4:45 PM - 5:00 PM
[AOS17-12] Exploring microbial diversity and carbon storage capacity of mangrove sediments through spatiotemporal studies
Keywords:Mangrove, Metagenome, Microbial community
Mangroves are coastal ecosystems found in the tropical and subtropical intertidal zones, where the repetition of submerged and dried conditions shape a unique microbial community in the sediment. Mangrove ecosystems capture and sequester CO2 through photosynthesis. Mangrove sediments are often exposed to anaerobic conditions, preventing the biodegradation of organic matter by microbes, which may contribute to their high carbon sequestration. However, the key microbial members in mangrove sediments and the effects of location and tidal conditions on the microbial community remain to be investigated.
We conducted comprehensive investigations of microbial diversity in mangrove sediments using shotgun metagenomic sequences and assemblies. Sediment samples were collected spatiotemporally from southwestern Japan: monolayer (Okinawa Is.) or multilayer (Iriomote Is.) at low tide. Additionally, some high-tide samples were also collected. We extracted DNA using a DNeasy PowerMax Soil Kit (QIAGEN, Japan), and sequenced it using a DNBSEQ-T7RS platform (PE150; MGI Tech, China) by Genome-Lead Ltd. (Kagawa, Japan). Obtained reads were subjected to quality filtering using fastp v. 0.23.2. Taxonomic profiling was estimated by kaiju v. 1.9.2. Microbial community structures were estimated using the protein-level classification, indicating that phylum Pseudomonadota decreased and phylum Chloroflexota increased with sediment depth at low tide. Phylum Thermodesulfobacteriota, which are responsible for sulfate reduction, were found at a wide range of depths. Regarding phylum Choroflexota, class Anaerolinea was more abundant in the surface layer, and the proportion of class Dehalococcoidia increased with depth. The k-mer spectrum estimated using simka v. 1.5.3 suggested that microbial communities differ among localities rather than tidal conditions in both islands.
In addition, to reconstruct metagenome-assembled genomes (MAGs), the clean reads were assembled using MEGAHIT v. 1.2.9, and the assemblies of less than 1,000 bp were removed using the seqkit v. 2.4.0. We then performed metagenome binning using three algorithms, MetaBAT2 v. 2.15.15, MaxBin2 v. 2.2.7, and CONCOCT v. 1.1.0, and dereplicated and merged using the bin_refinement module of MetaWRAP v. 1.3.2. Completeness and contamination values of bins were calculated using CheckM2 v. 1.0.2, and taxonomic assignment of MAGs was performed using GTDB-Tk2 v. 2.3.2. Ortholog search using orthofinger v. 2.5.5 against MAGs and the total organic carbon (TOC) value of sediments detected 12 candidate gene groups that are specific in the high TOC group.
In this talk, we would like to discuss the genomic characteristics of microorganisms that are potentially involved in carbon cycling and sequestration in mangrove sediments.
We conducted comprehensive investigations of microbial diversity in mangrove sediments using shotgun metagenomic sequences and assemblies. Sediment samples were collected spatiotemporally from southwestern Japan: monolayer (Okinawa Is.) or multilayer (Iriomote Is.) at low tide. Additionally, some high-tide samples were also collected. We extracted DNA using a DNeasy PowerMax Soil Kit (QIAGEN, Japan), and sequenced it using a DNBSEQ-T7RS platform (PE150; MGI Tech, China) by Genome-Lead Ltd. (Kagawa, Japan). Obtained reads were subjected to quality filtering using fastp v. 0.23.2. Taxonomic profiling was estimated by kaiju v. 1.9.2. Microbial community structures were estimated using the protein-level classification, indicating that phylum Pseudomonadota decreased and phylum Chloroflexota increased with sediment depth at low tide. Phylum Thermodesulfobacteriota, which are responsible for sulfate reduction, were found at a wide range of depths. Regarding phylum Choroflexota, class Anaerolinea was more abundant in the surface layer, and the proportion of class Dehalococcoidia increased with depth. The k-mer spectrum estimated using simka v. 1.5.3 suggested that microbial communities differ among localities rather than tidal conditions in both islands.
In addition, to reconstruct metagenome-assembled genomes (MAGs), the clean reads were assembled using MEGAHIT v. 1.2.9, and the assemblies of less than 1,000 bp were removed using the seqkit v. 2.4.0. We then performed metagenome binning using three algorithms, MetaBAT2 v. 2.15.15, MaxBin2 v. 2.2.7, and CONCOCT v. 1.1.0, and dereplicated and merged using the bin_refinement module of MetaWRAP v. 1.3.2. Completeness and contamination values of bins were calculated using CheckM2 v. 1.0.2, and taxonomic assignment of MAGs was performed using GTDB-Tk2 v. 2.3.2. Ortholog search using orthofinger v. 2.5.5 against MAGs and the total organic carbon (TOC) value of sediments detected 12 candidate gene groups that are specific in the high TOC group.
In this talk, we would like to discuss the genomic characteristics of microorganisms that are potentially involved in carbon cycling and sequestration in mangrove sediments.