenous HS amendment attenuates in sediment with high native HS concentration. Metagenomic binning further reveals multiple cytochromes forming a complete EET-coupled denitrification electron transport chain. Our findings elucidate the microbial mechanisms underlying electron shuttling-driven denitrification in lakes, thereby expanding the understanding of biogeochemical cycles.

BackgroundMicroorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.ResultsWe observed that the water column microbiome significantly varied by season (R2 = 0.59, P = 0.003). Temperature (R2 = 0.27, P = 0.004), dissolved organic matter (R2 = 0.13, P = 0.004), and dissolved oxygen (R2 = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.ConclusionsOur work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.

Understanding human-driven environmental impacts on microbial community distribution, abundance, and function remains a central challenge in microbial ecology. In particular, the drivers of temporal succession in community membership following perturbation remain unclear. Great Salt Lake, Utah, bears clear hallmarks of human disturbance, including a rock-filled railroad causeway that sequestered its northern arm from freshwater river influx, leading to localized hypersalination and food web collapse. Following decades of riverine water diversion, the southern arm of this terminal lake reached a historic low elevation during a time of increased climatic change, placing strong environmental pressure on the robust saline ecosystem. Here, we use molecular methods to report microbial community composition during this severe drought year at sites across the lake, including where the north and south arm waters contact. At sites of hypersaline water intrusion, we observe surprising stability in the north arm community composition, in contrast with strong perturbation in the south arm community structure. We use hydrodynamic modeling to pinpoint physical water flow dynamics as a key driver of these community shifts. At hypersaline north arm sites far from hyposaline water intrusion, abundance shifts were detected in predatory and parasitic taxa, a discovery that reveals surprising ecological dynamics in saturated hypersaline systems. In sum, this study demonstrates drastic hypersaline microbial community shifts during salinity and extreme weather perturbations.ImportanceThe Great Salt Lake ecosystem is rapidly drying due to climate warming and human consumptive water use that diverts riverine input to the lake's south arm. In 2022, the lake dried to reach its lowest elevation in recorded history, dehydrating microbial mats and exposing the toxic dust of the lakebed. This endangers food webs, industry, and human health. In response, Utah agencies are regulating Great Salt Lake salinity with ongoing adaptive structural engineering interventions. We hypothesized that these interferences would lead to dynamic mixing of microbial communities across a salinity gradient. We find that physical mixing drives dynamic, ongoing diversity loss and food web disruption at these sites of intervention, providing insights into how salinity regulation could be improved.