Estuarine microbial networks and relationships vary between environmentally distinct communities

Sean R Anderson; Elizabeth L Harvey

doi:10.7717/peerj.14005

Estuarine microbial networks and relationships vary between environmentally distinct communities

PeerJ. 2022 Sep 20:10:e14005. doi: 10.7717/peerj.14005. eCollection 2022.

Authors

Sean R Anderson^{1

2}, Elizabeth L Harvey³

Affiliations

¹ Northern Gulf Institute, Mississippi State University, Mississippi State, MS, United States of America.
² Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, United States of America.
³ Department of Biological Sciences, University of New Hampshire, Durham, NH, United States of America.

Abstract

Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO₃, and SiO₄; only NH₄ was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.

Keywords: Amplicon metabarcoding; Estuaries; Microbes; Networks; Nutrients; Prokaryotes; Protists; Relationships; Temperature.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Archaea / genetics
Bacteria* / genetics
Biodiversity
Ecosystem*
Eukaryota / genetics
Prokaryotic Cells

Grants and funding

This work is funded by a Sloan Research Fellowship to Elizabeth Harvey, and a National Science Foundation Grant (OCE-1831625) that supported the collaboration of Sean R Anderson, Margot Chisholm, and Elizabeth Harvey during the summer of 2020. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.