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Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

机译：个体生理适应性使长期培养期间选定的细菌类群流行

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Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55?days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter. In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects (“bottle effect”) may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55?days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called “bottle effect,” which is well known to occur during enclosure experiments.
机译：外壳实验经常用于研究环境条件变化对微生物组合的影响。然而，迄今为止，孵化本身如何挑战复杂的细菌群落尚不清楚。在这项研究中，通过长期分批孵育，结合了元蛋白质组分析，16S rRNA基因分析和细胞计数，评估了来自海洋，中盐和寡盐条件下的细菌群落。在实验的早期，这三个细菌群落高度不同，其组成也有很大差异。在实验的早期阶段，用陆源溶解的有机碳处理围护结构与对照围护结构相比，存在显着差异。但是，在55天后，在海洋和中卤条件下，被操纵和控制围栏中的细菌群落全部被γ-变形杆菌海绵状杆菌所控制。在寡盐环抱中，hgc组的放线菌群I（hgc-I）在培养后期仍保持丰富。元蛋白质组学分析表明，除了先前描述的放牧抗性之外，使用基于外膜的内部能量存储的能力还可以使γ-变形杆菌海绵状细菌在长期孵育中占主导地位。在低盐条件下，外部顽固碳的利用似乎更为重要（hgc-I）。复杂的自然微生物群落的封闭实验是研究操纵效果的重要工具。但是，特定物种的特性（例如单个碳存储策略）可能会导致与操作无关的影响，因此在解释封闭环境的结果时需要考虑这些因素。在微生物生态学中，封闭环境研究通常用于调查单个环境因素对封闭环境的影响。复杂的细菌群落。但是，除了操作外，由于外壳本身，可能会发生意想不到的效果（“瓶效应”）。在这项研究中，我们分析了来自波罗的海的三种不同盐度的细菌群落，比较了它们在孵化初期和孵化55天后的组成和生理活性。我们的结果表明，内部碳存储策略会影响某些细菌物种的成功，而与实验操作无关。因此，尽管封闭试验仍然是环境研究中的有效工具，但必须严格遵循微生物群落组成的变化。长期批量封闭过程中对元蛋白质组的这一研究扩展了我们对所谓的“瓶效应”的当前理解，众所周知，这种效应是在封闭实验中发生的。

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