Prokaryotic Diversity in Oxygen Depleted Waters of the Bay of Bengal Inferred Using Culture-Dependent and -Independent Methods

Abstract

There are regions in the world oceans where oxygen saturation is at its lowest, evident at depths between shelf to upper bathyal zone. These regions are known as Oxygen Minimum Zones (OMZs), which reportedly support phylogenetically diverse microbes. In this study, we aimed to characterize prokaryotic diversity in the water samples collected from 43, 200 and 1000 m depth of the Bay of Bengal Time Series location (BoBTS-18.0027°N, 89.0174°E) in the OMZ region. Illumina sequencing generated 3,921,854 reads of 16S rRNA gene amplicons, which corresponded to 5778 operational taxonomic units. The distribution of bacteria at class level varied with depth and oxygen concentration. a-Proteobacteria was found in abundance in 43 m and 1000 m depth water samples. c-Proteobacteria was prominently detected in oxygen-depleted depths of 200 m and 1000 m. AB16 (Marine Group A, originally SAR406) was restricted at dissolved oxygen concentration of 1.5 lM at 200 m. Archaeal members were observed in low abundance (2%), with a high occurrence of phylum Euryarchaeota at 43 m, while Crenarchaeota was detected only at 200 m depth. Select bacterial cultures were screened for their ability to reduce nitrate in vitro, to obtain insights into their possible role in the nitrogen cycle. A total of 156 bacterial isolates clustered majorly with Alcanivorax, Bacillus, Erythrobacter, Halomonas, Idiomarina and Marinobacter. Among them, 11 bacterial genera showed positive nitrate reduction in the Griess test. A large percentage (63.55%) of 16S rRNA gene amplicons corresponded to unidentified OTUs at genus or higher taxonomic levels, suggesting a greater undiscovered prokaryotic diversity in this oxygen depleted region.

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

“…Recently, similar to the present study in the BoBTS, V3 hyper-variable region of 16S rRNA genes was sequenced (97% sequence similarity), reported high diversity at the core and lower OMZ than the surface. Due to restricted sampled depths and higher DO concentration within the core OMZ (1.5 µM) than the present study (0.6 µM) (Fernandes et al, 2019), this could be a reason for such divergent findings. Bryant et al (2012) speculated lower redox potentials and less readily available organic matter conditions in the core OMZ of ETSP to be one of the reasons of low energy availability and thus the cause of reduced microbial richness.…”

“…It was observed that in the present study higher OTU richness could be recovered at ASTS with the use of high throughput sequencing. However, at BoBTS, higher OTU richness was reported in Fernandes et al (2019) where similar molecular identification method was employed. Notably, the DO concentration observed during Fernandes et al (2019) study was higher than those observed in BoBTS-OMZ in the present study.…”

“…Other taxa at class-level including the Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Nitrospinia, Planctomycetacia, and SAR406 clade were also well-reported however varied along the depths and sites sampled in the Indian Ocean OMZs (Fuchs et al, 2005;Bandekar et al, 2018;Fernandes et al, 2019). Pelagic nitrogen and sulfur cycling in the OMZs of the Indian Ocean have recently revealed presence of nitrate-reducing and sulfur-oxidizing bacteria based on biochemical of culture-dependent studies (Mulla et al, 2017;Menezes et al, 2018;Fernandes et al, 2019). Metagenomic analysis in the AS OMZ have revealed presence of denitrifiers and annamox bacteria (Bandekar et al, 2018).…”

“…Culture-dependent and independent analysis of the AS and BoB OMZ and non-OMZ waters have shown a high representation of δ-Proteobacteria and γ-Proteobacteria affiliated to Proteobacteria (Riemann et al, 1999;Fuchs et al, 2005;Divya et al, 2011;Jain et al, 2014;Wang et al, 2016;Bristow et al, 2017;Mulla et al, 2017;Bandekar et al, 2018;Qian et al, 2018;Rajpathak et al, 2018;Fernandes et al, 2019;Paingankar et al, 2019). Other taxa at class-level including the Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Nitrospinia, Planctomycetacia, and SAR406 clade were also well-reported however varied along the depths and sites sampled in the Indian Ocean OMZs (Fuchs et al, 2005;Bandekar et al, 2018;Fernandes et al, 2019). Pelagic nitrogen and sulfur cycling in the OMZs of the Indian Ocean have recently revealed presence of nitrate-reducing and sulfur-oxidizing bacteria based on biochemical of culture-dependent studies (Mulla et al, 2017;Menezes et al, 2018;Fernandes et al, 2019).…”

Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers

“…Large amounts of particulate and dissolved organic matter are characteristic of the watercourses flowing into the Bay of Bengal. Gammaproteobacteria and Alphaproteobacteria dominated the bacterial community composition of the waters of the Bay of Bengal (Ghosh and Bhadury, 2018;Rajpathak et al, 2018;Fernandes et al, 2019;Dhal et al, 2020) and these classes together with Deltaproteobacteria were detected abundantly in sediments of the Sundarbans (Basak et al, 2015). In this study, Deltaproteobacteria were mainly represented by Geobacter at K8 with relevance for the arsenic cycle (Gnanaprakasam et al, 2017).…”