Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems

Abstract

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants

“…Our results showed that bacterial species had the highest relative abundance in both habitats (98%) compared to Archaea (0.22%) and Eukaryota (1.77%), whereas the most abundant bacterial Phyla are Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria and Firmicutes, accounting for approximately 85% of the sequences in rhizosphere soil samples. These Phyla have been described as widespread and often abundant in other different soil samples (Aislabie et al, 2013;Imchen et al, 2017;Lauber et al, 2009;Yang, 2015), including Antarctic soils (Bottos et al, 2014;da Silva et al, 2017;Teixeira et al, 2013) and may constitute a core root microbiome playing a pivotal role in plant growth promotion, nutrient acquisition and abiotic stress tolerance (Chen et al, 2017). Proteobacteria is a metabolically diverse group that has been related to nutrient cycling, including carbon, nitrogen and sulfur, by degrading soluble organic molecules such as organic acids, aminoacids and sugars (Eilers et al, 2010).…”

Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities

“…Parameters applied were maximum E-value of 1 × 10 −5 , a minimum percentage identity of 60%, and a minimum alignment length of 15. For functional analysis comparisons, subsystems were implied to assign functional roles to genes [22,23].…”

Insights into Antagonistic Interactions of Multidrug Resistant Bacteria in Mangrove Sediments from the South Indian State of Kerala

“…Mangrove sediment samples were collected from eight different locations along the coastal region of Kerala according to our previous study on the Kerala mangrove resistome (Table 1) [10,11]. These mangrove ecosystems have indirect mild exposure to sewage from anthropogenic activities.…”

“…Table 1. Sampling locations spanning the north and central Kerala (India) were surveyed according to our previous studies [10,11] and mangrove sediments were collected in triplicate from the upper 5-10 cm in sterile sampling bags. The sampling locations and their codes are provided in first and second column, respectively.…”