Wang Xiangyu, Lv Yongxin, Zhao Weishu, Xiao Xiang, Wang Jing
State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China.
mSystems. 2025 Jul 11:e0058125. doi: 10.1128/msystems.00581-25.
Hadal trenches, the Earth's deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions.
Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.
超深渊海沟是地球上最深的海洋环境，其中蕴藏着丰富的微生物群落，这些微生物群落在极端条件下促进难降解溶解有机物（RDOM）的周转。然而，微生物对D-氨基酸（D-AA）库（深海RDOM的重要组成部分）的影响在很大程度上仍不清楚。为了填补这一知识空白，我们精心构建了一个全面的D-AA功能基因参考数据库，用于从宏基因组数据中准确识别D-AA代谢潜力。利用这个数据库，我们在马里亚纳海沟的水柱和沉积物中，识别出了各种与中心碳代谢和氨氧化基因密切相关的D-AA合成代谢和分解代谢基因。此外，93.6%的回收细菌和古菌基因组至少包含这些D-AA功能基因中的一个，极大地扩展了我们对潜在D-AA利用者的认识。值得注意的是，我们发现谷氨酸消旋酶（一种以前被认为是细菌特有的酶）在氨氧化古菌中普遍存在。这一发现表明，D-谷氨酸可能通过这一关键微生物类群融入超深渊碳和氮循环。最后，我们观察到随着水深增加，D-AA的产生和降解潜力均有所增加，近底海水的水平高于沉积物。这些发现表明，多样的微生物类群促进了超深渊区域D-AA周转的增加，这可能代表了对极端超深渊条件的一种常见适应性反应。
深海微生物在RDOM的周转中起着关键作用。在本研究中，我们调查了D-AA的代谢潜力，D-AA是RDOM的重要组成部分，用于指示有机物的难降解性。通过阐明D-AA代谢的遗传特征及相关微生物类群，我们观察到D-AA代谢是一种在最深海洋中普遍存在的基本生态功能。我们在更深环境中发现更高的D-AA周转潜力，这挑战了D-AA一直难降解的传统观点，表明D-AA周转可能依赖于环境。这一见解为理解RDOM周转提供了一个新范式，对海洋生物地球化学具有广泛影响。
