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Applied and Environmental Microbiology, April 2001, p. 1751-1765, Vol. 67, No. 4
School of Biosphere Sciences, Hiroshima
University, Higashi-hiroshima 739-8528,1 and
Deep-Sea Research Department, Japan Marine Science and
Technology Center, Yokosuka 237-0061,2 Japan
Received 22 September 2000/Accepted 2 February 2001
The phylogenetic diversity of the ribulose-1,5-bisphosphate
carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of
deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated
from seven samples, including samples from the Mid-Atlantic Ridge and
various deep-sea habitats around Japan. The kinds of samples were
hydrothermal vent water and chimney fragment; reducing sediments from a
bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing
tissues of the vent mussel, Bathymodiolus sp., and the seep
vestimentiferan tubeworm, Lamellibrachia sp. The RuBisCO
genes that encode both form I and form II large subunits (cbbL and cbbM) were amplified by PCR from the
seven deep-sea sample DNA populations, cloned, and sequenced. From each
sample, 50 cbbL clones and 50 cbbM clones, if
amplified, were recovered and sequenced to group them into operational
taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total cbbL clones, and a total of 24 OTUs were recorded
from the 250 total cbbM clones. All the current OTUs have
the characteristic RuBisCO amino acid motif sequences that exist in
other RuBisCOs. The recorded OTUs were related to different RuBisCO
groups of proteobacteria, cyanobacteria, and eukarya. The diversity of
the RuBisCO genes may be correlated with certain characteristics of the
microbial habitats. The RuBisCO sequences from the symbiont-bearing
tissues showed a phylogenetic relationship with those from the ambient
bacteria. Also, the RuBisCO sequences of known species of thiobacilli
and those from widely distributed marine habitats were closely
related to each other. This suggests that the
Thiobacillus-related RuBisCO may be distributed globally
and contribute to the primary production in the deep sea.
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.4.1751-1765.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Phylogenetic Diversity of Ribulose-1,5-Bisphosphate
Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea
Microorganisms
*
Corresponding author. Mailing address: School of
Biosphere Sciences, Hiroshima University, 1-4-4 Kagamiyama,
Higashi-hiroshima 739-8528, Japan. Phone: 81-824-24-7986. Fax:
81-824-22-7059. E-mail: takn{at}hiroshima-u.ac.jp.
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