Taxonomic diversity of bacteria from mangrove sediments of Goa: metagenomic and functional analysis

Abstract

The present study compared the taxonomic diversity and evaluated the functional attributes of the bacterial species from Mandovi and Zuari mangrove sediments, Goa, using paired-end amplicon sequencing of 16S rDNA and culture-based analyses, respectively. 16S rDNA sequencing revealed Proteobacteria, Firmicutes, and Actinobacteria as the dominant phyla in both the sediments. However, the abundance of these phyla significantly differed between the samples. Bacteroidetes from Mandovi sediment, and Acidobacteria and Gemmatimonadetes from Zuari sediment were the other exclusive major phyla. Chloroflexi, Cyanobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia, and WS3 were the minor phyla observed in both. However, a significant difference in the distribution of minor phyla and lower bacterial taxa under each phylum was noted between the sediments, indicating that the resident microbial flora completely differed between them. This was further validated by high values from distance matrix analyses between the samples. In addition, the pathogenic Vibrio sp. was recorded exclusively in Mandovi sediment, while higher abundance of ecologically important bacterial classes including Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Bacilli was observed in Zuari sediment. Taken together, the data indicated that Zuari sediment was taxonomically richer than Mandovi sediment, while a greater incidence of anthropogenic activities occurred in the latter. This observation was further validated by non-parametric richness estimators which were found to be higher for Zuari sediment. The cultured bacterial isolates, all identified as Firmicutes, were tested for activities related to biofertilization and production of enzymes to be used for bioremediation and chemotherapeutic applications. Higher number of bacterial isolates from Mandovi was found to produce indole-acetic-acid, tannase, xylanase, and glutaminase enzymes, and could solubilize phosphate. In contrast, higher proportion of bacterial isolates from Zuari sediment were capable of producing amylase, cellulase, gelatinase, laccase, lipase, protease, and asparaginase enzymes, emphasizing the fact that the Zuari mangrove sediment is a rich reservoir for economically and biotechnologically important bacterial species.

The Study of Microbial Diversity in Mangrove Wetland Ecological System Based on a 16S rDNA Library

“…Phylogenetic analysis revealed that the 50 bacterial clones fell into at least eight major lineages of the bacterial domain: the α-, γ-, δ-, ε-proteobacteria, Bacteroidetes, Planctomycetes, Actinobacteria, and Verrucomicrobia groups. The Proteobacteria group was predominant in the mangrove sediments and this agreed with a report that this group is the major type in most environments [18]. A total of 50 clones, represented by 35 sequence types and accounting for 70% of the gene library, grouped within the four subdivisions of the Proteobacteria.…”

Molecular identification of bacterial isolates from the rhizospheres of four mangrove species in Kenya

“…The results from morphological characterization indicated that the majority of the isolates were circular in form, cream in color, raised elevation, had entire margins and were gram positive. Morphological features have been widely used by most researchers for preliminary identification and placing of bacterial isolates into different morphotypes (Anna et al, 2018;Haldar and Nazareth, 2018;Saseeswari et al, 2016). Although useful, the information on morphological characters is insufficient to be used for final bacterial identification and, therefore, has to be supplemented with other data including the DNA relatedness studies, DNA-DNA hybridization, small subunit (SSU) sequences, cell wall composition and other characterization (Sarker et al, 2015).…”

“…The phylum Firmicutes was the second most dominant and represented by members of the genus Bacillus. Several other studies have reported the occurrence of bacterial species from the genus Bacillus in mangrove habitats (Anna et al, 2018;Haldar and Nazareth, 2018;Mo et al, 2020). One of the reasons is that Bacillus species are easy to culture, and some can form endospores, whose primary function is to ensure their survival under harsh environmental conditions.…”

Invited Review: Biodiversity of Plant Polysaccharide-Degrading Bacteria in Mangrove Ecosystem

“…It was reported that B. subtilis cho40 isolated from the mangrove area of Mandovi estuary, India, can produce a novel halotolerant xylanase (Khandeparker et al 2011). Haldar and Nazareth (2018) isolated 11 xylan-degrading bacteria belonging to B. toyonensis, L. macroides and S. pasteuri from Mandovi estuary and three strains, B. toyonensis, L. macroides and S. hominis from Zuari esturay, Goa, India. Our team also isolated two xylan-degrading bacteria, Mangrovimonas-like bacterium TPBH4 and M. xylaniphage ST2L12 from two mangrove sediments, Taman Paya Bakau and Matang Mangrove Forest, Malaysia, respectively (Dinesh et al 2017;.…”