Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea

被引:16
作者
Wemheuer, Bernd [1 ,2 ]
Wemheuer, Franziska [1 ,3 ]
Meier, Dimitri [1 ]
Billerbeck, Sara [4 ]
Giebel, Helge-Ansgar [4 ]
Simon, Meinhard [4 ]
Scherber, Christoph [5 ]
Daniel, Rolf [1 ]
机构
[1] Univ Gottingen, Inst Microbiol & Genet, Grisebachstr 8, D-37077 Gottingen, Germany
[2] Univ New South Wales, Sch Biol Earth & Environm Sci, Ctr Marine Bioinnovat, Sydney, NSW 2052, Australia
[3] Univ New South Wales, Sch Biol Earth & Environm Sci, Evolut & Ecol Res Ctr, Sydney, NSW 2052, Australia
[4] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm ICBM, Carl von Ossietzky Str 9-11, D-26111 Oldenburg, Germany
[5] Univ Munster, Inst Landscape Ecol, Heisenbergstr 2, D-48149 Munster, Germany
关键词
microbial diversity; microbial ecology; structural modelling; functional predictions; marine microbiology; DISSOLVED ORGANIC-MATTER; 16S RIBOSOMAL-RNA; FREE AMINO-ACIDS; MARINE BACTERIOPLANKTON; BACTERIAL COMMUNITIES; DIVERSITY; BLOOM; OCEAN; DYNAMICS; CLADE;
D O I
10.3390/microorganisms5040068
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.
引用
收藏
页数:16
相关论文
共 61 条
[11]   QIIME allows analysis of high-throughput community sequencing data [J].
Caporaso, J. Gregory ;
Kuczynski, Justin ;
Stombaugh, Jesse ;
Bittinger, Kyle ;
Bushman, Frederic D. ;
Costello, Elizabeth K. ;
Fierer, Noah ;
Pena, Antonio Gonzalez ;
Goodrich, Julia K. ;
Gordon, Jeffrey I. ;
Huttley, Gavin A. ;
Kelley, Scott T. ;
Knights, Dan ;
Koenig, Jeremy E. ;
Ley, Ruth E. ;
Lozupone, Catherine A. ;
McDonald, Daniel ;
Muegge, Brian D. ;
Pirrung, Meg ;
Reeder, Jens ;
Sevinsky, Joel R. ;
Tumbaugh, Peter J. ;
Walters, William A. ;
Widmann, Jeremy ;
Yatsunenko, Tanya ;
Zaneveld, Jesse ;
Knight, Rob .
NATURE METHODS, 2010, 7 (05) :335-336
[12]   Associating microbiome composition with environmental covariates using generalized UniFrac distances [J].
Chen, Jun ;
Bittinger, Kyle ;
Charlson, Emily S. ;
Hoffmann, Christian ;
Lewis, James ;
Wu, Gary D. ;
Collman, Ronald G. ;
Bushman, Frederic D. ;
Li, Hongzhe .
BIOINFORMATICS, 2012, 28 (16) :2106-2113
[13]   Comparison between MICRO-CARD-FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic [J].
De Corte, Daniele ;
Sintes, Eva ;
Yokokawa, Taichi ;
Herndl, Gerhard J. .
ENVIRONMENTAL MICROBIOLOGY REPORTS, 2013, 5 (02) :272-281
[14]   The microbial ocean from genomes to biomes [J].
DeLong, Edward F. .
NATURE, 2009, 459 (7244) :200-206
[15]   STOCKS AND DYNAMICS OF BACTERIOPLANKTON CARBON DURING THE SPRING BLOOM IN THE EASTERN NORTH-ATLANTIC OCEAN [J].
DUCKLOW, HW ;
KIRCHMAN, DL ;
QUINBY, HL ;
CARLSON, CA ;
DAM, HG .
DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, 1993, 40 (1-2) :245-263
[16]   Search and clustering orders of magnitude faster than BLAST [J].
Edgar, Robert C. .
BIOINFORMATICS, 2010, 26 (19) :2460-2461
[17]   Marine microbial community dynamics and their ecological interpretation [J].
Fuhrman, Jed A. ;
Cram, Jacob A. ;
Needham, David M. .
NATURE REVIEWS MICROBIOLOGY, 2015, 13 (03) :133-146
[18]   Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing [J].
Gentile, Gabriella ;
Giuliano, Laura ;
D'Auria, Giuseppe ;
Smedile, Francesco ;
Azzaro, Maurizio ;
De Domenico, Maria ;
Yakimov, Michail M. .
ENVIRONMENTAL MICROBIOLOGY, 2006, 8 (12) :2150-2161
[19]   Planktomarina temperata gen. nov., sp nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea [J].
Giebel, Helge-Ansgar ;
Kalhoefer, Daniela ;
Gahl-Janssen, Renate ;
Choo, Yoe-Jin ;
Lee, Kiyoung ;
Cho, Jang-Cheon ;
Tindall, Brian J. ;
Rhiel, Erhard ;
Beardsley, Christine ;
Aydogmus, Oemer O. ;
Voget, Sonja ;
Daniel, Rolf ;
Simon, Meinhard ;
Brinkhoff, Thorsten .
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013, 63 :4207-4217
[20]   Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate [J].
Giebel, Helge-Ansgar ;
Kalhoefer, Daniela ;
Lemke, Andreas ;
Thole, Sebastian ;
Gahl-Janssen, Renate ;
Simon, Meinhard ;
Brinkhoff, Thorsten .
ISME JOURNAL, 2011, 5 (01) :8-19