A holistic genome dataset of bacteria and archaea of mangrove sediments

Abstract

Background: Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contribute to pivotal ecological functions in mangrove ecosystems. However, the study of mangrove sediment microbiomes is limited.

Findings: Here, we applied metagenome sequencing analysis of microbial communities in mangrove sediments across Southeast China from 2014 to 2020. This genome dataset includes 966 metagenome-assembled genomes with ≥50% completeness and ≤10% contamination generated from 6 groups of samples. Phylogenomic analysis and taxonomy classification show that mangrove sediments are inhabited by microbial communities with high species diversity. Thermoplasmatota, Thermoproteota, and Asgardarchaeota in archaea, as well as Proteobacteria, Desulfobacterota, Chloroflexota, Acidobacteriota, and Gemmatimonadota in bacteria, dominate the mangrove sediments across Southeast China. Functional analyses suggest that the microbial communities may contribute to carbon, nitrogen, and sulfur cycling in mangrove sediments.

Conclusions: These combined microbial genomes provide an important complement of global mangrove genome datasets and may serve as a foundational resource for enhancing our understanding of the composition and functions of mangrove sediment microbiomes.

Keywords: mangrove wetland; metagenome sequencing; metagenome-assembled genomes; microbial composition; sediment microbiome.

Figure 1:

Geographical distribution of metagenome-assembled genomes. (A) A total of 966 MAGs were recovered from the mangrove sediment metagenomes. Most metagenomes were reassembled for this work using the latest state-of-the-art assembly pipeline. These genomes form the MSM catalog. All MAGs were ≥50% complete and ≤5% contaminated. (B) Geographic distribution of the 6 groups of sediment sites where metagenomic sequencing data were collected. (C) Genome statistics for the representative species of nonredundant MAGs, showing the minimum value, first quartile, median, third quartile, and maximum value.

Figure 2:

Functional annotation and taxonomic classification of the MSM catalog. (A) Functional annotations at the eggNOG category level. S: Function unknown. (B) An overview of annotations for the nonredundant gene catalog. Nonannotation indicates that these genes were not annotated in at least one of the following databases: eggNOG, KEGG, UniRef 90, VFDB, CARD, and CAZy. (C) Number of genes with functional annotations across the 6 functional databases.

Figure 3:

Primary metabolic processes and functional genes in the mangrove sediments. (A) Conceptual diagram of primary metabolic processes. The colors of the arrows represent the metabolic processes. Orange: methane cycle. Green: sulfur cycle. Blue: nitrogen cycle. (B) The abundance of genes implicated in methane, sulfur, and nitrogen cycles. Each row represents a gene, and each column represents a sampling group. For each gene, the total abundance of all samples was logarithmically transformed and shown on the right side (white-green block). The respective abundances of samples were logarithmically transformed and scaled by row (blue-red block).

Figure 4:

Taxonomic classification (domain and phylum levels) of the species-level representative MAGs. (A) The relative abundance of each archaeal or bacterial phylum, the coverage of each MAG was calculated using CoverM (version 0.6.1). (B) Genome statistics for the representative species of nonredundant MAGs. (C) The results of PCoA for the total microbial community in different sampling groups. (D) Taxonomic novelty of the representative species.

Figure 5:

Phylogenomic analysis of archaeal MAGs. The phylogenetic tree was constructed from 43 MAGs from this study. The number of MAGs in each phylum is indicated in parentheses after the phylum name. The bootstrap values >0.9 are shown as red dots on nodes. The tree is unrooted.

Figure 6:

Phylogenomic analysis of bacterial MAGs. The phylogenetic tree was constructed from 686 MAGs from this study. The number of MAGs in each phylum is indicated in parentheses after the phylum name. The bootstrap values >0.9 are shown as red dots on nodes. The tree is unrooted.