Needham David M, Sachdeva Rohan, Fuhrman Jed A
Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
ISME J. 2017 Jul;11(7):1614-1629. doi: 10.1038/ismej.2017.29. Epub 2017 Apr 11.
Numerous ecological processes, such as bacteriophage infection and phytoplankton-bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomic units (OTUs), of bacteria, archaea, phytoplankton chloroplasts (all via 16S or intergenic spacer (ITS) sequences) and T4-like-myoviruses (via g23 major capsid protein gene sequence). The extent of microdiversity varied between genes (ITS most, g23 least) and only temporally common taxa were highly microdiverse. Overall, 60% of taxa exhibited microdiversity; 59% of these had subtypes that changed significantly as a proportion of the parent taxon, indicating ecologically distinct taxa. Pairwise correlations between prokaryotes and myoviruses or phytoplankton (for example, highly microdiverse Chrysochromulina sp.) improved when using single-base variants. Correlations between myoviruses and SAR11 increased in number (172 vs 9, Spearman>0.65) and became stronger (0.61 vs 0.58, t-test: P<0.001) when using SAR11 ITS single-base variants vs OTUs. Whole-community correlation between SAR11 and myoviruses was much improved when using ITS single-base variants vs OTUs, with Mantel rho=0.49 vs 0.27; these results are consistent with strain-specific interactions. Mantel correlations suggested >1 μm (attached/large) prokaryotes are a major myovirus source. Consideration of microdiversity improved observation of apparent host and virus networks, and provided insights into the ecological and evolutionary factors influencing the success of lineages, with important implications to ecosystem resilience and microbial function.
许多生态过程，如噬菌体感染和浮游植物与细菌的相互作用，通常通过菌株特异性机制发生。因此，研究微生物动态的成因应受益于高分辨率的分类特征。在南加州沿岸浮游植物大量繁殖后的5个多月里，我们每天至每周进行采样，研究了细菌、古菌、浮游植物叶绿体（均通过16S或基因间隔区（ITS）序列）和T4样肌病毒（通过g23主要衣壳蛋白基因序列）的微多样性程度，即99%序列相似性聚类（操作分类单元，OTU）内的显著变异。微多样性程度因基因而异（ITS最高，g23最低），只有在时间上常见的分类群具有高度微多样性。总体而言，60%的分类群表现出微多样性；其中59%具有亚型，这些亚型作为亲本分类群的一部分发生了显著变化，表明存在生态上不同的分类群。使用单碱基变体时，原核生物与肌病毒或浮游植物之间的成对相关性（例如，高度微多样的金藻属物种）得到改善。当使用SAR11 ITS单碱基变体而非OTU时，肌病毒与SAR11之间的相关性数量增加（172对9，斯皮尔曼相关系数>0.65）且变得更强（0.61对0.58，t检验：P<0.001）。使用ITS单碱基变体而非OTU时，SAR11与肌病毒之间的全群落相关性有很大改善，Mantel相关系数为0.49对0.27；这些结果与菌株特异性相互作用一致。Mantel相关性表明，大于1μm（附着/大型）的原核生物是主要的肌病毒来源。对微多样性的考虑改善了对明显宿主和病毒网络的观察，并为影响谱系成功的生态和进化因素提供了见解，对生态系统恢复力和微生物功能具有重要意义。
