The microbiome of Brazilian mangrove sediments as revealed by metagenomics

Abstract

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2)S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

Figure 1. Location of mangroves and composition of each analysed dataset.

Codes indicate the name attributed to the datasets analyzed by metagenome.

Figure 2. Taxonomic affiliation of metagenomic reads.

(a) SSU rRNA sequences from the datasets were classified by BLASTN against the RDPII database using Classifier v 2.2 software. (b) Differential proportion of sequences assigned within the phylum Proteobacteria. (c) Results for complete datasets evaluated by BLASTX analysis against the SEED database using MG-RAST v 2.0 software. Others assignment methodologies are presented in the supplemental material (Supplementary Figure S1 and Table S1).

Figure 3. Profile scatter plot indicating the relative proportion of sequences at the 5 level (MG-RAST annotation) determined using STAMP software.

Figure 4. Functional assignment of metagenome sequences.

(a) BLASTX analysis against the COGs database; read numbers were assigned to specific COG functional categories, and (b) BLASTX analysis against the NCBI-NR database conducted using MEGAN 4.0 software; reads numbers were assigned to specific KEGG identifiers.

Figure 5. Part of a SEED-based functional analysis of mangrove metagenomes.

Each item represents a functional role in the SEED and is labelled by the number of reads assigned in each dataset: (a) carbon fixation and methane metabolism; (b) nitrogen metabolism; and (c) sulphur metabolism. Boxes indicate the KEGG characteristic identified, and numbers in circles indicate the number of sequences from each metagenome affiliated with the KEGG function.

Figure 6. Taxonomic affiliation of main microbial groups involved in methane, nitrogen, and sulphur transformations in mangroves.

Reads assigned by MEGAN 4.0 software were based on BLASTX vs. NCBI-NR. Numbers refer to the complete table which is part Supplementary Figure S2.

Figure 7. Principal component analysis of metagenomes based on taxonomic affiliation of reads determined using MG-RAST.

The percentages of variance explained in each axis are indicated.