While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera “Candidatus Planktophila” (acI-A) and “Candidatus Nanopelagicus” (acI-B) and the proteobacterial genus “Candidatus Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community by-product. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies.

中文翻译：

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流线型和丰富的浮游细菌在功能群组中茁壮成长

虽然挑剔的微生物在其自然群落中可能丰富且无处不在，但由于营养缺陷或其他依赖性，许多微生物无法在实验室中无菌生长。为了克服营养缺陷，这些微生物依赖于它们周围的群体。一个群组可能由亲属（生态型）或更远亲的生物（社区）组成，合作是互惠的或非互惠的和昂贵的（黑皇后假设）或无成本的（副产品）。这些代谢伙伴关系（无论是在单一物种种群还是社区级别）使这些谱系在自然界中占主导地位并共存。在这里，我们研究了这些合作模型的相关性，以解释双混相中营养淡水湖中占主导地位的挑剔浮游细菌的丰度和普遍性。Candidatus Planktophila”（acI-A）和“ Candidatus Nanopelagicus”（acI-B）以及变形菌属“ Candidatus Fonsibacter”（LD12）。虽然“ Ca . 浮游生物”和“ Ca. Fonsibacter”在它们的自然栖息地没有相关性，它们有可能在实验室环境中互补。我们还调查了双功能的过氧化氢酶，过氧化物酶的katG（共同利益，其中“钙。Planktophila”取决于），并在湖中的最有可能的供应商。此外，我们发现虽然生态型和社区合作相结合可以解释“ Ca . Planktophila”种群丰度，“ Ca ”的成功。Nanopelagicus”和“ Ca。Fonsibacter”更好地解释为社区副产品。“ Ca 的生态型分化。Fonsibacter”作为一种逃避捕食的手段得到了支持，但不是为了克服营养缺陷。