Data Sheet 1_Metagenomics-assembled genomes reveal microbial metabolic adaptation to athalassohaline environment, the case Lake Barkol, China.pdf

Salt-tolerant and halophilic microorganisms are critical drivers of ecosystem stability and biogeochemical cycling in athalassohaline environments. Lake Barkol, a high-altitude inland saline lake, provides a valuable natural setting for investigating microbial community dynamics and adaptation mechanisms under extreme salinity. In this study, we employed high-throughput metagenomic sequencing to characterize the taxonomic composition, metabolic potential, and ecological functions of microbial communities in both water and sediment samples from Lake Barkol. We reconstructed 309 metagenome-assembled genomes (MAGs), comprising 279 bacterial and 30 archaeal genomes. Notably, approximately 97% of the MAGs could not be classified at the species level, indicating substantial taxonomic novelty in this ecosystem. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Desulfobacterota, Planctomycetota, and Verrucomicrobiota, while archaeal communities were primarily composed of Halobacteriota, Thermoplasmatota, and Nanoarchaeota. Metabolic reconstruction revealed the presence of diverse carbon fixation pathways, including the Calvin-Benson-Bassham (CBB) cycle, the Arnon-Buchanan reductive tricarboxylic acid (rTCA) cycle, and the Wood-Ljungdahl pathway. Autotrophic sulfur-oxidizing bacteria, alongside members of Cyanobacteria and Desulfobacterota, were implicated in primary production and carbon assimilation. Nitrogen metabolism was predominantly mediated by Gammaproteobacteria, with evidence for both nitrogen fixation and denitrification processes. Sulfur cycling was largely driven by Desulfobacterota and Pseudomonadota, contributing to sulfate reduction and sulfur oxidation pathways. Microbial communities exhibited distinct osmoadaptation strategies. The “salt-in” strategy was characterized by ion transport systems such as Trk/Ktr potassium uptake and Na+/H+ antiporters, enabling active intracellular ion homeostasis. In contrast, the “salt-out” strategy involved the biosynthesis and uptake of compatible solutes including ectoine, trehalose, and glycine betaine. These strategies were differentially enriched between water and sediment habitats, suggesting spatially distinct adaptive responses to local salinity gradients and nutrient regimes. Additionally, genes encoding microbial rhodopsins were widely distributed, suggesting that rhodopsin-based phototrophy may contribute to supplemental energy acquisition under osmotic stress conditions. The integration of functional and taxonomic data highlights the metabolic versatility and ecological roles of microbial taxa in sustaining biogeochemical processes under hypersaline conditions. Overall, this study reveals extensive taxonomic novelty and functional plasticity among microbial communities in Lake Barkol and underscores the influence of salinity in structuring microbial assemblages and metabolic pathways in athalassohaline ecosystems.

嗜盐与耐盐微生物是非海水型高盐环境（athalassohaline environments）中生态系统稳定与生物地球化学循环的核心驱动因子。巴里坤湖（Lake Barkol）作为一处高海拔内陆咸水湖，为研究极端盐度下微生物群落动态与适应机制提供了极具价值的天然研究场景。本研究采用高通量宏基因组测序技术，对巴里坤湖水体与沉积物样本中的微生物群落的分类组成、代谢潜力及生态功能进行解析。本研究共重构得到309个宏基因组组装基因组（metagenome-assembled genomes, MAGs），其中包含279条细菌基因组与30条古菌基因组。值得注意的是，约97%的MAGs无法在物种水平完成分类注释，表明该生态系统中存在大量未被发掘的分类学新类群。优势细菌类群隶属于变形菌门（Pseudomonadota）、拟杆菌门（Bacteroidota）、脱硫杆菌门（Desulfobacterota）、浮霉菌门（Planctomycetota）及疣微菌门（Verrucomicrobiota）；古菌群落则主要由盐杆菌门（Halobacteriota）、热原体门（Thermoplasmatota）与纳米古菌门（Nanoarchaeota）构成。代谢重构分析揭示了多种碳固定途径的存在，包括卡尔文-本森-巴斯汉姆（Calvin-Benson-Bassham, CBB）循环、阿诺-布坎南还原性三羧酸（Arnon-Buchanan reductive tricarboxylic acid, rTCA）循环以及伍德-隆德哈尔（Wood-Ljungdahl）途径。自养型硫氧化细菌、蓝细菌（Cyanobacteria）以及脱硫杆菌门成员共同参与了初级生产与碳同化过程。氮代谢过程主要由γ-变形菌纲（Gammaproteobacteria）介导，研究同时检测到固氮与反硝化过程的相关证据。硫循环过程主要由脱硫杆菌门与变形菌门驱动，参与了硫酸盐还原与硫氧化代谢途径。微生物群落展现出差异化的渗透压适应策略。‘嗜盐入胞’策略以离子转运系统为核心特征，例如Trk/Ktr钾离子摄取系统与Na+/H+逆向转运蛋白，可实现细胞内离子稳态的主动维持。与之相对的‘排盐’策略则涉及相容性溶质的生物合成与摄取，包括四氢嘧啶（ectoine）、海藻糖（trehalose）以及甘氨酸甜菜碱（glycine betaine）。这两类适应策略在水体与沉积物生境中呈现差异化富集特征，表明微生物群落针对局部盐度梯度与营养状况演化出了空间特异性的适应响应。此外，编码微生物视紫红质的基因广泛分布于群落中，表明基于视紫红质的光能营养作用可能在渗透压胁迫条件下为微生物提供额外的能量来源。功能与分类学数据的整合分析凸显了高盐环境下微生物类群的代谢多样性及其在维持生物地球化学循环过程中的生态功能。综上，本研究揭示了巴里坤湖微生物群落中广泛存在的分类学新类群与功能可塑性，并强调了盐度在非海水型高盐环境中对微生物群落组成与代谢途径的塑造作用。