Table_1_Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria.XLSX

Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria.

多糖（polysaccharides）的降解是多糖转化过程的核心步骤，而多糖降解酶（polysaccharide-degrading enzymes）在该过程中发挥关键作用。尽管目前在这类酶的鉴定领域已取得一定进展，但海洋微生物（marine microorganisms）中此类酶的多样性与系统发育分布（phylogenetic distribution）仍在很大程度上尚不明确，这阻碍了我们对海洋微生物在海洋碳循环（ocean carbon cycle）中生态功能的认知。本研究针对海洋细菌基因组中的九类多糖降解酶的系统发育分布展开探究。首先，我们手动构建了包含961个经实验验证的酶的参考序列数据库（reference sequence database）；基于该数据库，我们对2182个高质量海洋细菌基因组中的9335个酶序列完成了注释，揭示了6种酶在门水平、以及全部9种酶在更低分类阶元上的扩展分布范围。随后，系统发育分析表明，部分酶在属水平上的编码潜力与系统发育保守性存在进化枝内多样性（intra-clade diversity）。最后，我们的分析揭示了酶类间的相关性：褐藻酸裂解酶（alginate lyases）与其他酶类展现出最为广泛的关联；值得注意的是，几丁质酶（chitinases）在部分菌属中与纤维素酶（cellulases）、褐藻酸裂解酶及琼胶酶（agarases）呈负相关。这一结果表明，海洋细菌内的属水平生活方式分化（lifestyle differentiation）已多次发生，而多糖的利用或许是部分类群（lineages）近期生态分化的重要驱动因素。本研究拓展了我们对多糖降解酶系统发育分布的认知，并为海洋细菌的生态分化研究提供了新的见解。