Metagenomic data of Microbiota in Mangrove Soil from Lukut River, Malaysia

Metagenomics sequencing
The assembled genome contained 6736 shared genes between soil 1 and soil 3, 203,682 shared genes between soil 1 and soil 2, and 66,383 shared genes between soil 2 and soil 3 (Figure 1).

Comparative analysis of metabolic pathways of bacterial diversity
Function annotation based on the KEGG, as shown in Figure 2, reveals that most of the core genes found in mangrove soils are involved in metabolic pathways. The highest genes are involved in carbohydrate metabolism and followed by amino acid metabolism. In addition, the functional annotation based on eggNOG shows the genome isolated from the soils of mangrove trees’ rhizosphere mostly contains genes that are associated with energy production and conversion, amino acid transport, metabolism, replication, recombination and repair, as well as carbohydrate transport and metabolism pathways (Figure 3). In this study, the functional annotation based on the CAZy reveals six CAZy main functions as follows: Glycoside Hydrolase (GH), Glycosyl Transferase (GT), Polysaccharide Lyase (PL), Carbohydrate Esterases (CE), Auxiliary Activities (AA) and Carbohydrate-Binding Modules (CBM) were found in collected mangrove soils (Figure 4).

Metabolic pathways show the signature of bacteria and their function
Carbon fixation was found to be the most prevalent pathway, followed by methane, nitrogen, sulfur, atrazine, and dioxin degradation pathways (Figure 5). Further analysis identified Chloroflexi, Gaiellales bacterium and Acidobacteria as the major microbial taxa affiliated with the carbon fixation pathway. Methanotrophic bacteria, including Methyloceanibacter caenitepidi, M. superfactus, and M. marginalis were also detected (Figure 6). Additionally, several nitrogen-fixing bacteria, such as Chloroflexi bacterium, Acidobacteria bacterium, Actinobacteria bacterium, Frankia sp., proteobacteria bacterium, Betaproteobacteria bacterium, Anaerolineae bacterium, Bradyrhizobium liaoningense, Bradyrhizobium sp., Methyloceanibacter caenitepidi, Methyloceanibacter marginalis, Methyloceanibacter superfactus, Pseudolabrys taiwanensis, Bradyrhizobium manausense, Solirubrobacter sp., Solirubrobacter soli, and Phycicoccus jejuensis were identified (Figure 6).

Furthermore, we also found the presence of sulfate-reducing bacteria (SRB), such as Thiohalobacter thiocyanaticus, Acidobacteria bacterium, Woeseia oceani, Desulfobacteraceae bacterium, Desulfobacterales bacterium, Mycolicibacterium rhodesiae, Gaiellales bacterium, Deltaproteobacteria bacterium and Myxococcales bacterium in the collected soil samples (Figure 6). The heatmap in Figure 6 also shows the presence of various bacterial species classified in the Actinobacteria phylum, including Phycicoccus jejuensis, Solirubrobacterales bacterium, Mycolicibacterium rhodesiae, M. mariokaense, Solirubrobacter sp. and S. soli in the collected soils.