Linz Alexandra M, Crary Benjamin C, Shade Ashley, Owens Sarah, Gilbert Jack A, Knight Rob, McMahon Katherine D
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.
mSphere. 2017 Jun 28;2(3). doi: 10.1128/mSphere.00169-17. eCollection 2017 May-Jun.
Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including in polymictic lakes (i.e., lakes with multiple mixing events per year), in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and " Omnitrophica" in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including tribe acI-B2 and lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.
细菌在淡水生物地球化学循环中起着关键作用，但淡水细菌群落组成和动态的长期趋势尚未得到很好的描述。我们使用了来自八个沼泽湖的16S rRNA基因扩增子测序数据的多年时间序列，对淡水细菌群落进行普查，并观察丰度的年度和季节性趋势。我们研究的地点涵盖了一系列水柱混合频率，我们假设这与α和β多样性的趋势有关。每个湖泊和水层都包含一个独特的细菌群落，具有不同的丰富度水平和指示类群，这可能反映了所采样的每种湖泊类型的环境条件，包括多循环湖（即每年有多次混合事件的湖泊）中的 ，双循环湖（每年有两次混合事件，通常在春季和秋季）中的 ，以及寡循环湖（没有记录到混合事件的湖泊）中的“全营养菌”。每年在每个地点出现的群落也惊人地独特。尽管群落组成存在意想不到的年际变化，但我们在所有湖泊和水层中检测到了一个核心类群群落，包括acI - B2部落和PnecC谱系。尽管丰度趋势并非每年重复，但群落中的每个淡水谱系都有一种一致的生活方式，由持久性、丰度和变异性定义。我们的分析结果强调了长期多地点观测的重要性，因为仅分析一年的数据或一个湖泊的数据将无法让我们如此全面地描述这些淡水细菌群落的动态和组成。湖泊是研究细菌群落动态的优秀系统，因为它们有清晰的边界和强烈的环境梯度。我们的研究结果表明，细菌群落组成随年份变化，这一发现可能适用于其他生态系统，并对研究设计和解释有影响。从长期尺度上理解细菌群落的驱动因素和控制因素，将既能提高我们对细菌群落基本特性的认识，又能增强我们预测群落状态的能力。在这个特定的生态系统中，沼泽湖在全球碳循环中发挥着不成比例的重要作用，这里提供的信息最终可能有助于完善这些湖泊的碳预算。最后，本研究中的所有数据和代码都可公开获取。我们希望这将成为任何试图利用多年时间序列来回答自己的微生物生态学问题的人的资源。
