Metagenomic analysis of the marine coastal invertebrates of South Korea as assessed by Ilumina MiSeq

Kim, Hyewon; Kim, Hyunkyong; Hwang, Hee-seung; Kim, Won

doi:10.1080/19768354.2016.1271012

Cited by 12 publications

(10 citation statements)

References 29 publications

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“…This index is lower to the reported in this study (32,348–39,895). Kim et al obtained a richness of 334 OTUs in a consortium from marine coastal invertebrates of South Korea [41]. This value is lower than that achieved in this study (633 OUTs).…”

Section: Resultscontrasting

confidence: 75%

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

Blanco-Enríquez

Serna

Peralta-Pérez

et al. 2018

IJERPH

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Pollution of freshwater ecosystems from polycyclic aromatic hydrocarbons (PAHs) is a global concern. The US Environmental Protection Agency (EPA) has included the PAHs pyrene, phenanthrene, and naphthalene among the 16 priority compounds of special concern for their toxicological effects. The aim of this study was to adapt and characterize a microbial consortium from ore waste with the potential to remove these three PAHs from water. This microbial consortium was exposed to the target PAHs at levels of 5, 10, 20, 50, and 100 mg L−1 for 14 days. PAH bioremoval was measured using the analytical technique of solid phase microextraction, followed by gas chromatography mass spectrometry (SPME-GC/MS). The results revealed that up to 90% of the target PAHs can be removed from water after 14 days at a concentration level of 100 mg L−1. The predominant group of microorganisms identified at the phylum taxonomic level were the Proteobacteria, while the Actinobacteria were the predominant subgroup. The removal of phenanthrene, naphthalene, and pyrene predominantly occurred in specimens of genera Stenotrophomonas, Williamsia, and Chitinophagaceae, respectively. This study demonstrates that the use of specific microorganisms is an alternative method of reducing PAH levels in water.

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Section: Resultscontrasting

confidence: 75%

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

Blanco-Enríquez

Serna

Peralta-Pérez

et al. 2018

IJERPH

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“…Several studies of marine metagenomics have used the hypervariable regions of 18S, like V1–V2 26 , V4 27 , 28 , or V7 24 . The V8 region was chosen for our study on the basis of its low amplicon-length variability 29 .…”

Section: Introductionmentioning

confidence: 99%

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

Günther

Knebelsberger

Neumann

et al. 2018

Sci Rep

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We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.

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“…Then, 16S and 18S rRNA genes were used to identify cyanobacteria and microalgae, respectively, within the OPRs. Each sequencing sample was prepared in accordance with Illumina 16S and 18S metagenomic sequencing library protocols, as previously described ( (de Muinck et al, 2017 ; Kim et al, 2017 ). Briefly, for 16S rRNA, the internal transcribed spacer 2 (ITS2) region was amplified using PCR with the ITS3/ITS4 primer set ( de Muinck et al, 2017 ; Kim et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation

et al. 2020

PeerJ

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Metagenome studies have provided us with insights into the complex interactions of microorganisms with their environments and hosts. Few studies have focused on microalgae-associated metagenomes, and no study has addressed aquatic microalgae and their bacterial communities in open pond raceways (OPRs). This study explored the possibility of using microalgal biomasses from OPRs for biodiesel and biofertilizer production. The fatty acid profiles of the biomasses and the physical and chemical properties of derived fuels were evaluated. In addition, the phenotype-based environmental adaptation ability of soybean plants was assessed. The growth rate, biomass, and lipid productivity of microalgae were also examined during mass cultivation from April to November 2017. Metagenomics analysis using MiSeq identified ∼127 eukaryotic phylotypes following mass cultivation with (OPR 1) or without (OPR 3) a semitransparent film. Of these, ∼80 phylotypes were found in both OPRs, while 23 and 24 phylotypes were identified in OPRs 1 and 3, respectively. The phylotypes belonged to various genera, such as Desmodesmus, Pseudopediastrum, Tetradesmus, and Chlorella, of which, the dominant microalgal species was Desmodesmus sp. On average, OPRs 1 and 3 produced ∼8.6 and 9.9 g m−2 d−1 (0.307 and 0.309 DW L−1) of total biomass, respectively, of which 14.0 and 13.3 wt% respectively, was lipid content. Fatty acid profiling revealed that total saturated fatty acids (mainly C16:0) of biodiesel obtained from the microalgal biomasses in OPRs 1 and 3 were 34.93% and 32.85%, respectively; total monounsaturated fatty acids (C16:1 and C18:1) were 32.40% and 31.64%, respectively; and polyunsaturated fatty acids (including C18:3) were 32.68% and 35.50%, respectively. Fuel properties determined by empirical equations were within the limits of biodiesel standards ASTM D6751 and EN 14214. Culture solutions with or without microalgal biomasses enhanced the environmental adaptation ability of soybean plants, increasing their seed production. Therefore, microalgal biomass produced through mass cultivation is excellent feedstock for producing high-quality biodiesel and biofertilizer.

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Metagenomic analysis of the marine coastal invertebrates of South Korea as assessed by Ilumina MiSeq

Cited by 12 publications

References 29 publications

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation

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