Isolation of lindane- and endosulfan-degrading bacteria and dominance analysis in the microbial communities by culture-dependent and independent methods.

Bioremediation for lindane and endosulfan removal is a cost-effective approach, but its effectiveness depends on the ability to isolate degrading functionalized microorganisms. Researchers have isolated many lindane and endosulfan degrading bacteria from enrichment cultures based on culture-dependent methods during the past decades. However, it is unknown whether the isolated bacteria can reflect the indigenous predominant degraders in enriching cultures. In this study, we compared the culture-dependent method with selective medium isolation with culture-independent method (PacBio SMRT sequencing of full-length 16S rRNA amplicon) to analyze the bacterial communities from four distinct lindane (LA1 and LC1) and endosulfan (EA1 and EC1) enrichment cultures. From all the isolates we harvested from lindane (63 isolates) and endosulfan (61 isolates) enrichment cultures, their BLAST alignment can only match 5.49 % and 4.32 % of the bacterial operational taxonomic units (OTUs), respectively. Rhodanbacter lindaniclasticus and Pandoraea thiooxydans were the rarely seen potential degrading representatives that were simultaneously enriched and isolated. This study is the first comparative analysis of microbial communities from lindane and endosulfan enrichment culture using culture-dependent and culture-independent methods. Our results suggested that developing a target-specific and efficient microbial isolation method is necessary to harvest and study representative degrading bacteria in the community.