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In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay

  • Microbiology of Aquatic Systems
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Abstract

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.

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Acknowledgments

Thank you to Jim Cloern and the Water Quality of San Francisco Bay monitoring group (including but not limited to Tara Schraga, Jessica Dyke, Amy Kleckner, Jennifer Teschler, Charlie Martin, and Jan Thompson) at USGS and the R/V Polaris crew for facilitating our participation in numerous cruises. This work was supported in part by NSF CAREER grant OCE-0847266 from the Biological Oceanography program (to CAF), the Stanford McGee research grant (JD), and NSF GRFP and Amherst College Fellowships (to ANR). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Sequencing thanks to JGI CSP project 503022 to CAF. Special thanks to Tijana Glavino del Rio at JGI.

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  1. Julian Damashek

    Present address: Department of Biology, Utica College, Utica, NY, 13502, USA

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  1. Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA

    Anna N. Rasmussen, Julian Damashek & Christopher A. Francis

  2. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Emiley A. Eloe-Fadrosh

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  1. Anna N. Rasmussen
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Correspondence to Christopher A. Francis.

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Rasmussen, A.N., Damashek, J., Eloe-Fadrosh, E.A. et al. In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay. Microb Ecol 81, 601–616 (2021). https://doi.org/10.1007/s00248-020-01621-7

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