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Marine bacterial, archaeal and protistan association networks reveal ecological linkages

Steele, Joshua A. and Countway, Peter D. and Xia, Li and Vigil, Patrick D. and Beman, J. Michael and Kim, Diane Y. and Chow, Chery-Emiliane T. and Sachdeva, Rohan and Jones, Adriane C. and Schwalbach, Michael S. and Rose, Julie M. and Hewson, Ian and Patel, Anand and Sun, Fengzhu and Caron, David A. and Fuhrman, Jed A. (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME Journal, 5 (9). pp. 1414-1425. ISSN 1751-7362. https://resolver.caltech.edu/CaltechAUTHORS:20111109-071212431

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Abstract

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible ‘keystone’ species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/ismej.2011.24DOIArticle
http://www.nature.com/ismej/journal/v5/n9/full/ismej201124a.htmlPublisherArticle
ORCID:
AuthorORCID
Patel, Anand0000-0001-6319-658X
Sun, Fengzhu0000-0002-8552-043X
Additional Information:© 2011 International Society for Microbial Ecology. Received 2 November 2010; Revised 4 February 2011; Accepted 4 February 2011; Published online 24 March 2011. We thank the captain and crew of the R/V Seawatch, M. Neumann and R. Smith for oxygen, salinity and chlorophyll data; Z. Zheng for nutrient data. We thank D. Capone, W. Ziebis, J. Devinny D. Keifer and E. Berlow for helpful comments on earlier versions of this manuscript, and anonymous reviewers for their careful reading and excellent comments that improved this paper. The US National Science Foundation Microbial Observatories and Biological Oceanography programs funded this research, grants 0703159, 0623575 and 0648581.
Funders:
Funding AgencyGrant Number
NSFMCB-0703159
NSFOCE-0623575
NSFOCE-0648581
Subject Keywords:co-occurrence patterns; stramenopiles; dinoflagellates; SAR11; cyanobacteria; time series
Issue or Number:9
Record Number:CaltechAUTHORS:20111109-071212431
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20111109-071212431
Official Citation:Marine bacterial, archaeal and protistan association networks reveal ecological linkages Joshua A Steele, Peter D Countway, Li Xia, Patrick D Vigil, J Michael Beman, Diane Y Kim, Cheryl-Emiliane T Chow, Rohan Sachdeva, Adriane C Jones, Michael S Schwalbach, Julie M Rose, Ian Hewson, Anand Patel, Fengzhu Sun, David A Caron and Jed A Fuhrman ISME J 5: 1414-1425; advance online publication, March 24, 2011; doi:10.1038/ismej.2011.24
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27689
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:09 Nov 2011 15:42
Last Modified:09 Mar 2020 13:19

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