DataSheet_1_Pathway-Centric Analysis of Microbial Metabolic Potential and Expression Along Nutrient and Energy Gradients in the Western Atlantic Ocean.zip

Microbial communities play integral roles in driving nutrient and energy transformations in the ocean, collectively contributing to fundamental biogeochemical cycles. Although it is well known that these communities are stratified within the water column, there remains limited knowledge of how metabolic pathways are distributed and expressed. Here, we investigate pathway distribution and expression patterns from surface (5 m) to deep dark ocean (4000 m) at three stations along a 2765 km transect in the western South Atlantic Ocean. This study is based on new data, consisting of 43 samples for 16S rRNA gene sequencing, 20 samples for metagenomics and 19 samples for metatranscriptomics. Consistent with previous observations, we observed vertical zonation of microbial community structure largely partitioned between light and dark ocean waters. The metabolic pathways inferred from genomic sequence information and gene expression stratified with depth. For example, expression of photosynthetic pathways increased in sunlit waters. Conversely, expression of pathways related to carbon conversion processes, particularly those involving recalcitrant and organic carbon degradation pathways (i.e., oxidation of formaldehyde) increased in dark ocean waters. We also observed correlations between indicator taxa for specific depths with the selective expression of metabolic pathways. For example, SAR202, prevalent in deep waters, was strongly correlated with expression of the methanol oxidation pathway. From a biogeographic perspective, microbial communities along the transect encoded similar metabolic potential with some latitudinal stratification in gene expression. For example, at a station influenced by input from the Amazon River, expression of pathways related to oxidative stress was increased. Finally, when pairing distinct correlations between specific particulate metabolites (e.g., DMSP, AMP and MTA) and both the taxonomic microbial community and metatranscriptomic pathways across depth and space, we were able to observe how changes in the marine metabolite pool may be influenced by microbial function and vice versa. Taken together, these results indicate that marine microbial communities encode a core repertoire of widely distributed metabolic pathways that are differentially regulated along nutrient and energy gradients. Such pathway distribution patterns are consistent with robustness in microbial food webs and indicate a high degree of functional redundancy.

海洋微生物群落（Microbial communities）在驱动海洋营养与能量转化过程中发挥着不可或缺的核心作用，共同参与了基础生物地球化学循环（biogeochemical cycles）。尽管学界已明确这类群落在水体中存在分层分布现象，但针对其代谢通路的分布与表达模式的认知仍较为有限。本研究以南大西洋西部一条2765公里的断面为研究区域，选取3个采样站位，对从表层海水（5米）至深层黑暗海洋（4000米）的代谢通路分布与表达模式展开分析。本研究基于全新测序数据，其中包含用于16S核糖体RNA基因测序（16S rRNA gene sequencing）的样本43份、宏基因组学（metagenomics）测序样本20份以及宏转录组学（metatranscriptomics）测序样本19份。
与既往研究结果一致，本研究观测到微生物群落结构呈现垂直分带特征，且主要在透光与非透光海水区域间形成明显分区。基于基因组序列信息与基因表达数据推断得到的代谢通路，同样随水深呈现分层分布特征。例如，光合代谢通路的表达量在透光水体中显著上调；与之相反，参与碳转化过程的代谢通路（尤其是难降解有机碳降解通路，如甲醛氧化通路）的表达量在黑暗海洋水体中显著升高。本研究还观测到特定深度的指示类群（indicator taxa）与代谢通路的选择性表达之间存在显著关联。例如，在深水环境中广泛存在的SAR202类群，与甲醇氧化通路的表达量呈现强相关性。
从生物地理学视角来看，该断面上的微生物群落拥有相似的代谢潜能，但基因表达存在一定的纬向分层特征。例如，在受亚马逊河输入影响的站位中，与氧化应激相关的代谢通路表达量显著上调。最后，通过整合特定颗粒态代谢物（如DMSP、AMP、MTA）与分类学微生物群落、宏转录组通路在不同水深与空间尺度下的独特关联，我们得以解析海洋代谢物库的变化如何受微生物功能调控，反之亦然。
综合来看，本研究结果表明，海洋微生物群落拥有一套广泛分布的核心代谢通路全集，且这些通路会随营养与能量梯度发生差异化调控。这类通路分布模式与微生物食物网的稳定性特征相符，同时也反映出极高水平的功能冗余性。