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. 2018 Dec 17;13(12):e0208230.
doi: 10.1371/journal.pone.0208230. eCollection 2018.

Microbial community composition and diversity in the Indian Ocean deep sea REY-rich muds

Shuyan Wang  1   2   3 , Miao Yu  4 , Jiaqiang Wei  1   2   3 , Mu Huang  4 , Xuefa Shi  4 , Hao Chen  1   2   3
Affiliations

Microbial community composition and diversity in the Indian Ocean deep sea REY-rich muds

Shuyan Wang et al. PLoS One. .

Abstract

Studies about the composition and diversity of microbial community in the Rare Earth Elements-rich muds are limited. In this research, we conducted a characterization for the composition and diversity of bacterial and archaeal communities from rare earth elements-rich gravity core sediment at approximately 4800 meters deep in the Indian Ocean by Illumina high-throughput sequencing targeting 16S rRNA genes. The results showed that the most abundant bacteria were Proteobacteria, followed by Firmicutes and Actinobacteria. Amongst Proteobacteria, Gammaproteobacteria are present in all sections of this sediment core accounted for a particularly large proportion of bacterial sequences. Candidatus Nitrosopumilus, with a higher relative abundance in our samples, belongs to Thaumarchaeota. This is the first report on the composition and diversity of rare earth elements-rich muds microbial communities in the Indian Ocean deep sea.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Depth profiles of TN, TC, MC and REY contents at the studied site.
TN, total nitrogen; TC, total carbon; MC, moisture content; REY, rare earth elements.
Fig 2
Fig 2
Majority of sequences belonging to different bacteria a)/archaea b) phyla in core sediment.
Fig 3
Fig 3. Relative abundance of dominant bacterial groups observed in sediments.
Taxonomic distributions are depicted for the ranks of Phylum a), Class b), Order c) and Genera d). Each bar represents the relative abundance of each sample and each color represents a particular bacterial specie.
Fig 4
Fig 4. Relative abundance of dominant archaeal groups observed in sediments.
Taxonomic distributions are depicted for the ranks of Phylum a) and Genera b). Each bar represents the relative abundance of each sample and each color represents a particular bacterial specie.
Fig 5
Fig 5
Principal coordinate analysis (PCoA) plot on the weighted UniFrac distance matrix for bacteria a)/archaea b) community. Different colors and shapes points represent different groups. The I group were GC05. 02 to GC05.07; The II group were GC05.8 to GC05.12; The III group were GC05.13 to GC05.17; The IV group were GC05.18 to GC05.22 and the V group were GC05.23 to GC05.27. Points that were closer together on the ordination have communities that are more similar.
Fig 6
Fig 6. Redundancy analysis (RDA) of the relationship between the environmental factors and bacterial a)/archaeal b) flora composition.
Arrows represent environmental factors.
See this image and copyright information in PMC

References

    1. Xu XK, Zhu WZ, Wang ZJ, Witkamp GJ. Distributions of rare earths and heavy metals in field-grown maize after application of rare earth-containing fertilizer. Sci Total Environ 2005; 293 (1–3): 97–105. - PubMed
    1. Hatje V, Bruland KW, Flegal AR. Increases in anthropogenic gadolinium anomalies and rare earth element concentrations in San Francisco Bay over a twenty-year record. Environ Technol 2016; 50 (8): 4159–4168. - PubMed
    1. Yasuhiro K, Koichiro F, Kentaro N, Yutaro T, Kenichi K, Junichiro O, et al. Deep-sea mud in the Pacific Ocean as a potential resource for rare-earth elements. Nat Geosci 2011; 4 (8): 535–539.
    1. Jiao S, Liu ZS, Lin YB, Yang J, Chen WM, Wei GH. Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns. Soil Biol Biochem 2016; 98:64–73.
    1. Christian LL, Kelly SR, Zach A, Jay L, Noah F. Temporal variability in soil microbial communities across land-use types. The ISME Journal 2013;7 (8): 1641–1650 10.1038/ismej.2013.50 - DOI - PMC - PubMed

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