Institute of Marine Science and Technology, Shandong University, Qingdao, China.
Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.
Mol Ecol Resour. 2024 Jul;24(5):e13950. doi: 10.1111/1755-0998.13950. Epub 2024 Apr 3.
Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.
木质素作为一种丰富的有机碳，在全球碳循环中起着至关重要的作用。然而，我们对全球木质素降解微生物组的理解仍然难以捉摸。最大的障碍是缺乏一个全面而准确的功能基因数据库。在这里，我们首次开发了一个经过策展的功能基因数据库（LCdb），用于木质素降解微生物群落的宏基因组分析。通过 LCdb，我们描绘了一幅清晰的画面，描述了具有木质素降解潜力的全球生物地理群落。它们在分类和功能特征水平上表现出明显的生态位分化。陆地微生物组表现出最高的多样性，但相关性最低。特别是，有氧和厌氧降解途径所涉及的基因之间几乎没有相关性，表现出明显的功能冗余特性。相比之下，在水生群落中观察到增强的相关性，特别是在有氧和厌氧群体之间更紧密的联系，这是对较低多样性的响应。具体来说，dypB 和 dypA 在地球上广泛存在，表明它们在木质素解聚中起着重要作用。河口和海洋群落分别具有漆酶和 mnsod 基因。值得注意的是，古菌在木质素降解中的作用在海洋生态系统中得到了揭示。环境因素强烈影响功能特征，但对分类群的影响较弱。零模型分析进一步证实，功能特征的组成是确定性的，而分类组成是高度随机的，这表明环境选择的是功能基因而不是分类群。我们的研究不仅开发了一种有用的工具，通过宏基因组测序来研究木质素降解微生物群落，还增进了我们对这些全球微生物组生态特征的理解。
