Microbial Ecology

, 62:813

Phylogenetic Diversity and Ecological Pattern of Ammonia-oxidizing Archaea in the Surface Sediments of the Western Pacific

Environmental Microbiology

DOI: 10.1007/s00248-011-9901-0

Cite this article as:
Cao, H., Hong, Y., Li, M. et al. Microb Ecol (2011) 62: 813. doi:10.1007/s00248-011-9901-0


The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.

Supplementary material

248_2011_9901_MOESM1_ESM.doc (40 kb)
Table S1Statistical analysis of diversity and abundance (DOC 39 kb)
248_2011_9901_MOESM2_ESM.doc (230 kb)
Table S2Statistical analysis of physicochemical parameters and the diversity and abundance of nitrifying prokaryotes (DOC 229 kb)
248_2011_9901_MOESM3_ESM.doc (500 kb)
Figure S1Rarefaction curves of archaeal amoA gene sequences retrieved from the northern SCS on the basis of 5% distance cut-off calculated from DOTUR software (DOC 499 kb)
248_2011_9901_MOESM4_ESM.doc (168 kb)
Figure S2Rarefaction curves of archaeal amoA gene sequences retrieved from the western Pacific on the basis of 5% distance cut-off calculated from DOTUR software (DOC 167 kb)
248_2011_9901_MOESM5_ESM.pdf (2.6 mb)
Figure S3A further expanded information of Fig. 2 (PDF 2709 kb)
248_2011_9901_MOESM6_ESM.doc (146 kb)
Figure S4Principal coordinate analysis (PCoA) (a) for the archaeal amoA gene sequences from the whole northern SCS based on the online UniFrac software (DOC 145 kb)
248_2011_9901_MOESM7_ESM.doc (336 kb)
Figure S5Principal coordinate analysis (PCoA) for the all archaeal amoA gene sequences from the western Pacific represent of every clone library according to the online UniFrac software (DOC 336 kb)
248_2011_9901_MOESM8_ESM.doc (144 kb)
Figure S6Multivariate regression tree (MRT) analysis of the interaction between archaeal amoA lineage abundance (in term of sequence number) and environmental parameters. Columns under each leaf represent the mean of normalized AOA lineage abundance for each lineage significantly correlated with environmental parameters (DOC 144 kb)

Copyright information

© The Author(s) 2011

Authors and Affiliations

  1. 1.School of Biological SciencesThe University of Hong KongHong KongChina
  2. 2.State Key Laboratory of Oceanography in the Tropics, South China Sea Institute of Oceanography, Chinese Academy of SciencesGuangzhouChina