Agulhas Current Properties Shape Microbial Community Diversity and Potential Functionality

Phoma, Sandra; Vikram, Surendra; Jansson, Janet K.; Ansorge, Isabelle J.; Cowan, Don A.; Van de Peer, Yves; Makhalanyane, Thulani P.

doi:10.1038/s41598-018-28939-0

Agulhas Current Properties Shape Microbial Community Diversity and Potential Functionality

Journal Article · Thu Jul 12 00:00:00 EDT 2018 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-018-28939-0· OSTI ID:1491161

Phoma, Sandra ^[1]; Vikram, Surendra ^[1]; Jansson, Janet K. ^[2]; Ansorge, Isabelle J. ^[3]; Cowan, Don A. ^[1]; Van de Peer, Yves ^[4]; ^[1]

Univ. of Pretoria (South Africa)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Univ. of Cape Town (South Africa)
Univ. of Pretoria (South Africa); VIB Centre for Plant Systems Biology, Ghent (Belgium); Ghent Univ. (Belgium)

Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas current system and the Subtropical convergence in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for oxygen minimum zone communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulphur cycling capacity is the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas current system, particularly depth-related parameters, substantially influence microbial community structure. While the capacity for biogeochemical cycling of nitrogen and sulphur is linked primarily by the dominant Gammaproteobacterial taxa, ecologically rare taxa drive carbon cycling.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1491161

Report Number(s):: PNNL-SA--135321

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 8; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (108)

The Dynamical Subtropical Front: The Dynamical Subtropical Front Graham, Robert M.; De Boer, Agatha M. Journal of Geophysical Research: Oceans, Vol. 118, Issue 10 https://doi.org/10.1002/jgrc.20408	journal	October 2013
Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN Huson, Daniel H.; Mitra, Suparna Methods in Molecular Biology https://doi.org/10.1007/978-1-61779-585-5_17	book	January 2012
First principles of terrestrial life: exemplars for potential extra-terrestrial biology von Hegner, Ian Theory in Biosciences, Vol. 141, Issue 3 https://doi.org/10.1007/s12064-022-00373-x	journal	July 2022
Phylogenetic analysis and biological characteristic tests of marine bacteria isolated from Southern Ocean (Indian sector) water Gupta, Pratibha; Balaji, Raju; Parani, M. Acta Oceanologica Sinica, Vol. 34, Issue 8 https://doi.org/10.1007/s13131-015-0709-5	journal	August 2015
Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc Estuarine, Coastal and Shelf Science, Vol. 154 https://doi.org/10.1016/j.ecss.2014.12.039	journal	March 2015
Differential impact of lytic viruses on the taxonomical resolution of freshwater bacterioplankton community structure Keshri, Jitendra; Pradeep Ram, Angia Sriram; Colombet, Jonathan Water Research, Vol. 124 https://doi.org/10.1016/j.watres.2017.07.053	journal	November 2017
The Agulhas Return Current Lutjeharms, J. R. E.; Ansorge, I. J. Journal of Marine Systems, Vol. 30, Issue 1-2 https://doi.org/10.1016/s0924-7963(01)00041-0	journal	August 2001
Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies Ting, Claire S.; Rocap, Gabrielle; King, Jonathan Trends in Microbiology, Vol. 10, Issue 3 https://doi.org/10.1016/s0966-842x(02)02319-3	journal	March 2002
An altimetry-based gravest empirical mode south of Africa: 2. Dynamic nature of the Antarctic Circumpolar Current fronts Swart, Sebastiaan; Speich, Sabrina Journal of Geophysical Research, Vol. 115, Issue C3 https://doi.org/10.1029/2009jc005300	journal	January 2010
New CNES-CLS09 global mean dynamic topography computed from the combination of GRACE data, altimetry, and in situ measurements Rio, M. H.; Guinehut, S.; Larnicol, G. Journal of Geophysical Research, Vol. 116, Issue C7 https://doi.org/10.1029/2010jc006505	journal	January 2011
Float experiment studies interocean exchanges at the tip of Africa Boebel, O.; Rae, C. D.; Garzoli, S. Eos, Transactions American Geophysical Union, Vol. 79, Issue 1 https://doi.org/10.1029/98eo00001	journal	January 1998
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea Herlemann, Daniel PR; Labrenz, Matthias; Jürgens, Klaus The ISME Journal, Vol. 5, Issue 10 https://doi.org/10.1038/ismej.2011.41	journal	April 2011
A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters Williams, Timothy J.; Long, Emilie; Evans, Flavia The ISME Journal, Vol. 6, Issue 10 https://doi.org/10.1038/ismej.2012.28	journal	April 2012
Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean Mattes, Timothy E.; Nunn, Brook L.; Marshall, Katharine T. The ISME Journal, Vol. 7, Issue 12 https://doi.org/10.1038/ismej.2013.113	journal	July 2013
Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton Schmidt, Helen F.; Sakowski, Eric G.; Williamson, Shannon J. The ISME Journal, Vol. 8, Issue 1 https://doi.org/10.1038/ismej.2013.124	journal	August 2013
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes The ISME Journal, Vol. 9, Issue 7 https://doi.org/10.1038/ismej.2014.254	journal	January 2015
Bacterial diversity and community composition from seasurface to subseafloor Walsh, Emily A.; Kirkpatrick, John B.; Rutherford, Scott D. The ISME Journal, Vol. 10, Issue 4 https://doi.org/10.1038/ismej.2015.175	journal	October 2015
Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre Bryant, Jessica A.; Aylward, Frank O.; Eppley, John M. The ISME Journal, Vol. 10, Issue 6 https://doi.org/10.1038/ismej.2015.221	journal	December 2015
SAR11 clade dominates ocean surface bacterioplankton communities Morris, Robert M.; Rappé, Michael S.; Connon, Stephanie A. Nature, Vol. 420, Issue 6917 https://doi.org/10.1038/nature01240	journal	December 2002
Photosynthesis genes in marine viruses yield proteins during host infection Lindell, Debbie; Jaffe, Jacob D.; Johnson, Zackary I. Nature, Vol. 438, Issue 7064 https://doi.org/10.1038/nature04111	journal	October 2005
Migration of the subtropical front as a modulator of glacial climate Bard, Edouard; Rickaby, Rosalind E. M. Nature, Vol. 460, Issue 7253 https://doi.org/10.1038/nature08189	journal	July 2009
On the role of the Agulhas system in ocean circulation and climate Beal, Lisa M.; De Ruijter, Wilhelmus P. M.; Biastoch, Arne Nature, Vol. 472, Issue 7344 https://doi.org/10.1038/nature09983	journal	April 2011
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses Roux, Simon; Brum, Jennifer R.; Dutilh, Bas E. Nature, Vol. 537, Issue 7622 https://doi.org/10.1038/nature19366	journal	September 2016
Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects Wilkins, David; van Sebille, Erik; Rintoul, Stephen R. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3457	journal	September 2013
Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability Mark Moore, C.; Mills, Matthew M.; Achterberg, Eric P. Nature Geoscience, Vol. 2, Issue 12 https://doi.org/10.1038/ngeo667	journal	November 2009
Ecology and exploration of the rare biosphere Lynch, Michael D. J.; Neufeld, Josh D. Nature Reviews Microbiology, Vol. 13, Issue 4 https://doi.org/10.1038/nrmicro3400	journal	March 2015
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing Karst, Søren M.; Ziels, Ryan M.; Kirkegaard, Rasmus H. Nature Methods, Vol. 18, Issue 2 https://doi.org/10.1038/s41592-020-01041-y	journal	January 2021
Site-specific molecular analysis of the bacteriota on worn spectacles Fritz, Birgit; März, Melanie; Weis, Severin Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-62186-6	journal	March 2020
Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi Hughes, Riley L.; Arnold, Charles D.; Young, Rebecca R. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-71922-x	journal	September 2020
Pole-to-pole biogeography of surface and deep marine bacterial communities Ghiglione, J. -F.; Galand, P. E.; Pommier, T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 43 https://doi.org/10.1073/pnas.1208160109	journal	October 2012
Marine bacteria exhibit a bipolar distribution Sul, W. J.; Oliver, T. A.; Ducklow, H. W. Proceedings of the National Academy of Sciences, Vol. 110, Issue 6 https://doi.org/10.1073/pnas.1212424110	journal	January 2013
Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus Flombaum, P.; Gallegos, J. L.; Gordillo, R. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 24 https://doi.org/10.1073/pnas.1307701110	journal	May 2013
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes Hawley, A. K.; Brewer, H. M.; Norbeck, A. D. Proceedings of the National Academy of Sciences, Vol. 111, Issue 31 https://doi.org/10.1073/pnas.1322132111	journal	July 2014
Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation Qin, W.; Amin, S. A.; Martens-Habbena, W. Proceedings of the National Academy of Sciences, Vol. 111, Issue 34 https://doi.org/10.1073/pnas.1324115111	journal	August 2014
Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean Pedler, B. E.; Aluwihare, L. I.; Azam, F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 20 https://doi.org/10.1073/pnas.1401887111	journal	April 2014
Drift in ocean currents impacts intergenerational microbial exposure to temperature Doblin, Martina A.; van Sebille, Erik Proceedings of the National Academy of Sciences, Vol. 113, Issue 20 https://doi.org/10.1073/pnas.1521093113	journal	May 2016
Search and clustering orders of magnitude faster than BLAST Edgar, Robert C. Bioinformatics, Vol. 26, Issue 19, p. 2460-2461 https://doi.org/10.1093/bioinformatics/btq461	journal	August 2010
Quality control and preprocessing of metagenomic datasets Schmieder, R.; Edwards, R. Bioinformatics, Vol. 27, Issue 6 https://doi.org/10.1093/bioinformatics/btr026	journal	January 2011
PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang, J.; Kobert, K.; Flouri, T. Bioinformatics, Vol. 30, Issue 5 https://doi.org/10.1093/bioinformatics/btt593	journal	October 2013
Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships Tabita, F. R.; Satagopan, S.; Hanson, T. E. Journal of Experimental Botany, Vol. 59, Issue 7 https://doi.org/10.1093/jxb/erm361	journal	June 2007
Microbe biogeography tracks water masses in a dynamic oceanic frontal system Djurhuus, Anni; Boersch-Supan, Philipp H.; Mikalsen, Svein-Ole Royal Society Open Science, Vol. 4, Issue 3 https://doi.org/10.1098/rsos.170033	journal	March 2017
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms Tabita, F. Robert; Hanson, Thomas E.; Satagopan, Sriram Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, Issue 1504 https://doi.org/10.1098/rstb.2008.0023	journal	May 2008
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons Haas, B. J.; Gevers, D.; Earl, A. M. Genome Research, Vol. 21, Issue 3 https://doi.org/10.1101/gr.112730.110	journal	January 2011
Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community: Functional capacity in Namib Hypoliths Vikram, Surendra; Guerrero, Leandro D.; Makhalanyane, Thulani P. Environmental Microbiology, Vol. 18, Issue 6 https://doi.org/10.1111/1462-2920.13088	journal	December 2015
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data Bengtsson-Palme, Johan; Hartmann, Martin; Eriksson, Karl Martin Molecular Ecology Resources, Vol. 15, Issue 6 https://doi.org/10.1111/1755-0998.12399	journal	March 2015
Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation Galand, Pierre E.; Lovejoy, Connie; Hamilton, Andrew K. Environmental Microbiology, Vol. 11, Issue 4 https://doi.org/10.1111/j.1462-2920.2008.01822.x	journal	April 2009
The Biogeochemical Cycles of Trace Metals in the Oceans Morel, F. M. M. Science, Vol. 300, Issue 5621 https://doi.org/10.1126/science.1083545	journal	May 2003
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior DeLong, E. F. Science, Vol. 311, Issue 5760 https://doi.org/10.1126/science.1120250	journal	January 2006
Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean Swan, B. K.; Martinez-Garcia, M.; Preston, C. M. Science, Vol. 333, Issue 6047 https://doi.org/10.1126/science.1203690	journal	September 2011
Uptake of Dissolved Organic Carbon by Gammaproteobacterial Subgroups in Coastal Waters of the West Antarctic Peninsula Nikrad, Mrinalini P.; Cottrell, Matthew T.; Kirchman, David L. Applied and Environmental Microbiology, Vol. 80, Issue 11 https://doi.org/10.1128/aem.00121-14	journal	March 2014
Seasonal Variations in the Region of the Agulhas Retroflection: Studies with Geosat and FRAM Quartly, G. D.; Srokosz, M. A. Journal of Physical Oceanography, Vol. 23, Issue 9 https://doi.org/10.1175/1520-0485(1993)023<2107:svitro>2.0.co;2	journal	September 1993
Capturing the Transport Variability of a Western Boundary Jet: Results from the Agulhas Current Time-Series Experiment (ACT) Beal, Lisa M.; Elipot, Shane; Houk, Adam Journal of Physical Oceanography, Vol. 45, Issue 5 https://doi.org/10.1175/jpo-d-14-0119.1	journal	May 2015
Variation Partitioning of Species data Matrices: Estimation and Comparison of Fractions Peres-Neto, Pedro R.; Legendre, Pierre; Dray, Stéphane Ecology, Vol. 87, Issue 10 https://doi.org/10.1890/0012-9658(2006)87[2614:vposdm]2.0.co;2	journal	October 2006
Oceanic variability in the western sector of Algoa Bay, South Africa Schumann, Eh; Churchill, Jrs; Zaayman, Hj African Journal of Marine Science, Vol. 27, Issue 1 https://doi.org/10.2989/18142320509504069	journal	January 2005
Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula Luria, Cm; Ducklow, Hw; Amaral-Zettler, La Aquatic Microbial Ecology, Vol. 73, Issue 2 https://doi.org/10.3354/ame01703	journal	October 2014
Effects of nitrate, phosphate and iron on the growth of macroalgae and benthic cyanobacteria from Cocos Lagoon, Guam Kuffner, Ib; Paul, Vj Marine Ecology Progress Series, Vol. 222 https://doi.org/10.3354/meps222063	journal	January 2001
Distinct bacterial groups contribute to carbon cycling during a naturally iron fertilized phytoplankton bloom in the Southern Ocean Obernosterer, Ingrid; Catala, Philippe; Lebaron, Philippe Limnology and Oceanography, Vol. 56, Issue 6 https://doi.org/10.4319/lo.2011.56.6.2391	journal	November 2011
SILVA Databases Quast, Christian; Pruesse, Elmar; Gerken, Jan Encyclopedia of Metagenomics https://doi.org/10.1007/978-1-4614-6418-1_250-6	book	January 2012
SILVA Databases Quast, Christian; Pruesse, Elmar; Gerken, Jan Encyclopedia of Metagenomics https://doi.org/10.1007/978-1-4899-7478-5_250	book	January 2015
Distribution of marine viruses and their potential hosts in Prydz Bay and adjacent Southern Ocean, Antarctic Liang, Y.; Bai, X.; Jiang, Y. Polar Biology, Vol. 39, Issue 2 https://doi.org/10.1007/s00300-015-1787-8	journal	September 2015
Structure and Transport of the Agulhas Current and Its Temporal Variability Bryden, Harry L.; Beal, Lisa M.; Duncan, Louise M. Journal of Oceanography, Vol. 61, Issue 3 https://doi.org/10.1007/s10872-005-0057-8	journal	June 2005
On the meridional extent and fronts of the Antarctic Circumpolar Current Orsi, Alejandro H.; Whitworth, Thomas; Nowlin, Worth D. Deep Sea Research Part I: Oceanographic Research Papers, Vol. 42, Issue 5 https://doi.org/10.1016/0967-0637(95)00021-W	journal	May 1995
The Agulhas Return Current Lutjeharms, J. R. E.; Ansorge, I. J. Journal of Marine Systems, Vol. 30, Issue 1-2 https://doi.org/10.1016/S0924-7963(01)00041-0	journal	August 2001
Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies Ting, Claire S.; Rocap, Gabrielle; King, Jonathan Trends in Microbiology, Vol. 10, Issue 3 https://doi.org/10.1016/S0966-842X(02)02319-3	journal	March 2002
Macronutrient and trace-metal geochemistry of an in situ iron-induced Southern Ocean bloom Frew, Russell; Bowie, Andrew; Croot, Peter Deep Sea Research Part II: Topical Studies in Oceanography, Vol. 48, Issue 11-12 https://doi.org/10.1016/S0967-0645(01)00004-2	journal	January 2001
Bacterioplankton carbon cycling along the Subtropical Frontal Zone off New Zealand Baltar, Federico; Stuck, Esther; Morales, Sergio Progress in Oceanography, Vol. 135 https://doi.org/10.1016/j.pocean.2015.05.019	journal	June 2015
Comparison of three velocity sections of the Agulhas Current and Agulhas Undercurrent Donohue, Kathleen A.; Firing, Eric; Beal, Lisa Journal of Geophysical Research: Oceans, Vol. 105, Issue C12 https://doi.org/10.1029/1999JC000201	journal	December 2000
Comparison of three velocity sections of the Agulhas Current and Agulhas Undercurrent Donohue, Kathleen A.; Firing, Eric; Beal, Lisa Journal of Geophysical Research: Oceans, Vol. 105, Issue C12 https://doi.org/10.1029/1999jc000201	journal	December 2000
An altimetry-based gravest empirical mode south of Africa: 2. Dynamic nature of the Antarctic Circumpolar Current fronts Swart, Sebastiaan; Speich, Sabrina Journal of Geophysical Research, Vol. 115, Issue C3 https://doi.org/10.1029/2009JC005300	journal	January 2010
New CNES-CLS09 global mean dynamic topography computed from the combination of GRACE data, altimetry, and in situ measurements Rio, M. H.; Guinehut, S.; Larnicol, G. Journal of Geophysical Research, Vol. 116, Issue C7 https://doi.org/10.1029/2010JC006505	journal	January 2011
Thermocline and intermediate water communication between the south Atlantic and Indian oceans Gordon, Arnold L.; Weiss, Ray F.; Smethie, William M. Journal of Geophysical Research, Vol. 97, Issue C5 https://doi.org/10.1029/92JC00485	journal	January 1992
Float experiment studies interocean exchanges at the tip of Africa Boebel, O.; Rae, C. D.; Garzoli, S. Eos, Transactions American Geophysical Union, Vol. 79, Issue 1 https://doi.org/10.1029/98EO00001	journal	January 1998
Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability Mark Moore, C.; Mills, Matthew M.; Achterberg, Eric P. Nature Geoscience, Vol. 2, Issue 12 https://doi.org/10.1038/NGEO667	journal	November 2009
Microbial community structure in the North Pacific ocean Brown, Mark V.; Philip, Gayle K.; Bunge, John A. The ISME Journal, Vol. 3, Issue 12 https://doi.org/10.1038/ismej.2009.86	journal	July 2009
Ocean currents shape the microbiome of Arctic marine sediments Hamdan, Leila J.; Coffin, Richard B.; Sikaroodi, Masoumeh The ISME Journal, Vol. 7, Issue 4 https://doi.org/10.1038/ismej.2012.143	journal	November 2012
Erratum: Evidence for successional development in Antarctic hypolithic bacterial communities Makhalanyane, Thulani P.; Valverde, Angel; Birkeland, Nils-Kåre The ISME Journal, Vol. 8, Issue 4 https://doi.org/10.1038/ismej.2013.230	journal	March 2014
Evidence for successional development in Antarctic hypolithic bacterial communities Makhalanyane, Thulani P.; Valverde, Angel; Birkeland, Nils-Kåre The ISME Journal, Vol. 7, Issue 11 https://doi.org/10.1038/ismej.2013.94	journal	June 2013
Metastable garnet in oceanic crust at the top of the lower mantle Kubo, Tomoaki; Ohtani, Eiji; Kondo, Tadashi Nature, Vol. 420, Issue 6917 https://doi.org/10.1038/nature01281	journal	December 2002
Unusual biology across a group comprising more than 15% of domain Bacteria Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C. Nature, Vol. 523, Issue 7559 https://doi.org/10.1038/nature14486	journal	June 2015
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
Prokaryotes: The unseen majority Whitman, W. B.; Coleman, D. C.; Wiebe, W. J. Proceedings of the National Academy of Sciences, Vol. 95, Issue 12 https://doi.org/10.1073/pnas.95.12.6578	journal	June 1998
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks Yilmaz, Pelin; Parfrey, Laura Wegener; Yarza, Pablo Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1209	journal	November 2013
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies Parada, Alma E.; Needham, David M.; Fuhrman, Jed A. Environmental Microbiology, Vol. 18, Issue 5 https://doi.org/10.1111/1462-2920.13023	journal	October 2015
Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean: Iceberg influence on bacterioplankton Dinasquet, Julie; Richert, Inga; Logares, Ramiro Environmental Microbiology, Vol. 19, Issue 6 https://doi.org/10.1111/1462-2920.13769	journal	May 2017
Oceanic fronts: transition zones for bacterioplankton community composition: Fronts delimit bacterioplankton communities Baltar, Federico; Currie, Kim; Stuck, Esther Environmental Microbiology Reports, Vol. 8, Issue 1 https://doi.org/10.1111/1758-2229.12362	journal	January 2016
Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes Mock, Thomas; Daines, Stuart J.; Geider, Richard Global Change Biology, Vol. 22, Issue 1 https://doi.org/10.1111/gcb.12983	journal	July 2015
Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing: BACTERIAL ASSEMBLAGES IN NORTH ATLANTIC OCEAN AgoguÉ, HÉLÈNe; Lamy, Dominique; Neal, Phillip R. Molecular Ecology, Vol. 20, Issue 2 https://doi.org/10.1111/j.1365-294X.2010.04932.x	journal	December 2010
Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea: BIOGEOGRAPHY OF PELAGIC BACTERIA IN THE RED SEA Ngugi, David Kamanda; Antunes, AndrÉ; Brune, Andreas Molecular Ecology, Vol. 21, Issue 2 https://doi.org/10.1111/j.1365-294X.2011.05378.x	journal	December 2011
Non-parametric multivariate analyses of changes in community structure Clarke, K. R. Austral Ecology, Vol. 18, Issue 1 https://doi.org/10.1111/j.1442-9993.1993.tb00438.x	journal	March 1993
Structure and function of the global ocean microbiome Sunagawa, S.; Coelho, L. P.; Chaffron, S. Science, Vol. 348, Issue 6237 https://doi.org/10.1126/science.1261359	journal	May 2015
Environmental characteristics of Agulhas rings affect interocean plankton transport Villar, E.; Farrant, G. K.; Follows, M. Science, Vol. 348, Issue 6237 https://doi.org/10.1126/science.1261447	journal	May 2015
Uptake of Dissolved Organic Carbon by Gammaproteobacterial Subgroups in Coastal Waters of the West Antarctic Peninsula Nikrad, Mrinalini P.; Cottrell, Matthew T.; Kirchman, David L. Applied and Environmental Microbiology, Vol. 80, Issue 11 https://doi.org/10.1128/AEM.00121-14	journal	March 2014
Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems Zehr, Jonathan P.; Kudela, Raphael M. Annual Review of Marine Science, Vol. 3, Issue 1 https://doi.org/10.1146/annurev-marine-120709-142819	journal	January 2011
Seasonal Variations in the Region of the Agulhas Retroflection: Studies with Geosat and FRAM Quartly, G. D.; Srokosz, M. A. Journal of Physical Oceanography, Vol. 23, Issue 9 https://doi.org/10.1175/1520-0485(1993)023<2107:SVITRO>2.0.CO;2	journal	September 1993
Capturing the Transport Variability of a Western Boundary Jet: Results from the Agulhas Current Time-Series Experiment (ACT) Beal, Lisa M.; Elipot, Shane; Houk, Adam Journal of Physical Oceanography, Vol. 45, Issue 5 https://doi.org/10.1175/JPO-D-14-0119.1	journal	May 2015
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Large-scale contamination of microbial isolate genomes by Illumina PhiX control Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/1944-3277-10-18	journal	March 2015
Polinton-like viruses are abundant in aquatic ecosystems Bellas, Christopher M.; Sommaruga, Ruben Microbiome, Vol. 9, Issue 1 https://doi.org/10.1186/s40168-020-00956-0	journal	January 2021
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible McMurdie, Paul J.; Holmes, Susan PLoS Computational Biology, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pcbi.1003531	journal	April 2014
Variation Partitioning of Species data Matrices: Estimation and Comparison of Fractions Peres-Neto, Pedro R.; Legendre, Pierre; Dray, Stéphane Ecology, Vol. 87, Issue 10 https://doi.org/10.1890/0012-9658(2006)87[2614:VPOSDM]2.0.CO;2	journal	October 2006
Chemotaxonomic investigation of phytoplankton in the shelf ecosystem of the KwaZulu-Natal Bight, South Africa Barlow, Rg; Lamont, T.; Gibberd, M-J African Journal of Marine Science, Vol. 37, Issue 4 https://doi.org/10.2989/1814232X.2015.1106976	journal	December 2015
Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre Walsh, Ea; Smith, Dc; Sogin, Ml Aquatic Microbial Ecology, Vol. 75, Issue 1 https://doi.org/10.3354/ame01746	journal	April 2015
Southern Ocean Phytoplankton in a Changing Climate Deppeler, Stacy L.; Davidson, Andrew T. Frontiers in Marine Science, Vol. 4 https://doi.org/10.3389/fmars.2017.00040	journal	February 2017
Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula Signori, Camila N.; Thomas, FranÃ§ois; Enrich-Prast, Alex Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00647	journal	December 2014
Bacterioplankton Biogeography of the Atlantic Ocean: A Case Study of the Distance-Decay Relationship Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00590	journal	April 2016
Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible McMurdie, Paul J.; Holmes, Susan arXiv https://doi.org/10.48550/arxiv.1310.0424	text	January 2013

Figures / Tables (5)

Similar Records

Phylogenetically conserved resource partitioning in the coastal microbial loop

Journal Article · Fri Aug 11 00:00:00 EDT 2017 · The ISME Journal · OSTI ID:1394611

Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

Journal Article · Mon Apr 07 00:00:00 EDT 2014 · Frontiers in Microbiology, 5:Article No. 109 · OSTI ID:1129289

Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

Journal Article · Tue Aug 18 00:00:00 EDT 2020 · mBio (Online) · OSTI ID:1651272

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Agulhas current
biogeochemistry
carbon
nitrogen
sulphur

Agulhas Current Properties Shape Microbial Community Diversity and Potential Functionality

Citation Formats

References (108)

Figures / Tables (5)

Similar Records

Related Subjects