Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake

Abstract

Loktak, one of the largest freshwater lakes of India, is known for floating islands (Phumdi), being made up of a heterogeneous biomass of vegetation and soil. This ecological site represents an exclusive environmental habitat wherein the rhizospheric microbial community of Phumdi plays a key role in biogeochemical cycling of nutrients. A culture-independent whole genome shotgun sequencing based metagenomic approach was employed to unravel the composition of the microbial community and its corresponding functional potential at this environmental habitat. Proteobacteria (51%) was found to be the most dominant bacterial phylum followed by Acidobacteria (10%), Actinobacteria (9%) and Bacteroidetes (7%). Furthermore, Loktak metagenome data were compared with available metagenomes from four other aquatic habitats, varying from pristine to highly polluted eutrophic habitats. The comparative metagenomics approach aided by statistical analysis revealed that Candidatus Solibacter, Bradyrhizobium, Candidatus Koribacter, Pedosphaera, Methylobacterium, Anaeromyxobacter, Sorangium, Opitutus and Acidobacterium genera are selectively dominant at this habitat. Correspondingly, 12 different functional categories were found to be exclusively prevalent at Phumdi compared to other freshwater habitats. These differential features have been attributed to the unique habitat at Phumdi and correlated to the phenomenon of bioremediation at Loktak Lake.

Quantification of the covariation of lake microbiomes and environmental variables using a machine learning‐based framework

“…Most of the other OTUs are from the Phyla Bacteroidetes and Proteobacteria. Many of the lowest distinct taxa we identified have previously been discussed as bioindicators for general ecosystem quality (Ignavibacteriales (Cordier, 2019), Limnobacter (Yang et al, 2019), and Sandaracinaceae (Wei et al, 2019)), certain environmental variables ( Opitutus (Puranik et al, 2016; Plassart et al, 2019), Alcaligenaceae (Sharuddin et al, 2017), Novosphingobium (Astudillo‐García et al, 2019; Reis et al, 2020), and NS11‐12 marine group (Coclet et al, 2019; Henson et al, 2018)), and human interference/impact/pollution ( Actibacter (Kegler et al, 2018), Fluviicola (Chen et al, 2019), and SC‐I‐84 (Pershina et al, 2015)). However, not all of these taxa have previously been identified in lake ecosystems, and most of the OTUs among these bacterial multitask bioindicators are assigned to taxa originally isolated from soil ecosystems (see Table 3).…”

Aquisphaera insulae sp. nov., a new member in the family Isosphaeraceae, isolated from the floating island of Loktak lake and emended description of the genus Aquisphaera

“…This lake is of ecological hotspot with remarkable ora and fauna diversity and declared as Ramsar site in 1990. Insight of the previous metagenome study (Puranik et al 2016) and during our survey for planctomycetes from India (Kumar et al, 2020a,b,c;Kaushik et al, 2020;Kumar et al 2021a,b), strain JC669 T was isolated from the rhizosphere soil of a plant from the oating island of the Loktak lake, whose 16S rRNA gene sequence identity was highest (96.8%) with A. giovannonii OJF2 T . We characterized strain JC669 T using a polyphasic approach and genomic information and compared the characters with the type species of the genus Aquisphaera, A. giovannonii .…”

“…1), which are heterogeneous biomass of vegetation, soil and organic matter at various decomposition stages (Reddy et al 2005). Phumdis constitute a dense rhizosphere extending up to the lake sediment and hence, serve as an ecological habitat for several groups of bacteria like Actinobacteria, Acidobacteria, Proteobacteria, Verrucomicrobia and Planctomycetes (Puranik et al 2016). This lake is of ecological hotspot with remarkable ora and fauna diversity and declared as Ramsar site in 1990.…”

Quantifying the information content of lake microbiomes using a machine learning-based framework

“…Most of the other OTUs are from the Phyla Bacteroidetes and Proteobacteria. Many of the lowest distinct taxa we identified have previously been discussed as bioindicators for general ecosystem quality (Ignavibacteriales [36], Limnobacter [64], and Sandaracinaceae [65]), certain environmental parameters (Opitutus [17,66], Alcaligenaceae [67], Novosphingobium [68,69], and NS11-12 marine group [70,71]), and human interference/impact/pollution (Actibacter [72], Fluviicola [73], and SC-I-84 [74]). However, not all of these taxa have previously been identified in lake ecosystems, and most of the OTUs among these bacterial multi-task bioindicators are assigned to taxa originally isolated from soil ecosystems (see table 3).…”