Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain.
Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA.
Microbiome. 2018 Jul 10;6(1):128. doi: 10.1186/s40168-018-0513-5.
The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.
Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth.
Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.
水生栖息地的透光层受到强烈的理化梯度影响。为了分析海洋微生物组的精细变化，我们在强分层期间从地中海的一个单一近海地点以 15 米的深度间隔收集了七个样本，以及两个在冬季当透光水柱混合时采集的样本。我们能够从这些宏基因组中恢复 94 个新的宏基因组组装基因组（MAG），并使用宏基因组招募检查透光层内关键海洋微生物的分布。
我们的结果表明，分层透光水柱内不同层的微生物组成存在显著差异。大多数微生物局限于不超过 30 米的离散水平层（狭生）。只有少数微生物，如 SAR11 类群的成员，出现在所有深度（广生）。在冬季混合期间，只有一些如假单胞菌的优势种群得到了促进。虽然大多数微生物在两个季节都出现，但一些群体，如 SAR116 类群和一些拟杆菌门和疣微菌门似乎在混合期间消失了。此外，我们发现一些以前被认为是季节性的微生物，如古菌或放线菌，在分层期间生活在透光层的更深层。不仅在分类学水平，而且在功能水平上，甚至在不同的类群中，都发现了与深度相关的强烈专业化，用于操纵和吸收特定的多糖。视蛋白序列（绿色或蓝色）也显示出与微生物分类学相关的狭窄深度分布，但与深度无关。
尽管这项研究仅限于地中海的一个单一地点，但它对我们理解海洋微生物群落在分层时如何在透光层内随深度变化具有深远的意义。我们的结果强调了在比较季节性变化时从水柱不同深度采集样本的重要性，并且对大多数情况下仅从一个单一深度采集样本的全球海洋研究具有重要意义。此外，我们的视角和方法（宏基因组组装和招募）广泛适用于其他宏基因组研究。
