title: Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea.
abstract: BACKGROUND
  Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing.
  
  
  RESULTS
  Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans.
  
  
  CONCLUSIONS
  Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.
authors: Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan. chtzeng@gmail.com.|Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. chtzeng@gmail.com.|Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. chtzeng@gmail.com.
authors: Ching-Hung
authors: CH
authors: Tseng
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. chiangpw@gate.sinica.edu.tw.
authors: Pei-Wen
authors: PW
authors: Chiang
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. hungchunlai0729@gmail.com.|Institute of Oceanography, National Taiwan University, Taipei, Taiwan. hungchunlai0729@gmail.com.
authors: Hung-Chun
authors: HC
authors: Lai
authors: Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan. fkshiah@rcec.sinica.edu.tw.
authors: Fuh-Kwo
authors: FK
authors: Shiah
authors: Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan. leontj@gate.sinica.edu.tw.
authors: Ting-Chang
authors: TC
authors: Hsu
authors: Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan. r90241213@gmail.com.
authors: Yi-Lung
authors: YL
authors: Chen
authors: Institute of Oceanography, National Taiwan University, Taipei, Taiwan. lswen@ntu.edu.tw.
authors: Liang-Saw
authors: LS
authors: Wen
authors: Institute of Oceanography, National Taiwan University, Taipei, Taiwan. cmtseng99@ntu.edu.tw.
authors: Chun-Mao
authors: CM
authors: Tseng
authors: Institute of Oceanography, National Taiwan University, Taipei, Taiwan. winyang@ntu.edu.tw.
authors: Wung-Yang
authors: WY
authors: Shieh
authors: Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia. isaam.saeed@gmail.com.
authors: Isaam
authors: I
authors: Saeed
authors: Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia. saman@unimelb.edu.au.
authors: Saman
authors: S
authors: Halgamuge
authors: Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan. sltang@gate.sinica.edu.tw.|Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. sltang@gate.sinica.edu.tw.|Institute of Oceanography, National Taiwan University, Taipei, Taiwan. sltang@gate.sinica.edu.tw.
authors: Sen-Lin
authors: SL
authors: Tang
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D002681:China; D016000:Cluster Analysis; D019295:Computational Biology; D005092:Exonucleases / Q000235:genetics / Q000378:metabolism; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D056186:Metagenomics; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D014510:Urease / Q000235:genetics / Q000378:metabolism; D014805:Vitamin B 12 / Q000096:biosynthesis
chemical_list: D026901:Membrane Transport Proteins; D012336:RNA, Ribosomal, 16S; D005092:Exonucleases; D014510:Urease; D014805:Vitamin B 12