ABSTRACT

Aquatic sediment accumulates organic matter and provides microenvironments for the growth of a diverse microbial community with key roles in the biogeochemical nutrient cycling of the lacustrine ecosystem. We investigated vertical and temporal variations of the sedimentary bacterial community composition in a shallow coastal site of eutrophic Lake Pamvotis (northwestern Greece) across 3 horizons between the surface and 5 cm below lake floor (cmblf) during transition to the cold period of the year (Oct–Dec). For this analysis we used Illumina sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene. Bacterial community composition was dominated by Proteobacteria, Bacteroidetes, and Chloroflexi. Rare operational taxonomic units (OTUs) represented 96.09% (standard deviation 0.61%) of richness per sample, contributing significantly to diversity, and only a few became abundant during the study. Abundant OTUs represented <0.005% of richness but accounted for 20–33% of reads in different samples, mainly associated with anaerobic/microaerobic taxa common in polluted aquatic systems, sludge digesters, or wastewater (e.g., Thiolamprovum pedioforme, Candidatus Competibacter, Petrimonas). About 50% of OTUs found at the surface persisted with depth while shared OTUs between any 2 months were always >70% of richness. Overall, sediment bacterial community composition was diverse but remained largely homogeneous in the sediment of this human-impacted ecosystem at the temporal and vertical scale studied here. The study revealed the potential of specific bacterial taxa (e.g., Anaerolineae, Bellilinea) to serve as monitors of specific pollutants (e.g., polycyclic aromatic hydrocarbons) as well as the need to investigate the role of the rare biosphere in ecosystem functioning.

摘要

水生沉积物积累有机物质并为多样化微生物群落的生长提供微环境，在湖泊生态系统的生物地球化学养分循环中起关键作用。我们调查了富营养化的 Pamvotis 湖（希腊西北部）浅海沿岸沉积细菌群落组成的垂直和时间变化，跨越地表和湖底以下 5 厘米（cmblf）之间的 3 个层位，在过渡到一年中的寒冷时期。 10 月至 12 月）。对于该分析，我们使用了 16S rRNA 基因的 V3-V4 高变区的 Illumina 测序。细菌群落结构是由主导变形菌，拟杆菌和绿弯菌门. 稀有操作分类单位 (OTU) 代表每个样本 96.09%（标准偏差 0.61%）的丰富度，对多样性有显着贡献，在研究期间只有少数变得丰富。丰富的 OTU 代表 <0.005% 的丰富度，但占不同样本中读数的 20-33%，主要与受污染的水生系统、污泥消化器或废水中常见的厌氧/微需氧类群有关（例如，Thiolamprovum pedioforme、Candidatus Competibacter、Petrimonas）。在地表发现的约 50% 的 OTU 随深度持续存在，而任何 2 个月之间共享的 OTU 总是> 70% 的丰富度。总体而言，沉积物细菌群落组成多种多样，但在此研究的时间和垂直尺度上，在这个受人类影响的生态系统的沉积物中，沉积物基本保持一致。该研究揭示了特定细菌类群（例如，厌氧菌亚科、贝利菌属）作为特定污染物（例如多环芳烃）的监测器的潜力，以及研究稀有生物圈在生态系统功能中的作用的必要性。