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Kole wetlands of Kerala are a complex ecological system and are known for the
higher productivity of rice. The Kole lands remain submerged under flood water for
about six months in a year and this seasonal alteration gives it both terrestrial and water
related properties which determine the ecosystem structure. Though several studies have
been conducted for exploring the diversity of fishes, birds, flora, butterflies, etc., in Kole
lands, no systematic studies have been made on rhizosphere microbial diversity.
This study was intended to analyze the bacterial diversity in the rice rhizosphere
ecosystem of Kole lands of Thrissur. Rhizosphere soil samples were collected from three
locations of Kole lands of Thrissur viz. Puzhakkal (Pzk), Mullassery (Mls) and Cherpu
(Chr) and analyzed for physico-chemical and biological properties. Culturable microflora
was enumerated using serial dilution plate method for bacteria, fungi, actinomycetes, N-
fixers, P, K and Zn-solubilizers. Twenty four predominant bacterial isolates were purified
and screened for PGP activities including production of IAA and ammonia and phosphate
solubilization. The bacterial diversity of the rhizosphere samples was analyzed by
metagenomic library construction and sequencing of V3-V4 regions of the 16S rRNA
gene, using Next Generation Sequencing (NGS) technology. The sequences thus obtained
were analyzed for the Operational Taxonomic Units (OTUs) using MEGAN and MG-
RAST server.
The analysis of physico-chemical parameters showed a comparatively low pH in
all the samples. An extreme low pH can reduce the availability of major and secondary
nutrients in the soil. The sample Pzk showed higher content of organic C. Culturable
microflora and microbial biomass C analysis also showed a slight increase in the sample
Pzk. The soil organic C content and microbial biomass C are reported to be positively
correlated. The microbial biomass C is the measure of the weight of the organisms
present.The predominant bacterial phyla in the rice rhizosphere of Kole lands of Thrissur
included Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes and
Nitrospirae. The bacterial population was found higher in the sample Puzhakkal and
comparatively lower in the sample Chr. Phylum Proteobacteria was found to be the most
predominant bacterial phylum in Pzk while, Chloroflexi was more predominant in Mls
and Chr. The classes Acidobacteria and Ktedonobacteria were found dominant in the
samples Mls and Chr and the Pzk sample was dominated by Acidobacteria and
Deltaproteobacteria. The phylum level bacterial diversity was found highest in the sample
Chr with 21 phyla while the genus level bacterial diversity was highest in the sample Mls.
The abundance of genera Desulfobacca, Thermoanaerobaculum, Thioalkalispira,
Anaerolinea,
Ktedonobacter,
Gemmatimonas,
Puedolabrys,
Sulfuricurvum,
Syntrophobacter, Haliangium, Geobacter and Syntrophorhabdus was observed in the
Kole land rice rhizosphere samples. Many of these genera are involved in geo-cycling of
nutrients like Fe, S and Mn and a few are used in waste water treatment. The species-
level bacterial diversity was found to be highest in the sample Mls as indicated by the
Chao1 and observed species indices.
The predominant archaeal phyla in the rice rhizosphere of Kole lands of Thrissur
included Euryarchaeota, Crenarchaeota and Thaumarchaeota. Archaea are still an under-
detected and little-studied part of the soil, so their full influence on global
biogeochemical cycles remains largely unexplored. This study has thrown light on the
diversity of bacterial and archaebacterial communities in the peculiar ecosystem of Kole
lands of Thrissur. Many of the biofertilizer organisms like Azospirillum, Paenibacillus,
Cellulosimicrobium and biocontrol agents like Bacillus and Pseudomonas could be
detected, which could be cultured and used as potential acid tolerant biofertilizers and
PGPR. Many of the ‘Unclassified’ genera could be novel bacteria and more research is
needed to identify their taxonomic position and functional role in the ecosystem.