Open AccessBias of marker genes in PCR of anammox bacteria in natural habitats
Author(s) -
Cai Min,
Fei Ye,
Jiapeng Wu,
Qihang Wu,
Yu Wang,
Yiguo Hong
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0239736
Subject(s) - biology , 16s ribosomal rna , gene , bacteria , anammox , molecular marker , genetic marker , marker gene , genetics , ecology , microbiology and biotechnology , chemistry , denitrifying bacteria , organic chemistry , nitrogen , denitrification
The identification of anammox bacteria is mostly relied on PCR with various marker genes. However, the community composition revealed by different marker genes and whether the marker genes influence the resulted community composition remain unclear. We compared the community structure of anammox bacteria in enriched and natural environments revealed by 16S rRNA and functional genes ( hzo , hzsA and hzsB ) from public database and published papers. The genus of Ca . Scalindua showed the lowest similarities with other genera, especially for the hzsA gene (66.9%-68.6%). The 16S rRNA gene is the most commonly used marker gene in natural habitats with 151 out 221 papers in total. The anammox bacterial community composition is distributed according to the source of habitat regardless the use of various marker genes. The role of marker gene is limited with explanatory of 5.4% for variance of community composition, versus 20.5% of habitat. The effect of marker gene is mainly acted on freshwater habitat, which shows significant different community composition revealed by 16S rRNA and hzo , with Ca . Brocadia and Ca . Jettenia as dominant genus, respectively.