Dataset Information

Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.

ABSTRACT: There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating successional niche differentiation amongst soil biota. As predicted, early successional systems had greater abundance of genes associated with motility, but fewer genes relating to DNA/RNA/protein metabolism, cell division and cell cycle. Contrary to predictions, there were no significant differences in cell signaling, virulence and defense-related genes. Also, stress related genes were less abundant in later succession. The early successional system had lower taxonomic diversity but higher functional gene diversity. Over time, community characteristics changed progressively, but by the end of the experiment had not returned to the 'original' state of the system before disturbance. Results indicated a predictable sequence of gene functions and taxa following disturbance, analogous to ecosystem succession for large organisms. It is unclear if and when the system would return to its pre-disturbance state.

SUBMITTER: Choi S

PROVIDER: S-EPMC5442152 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.

Choi Soobeom S Song Hokyung H Tripathi Binu M BM Kerfahi Dorsaf D Kim Hyoki H Adams Jonathan M JM

Scientific reports 20170523 1

There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating s ...[more]

PMID: 28536449

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Project description:Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.Cd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.

Dataset Information

Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.

Publications

Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.

Similar Datasets

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