Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California

Abstract

A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.

Seasonal bacterial niche structures and chemolithoautotrophic ecotypes in a North Atlantic fjord

“…Monitoring programs that generate multi-disciplinary time-series datasets have been instrumental in detecting temporal patterns of change and seasonal shifts/cycles, alongside variability in environmental parameters and biological communities 6 , 7 . Furthermore, high-frequency sampling has allowed quantification of the impacts of short- and long-term stressors on coastal ecosystems specifically 8 – 10 and marine ecosystems in general 11 , 12 .…”

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing

“…The phylogenetic placement algorithms require a reference tree, a corresponding reference multiple sequence alignment, and a collection of query sequences: the output is a set of assignments of the query sequences to branches of the tree (Matsen et al 2012 ). This tool has been recently used to finely characterize microbial communities in coastal marine (Wilson et al 2021 ) and freshwater (Iniesto et al 2021 ) environments. Moreover, it has been applied to profile the gut microbiota in toxic and non-toxic puffer fish species (Li et al 2020 ) and to assign taxonomy to the white shrimp Litopenaeus vannamei gut oligotypes allowing to study the link between the presence and abundance of pathogenic opportunistic Vibrio species and atypical mass mortality (López-Cortés et al 2020 ).…”

Substantial microbial community shifts in response to an exceptional harmful algal bloom in coastal Southern California

“…These bacteria, archaea, and heterotrophic eukaryotes are particularly important for remineralizing bloom-derived organic matter (Buchan et al, 2014). Previous work has identified consistent taxonomic shifts in portions of the heterotrophic community in response to 'typical' sized blooms (Teeling et al, 2016;Wilson et al, 2021) and succession in the bacterial community has been observed following a HAB of Heterosigma akashiwo (Matcher et al, 2021). In particular, members of Flavobacteriales (Kirchman, 2002;Avci et al, 2020;Ferrer-Gonzalez et al, 2020;Matcher et al, 2021;Wilson et al, 2021) and Rhodobacterales Buchan et al, 2014) have both been shown to increase in response to phytoplankton-derived polysaccharides from variously sized blooms.…”