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Larkin AA, Blinebry SK, Howes C, Lin Y, Loftus SE, Schmaus CA, Zinser ER, Johnson ZI. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific. ISME JOURNAL 2016; 10:1555-67. [PMID: 26800235 DOI: 10.1038/ismej.2015.244] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/30/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023]
Abstract
The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some 'sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.
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Affiliation(s)
- Alyse A Larkin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sara K Blinebry
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Caroline Howes
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Yajuan Lin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sarah E Loftus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Carrie A Schmaus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zackary I Johnson
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
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Gifford SM, Sharma S, Moran MA. Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community. Front Microbiol 2014; 5:185. [PMID: 24795712 PMCID: PMC4006046 DOI: 10.3389/fmicb.2014.00185] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/03/2014] [Indexed: 11/13/2022] Open
Abstract
For bacterial communities containing hundreds to thousands of distinct populations, connecting functional processes and environmental dynamics at high taxonomic resolution has remained challenging. Here we use the expression of ribosomal proteins (%RP) as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in a coastal ocean time series encompassing both seasonal variability and diel dynamics. %RP patterns grouped the taxa into seven activity clusters with distinct profiles in functional gene expression and correlations with environmental gradients. Clusters 1-3 had their highest potential activity in the winter and fall, and included some of the most active taxa, while Clusters 4-7 had their highest potential activity in the spring and summer. Cluster 1 taxa were characterized by gene expression for motility and complex carbohydrate degradation (dominated by Gammaproteobacteria and Bacteroidetes), and Cluster 2 taxa by transcription of genes for amino acid and aromatic compound metabolism and aerobic anoxygenic phototrophy (Roseobacter). Other activity clusters were enriched in transcripts for proteorhodopsin and methylotrophy (Cluster 4; SAR11 and methylotrophs), photosynthesis and attachment (Clusters 5 and 7; Synechococcus, picoeukaryotes, Verucomicrobia, and Planctomycetes), and sulfur oxidation (Cluster 7; Gammaproteobacteria). The seasonal patterns in activity were overlain, and sometimes obscured, by large differences in %RP over shorter day-night timescales. Seventy-eight taxa, many of them heterotrophs, had a higher %RP activity index during the day than night, indicating a strong diel activity rhythm at this coastal site. Emerging from these taxonomically- and time-resolved estimates of in situ microbial activity are predictions of specific ecological groupings of microbial taxa in a dynamic coastal environment.
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Affiliation(s)
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of GeorgiaAthens, GA, USA
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