Phylogenetic analyses of archaeal ribosomal DNA sequences from salt pan sediment of Mumbai, India.
The archaeal diversity in salt pan sediment from Mumbai, India, was investigated by 16S rDNA-dependent molecular phylogeny. Small-subunit rRNA (16S rDNA) from salt pan sediment metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain archaea. Thirty-two unique phylotypes were obtained by PCR-based RFLP of 16S rRNA genes using endonucleases Hae111 and Msp1, which were most suitable to score the genetic diversity. These phylotypes spanned a wide range within the domain Archaea including both Crenarchaeota and Euryarcheaota. However, none of the retrieved Crenarchaeota sequences could be grouped with previously cultured Crenarchaeota. Of all the Euryarcheaota sequences, three sequences were related to Haloarchaea, two were related to cultured Methanosarcina sp., and the remaining sequences were affiliated with uncultured Methanosarcina sp., Methanogenium sp., and Methanolobus sp. Most of the sequences determined were closely related to the sequences that had been previously obtained from metagenome of a variety of marine environments. The phylogenetic study of a site investigated for the first time revealed the presence of a highly diverse archaeal population and may represent novel sequences and organisms specially adapted to the salt pan sediment of Mumbai. These findings are of fundamental value for understanding the complexity of salt pan ecosystems.
Ahmad
Nasier
N
Biotechnology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu-Tawi 180001, India.
Sharma
Sarika
S
Khan
Farrah G
FG
Kumar
Rajinder
R
Johri
Sarojini
S
Abdin
Malik Z
MZ
Qazi
Ghulam N
GN
D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D016172:DNA Fingerprinting; D017931:DNA Primers / Q000235:genetics; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D005838:Genotype; D019015:Geologic Sediments / Q000382:microbiology*; D007194:India; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D019642:RNA, Archaeal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
D017931:DNA Primers; D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S