Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover (“species” replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

尽管是北美西海岸最大的河口，但目前尚无对旧金山湾 (SFB) 水域微生物群落的深入调查。在这项研究中，我们分析了几个分类级别和空间范围（即北湾与南湾）的浮游细菌和古浮游生物群落，以揭示 alpha 和 beta 多样性的模式。我们使用 16S rRNA 基因的高通量测序在 2 年每月时间序列中沿 150 公里横断面收集的 177 个水柱样本中评估社区。在北湾，微生物群落由空间盐度变化构成，而在南湾，季节性变化主导群落动态。沿着北湾陡峭的盐度梯度，我们发现操作分类单位（OTU；97% 的同一性）比粗分类级别具有更高的位点特异性，并且周转率（“物种”替换）很高，揭示了来自新鲜和海洋最终成员的独特微咸群落（在寡卤、中卤和多卤样品中）。在较粗略的分类水平上（例如，门、纲），分类群广泛分布于盐度区（即存在/大量存在于大量样本中），而咸水群落似乎是新鲜群落和海洋群落的混合体。我们还观察到盐度相似的样本之间微咸社区的变化，这可能与北湾和南湾之间的水停留时间差异有关。在整个 SFB 中，悬浮颗粒物与丰富度呈正相关并影响 Beta 多样性的变化。在几个丰富的群体中，包括 SAR11 进化枝（占样本中多达 30% 的读数），OTU 似乎专门用于特定的盐度范围。其他一些生物也表现出明显的季节性丰度，包括聚球藻，Ca。Actinomarina 和Nitrosopumilus样 OTU。总体而言，这项研究代表了对 SFB 微生物群落的首次深入时空调查，并提供了对浮游微生物如何沿着盐度梯度专门针对不同生态位的见解。