Paver Sara F, Muratore Daniel, Newton Ryan J, Coleman Maureen L
Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA.
School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA.
mSystems. 2018 Nov 13;3(6). doi: 10.1128/mSystems.00232-18. eCollection 2018 Nov-Dec.
Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that , , , and contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.
海洋和淡水微生物群落系统发育不同，且栖息地类型之间的转变被认为不常见。我们通过对16S rRNA基因标签测序数据集进行荟萃分析，比较了海洋和淡水微生物的系统发育多样性，并确定了在海洋和淡水生态系统之间表现出显著高相似性或低相似性的特定谱系。正如预期的那样，海洋和淡水微生物群落在主要门类的相对丰度上存在差异，并且包含特定栖息地的谱系。同时，与预期相反，在两个栖息地都观察到了许多共享分类群。基于几个指标，我们发现， ， ，和 包含数量最多的密切相关的海洋和淡水序列，表明这些群体中相对较新的栖息地转变。以丰富的α-变形菌纲SAR11组为例，我们发现有证据表明，在淡水中以低但可重复的丰度检测到了超出公认的LD12进化枝的新谱系；这一证据不仅延伸到16S rRNA基因座，还延伸到整个基因组的核心基因。我们的结果表明，共享分类群很多，但往往在一种栖息地类型中偶尔出现且相对丰度较低，导致对海洋和淡水栖息地之间转变频率的低估。丰度接近或低于检测水平的稀有分类群，包括似乎最近跨越了盐度界限的谱系，可能具有使它们能够在环境受到干扰或条件变化时利用生态位扩展机会的适应性。微生物多样性在不同环境中的分布有助于深入了解创造和维持这种多样性的过程，以及推断群落将如何应对未来环境变化的潜力。我们整合了来自数十个淡水湖和海洋样本的数据集，以比较不同盐度的开阔水域栖息地的多样性。我们基于序列的方法的新颖组合揭示了可能最近经历了栖息地类型转变的谱系。这些分类群是研究盐度耐受性生理限制的有希望的目标。我们的发现有助于理解对微生物分布的生态和进化控制，并开启了关于特定谱系的可塑性和适应性的新问题。
