Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

Automated summary

Mangroves are highly productive ecosystems with diverse and unexplored microbial communities that play crucial roles in nutrient cycling and maintaining ecosystem services. This study explored the diversity and distribution of nitrogen-fixing and denitrifying bacteria in the rhizospheres of different mangrove species. The results showed that Gammaproteobacteria were predominant in both nitrogen fixation and denitrification. Culturable and unculturable analyses revealed the presence of unculturable groups as well as some culturable groups like Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized. PCR-DGGE analysis also identified 29 novel nifH sequences. Overall, mangrove ecosystems are a potential source for identifying novel microbial communities involved in nutrient cycling.