Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

Won, Nam‐Il; Kim, Kihwan; Kang, Jian; Park, Sang Rul; Lee, Hyuk Je

doi:10.3390/ijerph14020130

Cited by 46 publications

(31 citation statements)

References 41 publications

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“…Microbial communities in the sediments had higher diversity than in the water samples. This conclusion is reasonable as has been established through numerous studies of various aquatic ecosystems (Feng et al, 2009;Shulse et al, 2017;Sogin et al, 2006;Won et al, 2017). Higher microbial diversity in marine sediments is thought to be because sediments offer the surface for interaction of water column-derived organic matter with benthic microbial communities (Probandt et al, 2017).…”

Section: Discussionsupporting

confidence: 67%

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

Wambua

Gourlé

Villiers

et al. 2019

Preprint

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Microbial communities are essential components of natural ecosystems. Of the global oceans, the Indian Ocean remains the least studied in terms of its microbial diversity, despite it being a highly dynamic tropical water body. Metagenomics methods have significantly advanced studies in marine microbial ecology in recent years. Preliminary metabarcoding assessments are recommended to mitigate against the associated costs, prior to the metagenomics study, to give an impression of the diversity expected and determine the sequencing effort required.We report here the first metabarcoding survey of bacterial diversity of the western Indian Ocean (WIO) using samples used for optimizing environmental DNA (eDNA) isolation as pilot experiment for a metagenomic study investigating the coral-reef microbiome of the region. Sampling of water and sediment samples was done near-shore sublittoral and within the coral reef.About 3,000 microbial ribotypes were inferred, from which 41 phyla were uncovered. Sediments registered higher alpha diversity than seawater samples. The phylum Proteobacteria was dominant with its members constituting over 60% of the ribosomal sequence variants (RSVs). The other abundant bacteria were members of Bacteroidetes and Cyanobacteria phyla. We identified bacterial species with potential broad biotechnological applications, underscoring the WIO's richness and the usefulness of eDNA metabarcoding approaches in bioprospecting as well as monitoring and/or surveying marine ecosystems.

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Section: Discussionsupporting

confidence: 67%

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

Wambua

Gourlé

Villiers

et al. 2019

Preprint

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“…Marine environments represent the richest source of new genes, enzymes, and natural products [5]. Marine bacterial community structure is affected by several factors such as inorganic nutrient concentration [6], N [7,8], P [7], change in season, adjacent habitat [9], depth [8,10], oxygen [10], protist predation pressure [11], salinity [7,8,12], dominance of algae, particulate organic carbon, Si (OH) 4 [8], human disturbance, and sand mining activity [13].…”

Section: Introductionmentioning

confidence: 99%

“…The contemporary advances in NGS have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes [15]. NGS approach was employed to survey microbial communities from several marine environments such as the Gulf of Mexico [16,17], the Georgetown Coast, Malaysia [18], Malipo Beach, South Korea [19], the Canadian Arctic archipelago [8], and the South Sea, Korea [13].…”

Section: Introductionmentioning

confidence: 99%

Marine bacterial communities in the upper gulf of Thailand assessed by Illumina next-generation sequencing platform

Nimnoi

Pongsilp

2020

BMC Microbiol

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Background: The total bacterial community plays an important role in aquatic ecosystems. In this study, bacterial communities and diversity along the shores of the Upper Gulf of Thailand were first characterized. The association between bacterial communities and types of land use was also evaluated. Results: The bacterial communities and diversity of seawater in the Upper Gulf of Thailand, with regard to types of land use, were first revealed by using Illumina next-generation sequencing. A total of 4953 OTUs were observed from all samples in which 554 OTUs were common. The bacterial communities in sampling sites were significantly different from each other. The runoff water from three types of land use significantly affected the community richness and diversity of marine bacteria. Aquaculture sites contained the highest levels of community richness and diversity, followed by mangrove forests and tourist sites. Seawater physicochemical parameters including salinity, turbidity, TSS, total N, and BOD 5 , were significantly different when grouped by land use. The bacterial communities were mainly determined by salinity, total N, and total P. The species richness estimators and OTUs were positively correlated with turbidity. The top ten most abundant phyla and genera as well as the distribution of bacterial classes were characterized. The Proteobacteria constituted the largest proportions in all sampling sites, ranging between 67.31 and 78.80%. The numbers of the Marinobacterium, Neptuniibacter, Synechococcus, Candidatus Thiobios, hgcI clade (Actinobacteria), and Candidatus Pelagibacter were significantly different when grouped by land use. Conclusions: Type of land use significantly affected bacterial communities and diversity along the Upper Gulf of Thailand. Turbidity was the most influential parameter affecting the variation in bacterial community composition. Salinity, total N, and P were the ones of the important factors that shaped the bacterial communities. In addition, the variations of bacterial communities from site-to-site were greater than within-site. The Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Verrucomicrobia, Euryarchaeota, Planctomycetes, Firmicutes, Deep Sea DHVEG-6, and Marinimicrobia were the most and common phyla distributed across the Upper Gulf of Thailand.

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“…The Proteobacteria, especially DeltaProteobacteria and GammaProteobacteria, were found to be the most abundant in all three sediments. Won et al (2017) also showed that the Delta-and GammaProteobacteria were dominant in the sediment and deep sea samples from Korea. Two abundant orders of Deproteobacteria, Desulfobacterales in the Ongnyeon region and Desulfuromonadales in Yeongjong Island, include sulfate-reducing bacteria and sulfur-oxidizing bacteria, respectively.…”

Section: Discussionmentioning

confidence: 85%

“…In particular, due to intensive human activities, such as sewage discharge, excessive fertilizer use, land reclamation projects, and concentration of human civilization near coastal regions, coastal areas face serious ecosystem pollution which is reflected by over-nutrition and lower amounts of dissolved oxygen (Lee et al, 2011;Waycott et al, 2009). Tidal flats in the west coast wetlands of the Korean peninsula are known to be the fifth largest in the world, after the north coast of Europe, the wetlands of the Amazon, the east coast of Canada, and the eastern wetlands of America (Cho et al, 2004;Wilms et al, 2006;Won et al, 2017). The tidal flats of Incheon in Korea are known for their variety of geographical types.…”

Section: Introductionmentioning

confidence: 99%

Comparative microbial communities in tidal flats sediment on Incheon, South Korea

Choi

Jeong

Yoon

et al. 2018

J. Gen. Appl. Microbiol.

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Coastal ecosystems, play critical ecological roles of which tidal flats are a significant component of coastal wetlands, such as habitat and nutrient cycling in aquatic biology. Microbial communities in tidal flats are known to play vital roles of self-purification. And the microbial ecology of the sediment is easily affected by human activities and pollution. In this paper, we applied pyrosequencing technology to investigate microbial communities in three different tidal flats (Ganghwa Island, Ongnyeon land region and Yeongjong Island) on the Incheon, Korea peninsula. A total of 16,906 sequences were obtained. We used these sequences to identify the dominant phyla in the three tidal flats: Proteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. The composition of the bacterial community of Ganghwa Island and the Ongnyeon region were more similar to each other than they were to the bacterial community of Yeongjong Island. Simpson's dominance index of Yeongjong Island was higher than that of the other regions, and the Shannon diversity index of this region was the lowest. Previous research of samples in these regions indicated that the three tidal flats had similar geochemical characteristics. However, their bacterial communities were rather distinct. This might be because the analysis of microbial communities and physiochemical analysis have different perspectives. Therefore, the pyrosequencing of a bacterial community with physiochemical analysis is recommended as an effective monitoring tool for the comprehensive management of tidal flats.

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Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

Cited by 46 publications

References 41 publications

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

Marine bacterial communities in the upper gulf of Thailand assessed by Illumina next-generation sequencing platform

Comparative microbial communities in tidal flats sediment on Incheon, South Korea

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