Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing

Liu, Qian; Zhao, Qiannan; McMinn, Andrew; Yang, Eun Jin; Jiang, Yong

doi:10.1007/s42995-020-00062-y

Cited by 38 publications

(14 citation statements)

References 68 publications

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“…High-throughput sequencing technology is widely adopted for profiling the structure and diversity of microbial communities [1][2][3][4][5][6]. However, the results in different studies are not consistent and comparable as all processing steps from sampling to data analysis may introduce bias [7][8][9][10].…”

Section: Introductionmentioning

confidence: 99%

The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments

Shi

Kong

et al. 2022

Microorganisms

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DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities. Here, we studied the effects of three different DNA extraction kits on both prokaryotic and micro-eukaryotic communities by 16S and 18S rRNA gene amplicon sequencing, and further disentangled the influence of primer choice on the micro-eukaryotic communities. Our results showed that the FastDNA SPIN Kit for Soil and DNeasy PowerSoil Kit produced much higher DNA yield with good reproducibility, and observed more eukaryotic OTUs compared to the MinkaGene DNA extraction kit, but all three kits exhibited comparable ability in recovering bacterial alpha diversity. Of the two primer sets, both targeting the V4 region of the 18S rRNA gene, the TAR primer set detected higher number of unique OTUs than the EK primer set, while the EK primer set resulted in longer amplicons and better reproducibility between replicates. Based on our findings, we recommend using the DNeasy PowerSoil Kit with the EK primer set to capture the abundant micro-eukaryotic taxa from freshwater sediment samples. If a more complete picture of the eukaryotic microbial community is desired, the TAR primer set in combination with the FastDNA SPIN Kit is more efficient in this study.

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Section: Introductionmentioning

confidence: 99%

The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments

Shi

Kong

et al. 2022

Microorganisms

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“…Many novel molecular markers have recently been found, and they have been shown to help speed up diagnosis and improve outcomes for women with endometrial cancer. Gene expression profile data or protein chips have also been used to identify certain molecular markers, and a prognosis model has been developed [ 5 ]. These known prognostic indicators are challenging to utilise in clinical practice since they only apply to partial staging and/or tissue grade of endometrial cancer.…”

Section: Introductionmentioning

confidence: 99%

Research on Cancer Molecular Typing Based on High-Throughput Sequencing Technology

Dan

2021

Computational and Mathematical Methods in Medicine

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This paper studies the role of high-throughput measurement technology in cancer molecular typing. Based on the Dendrix algorithm, the model proposed in this paper selects the gene replication time as an inherent attribute that affects the frequency of gene mutations and adds it to the model. After setting the size of the gene set, compared with the Dendrix algorithm, the model does not need to delete the gene set that has been found in the process of searching the pathway, and it can find more driving pathway gene sets. Based on the high coverage and high exclusivity of the driving gene set in the pathway and the influence of gene covariates, this paper constructs an adaptive multiobjective optimization model. In order to overcome the problem of gene mutation heterogeneity, this model introduces gene covariates as the weight of gene mutation frequency so that the model is adaptive to each gene. The analysis of the research results shows the reliability of high-throughput sequencing technology.

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“…Furthermore, the higher prokaryotic abundance in vegetated sediments supplies more food for bacterivorous protists (Zheng et al, 2019 ), thus promoting the proportions and biomass of heterotrophs, such as flagellates, ciliates, and amoebae (Fenchel, 1969 ). Using molecular approaches, recent surveys on diversity of marine microeukaryotes have detected abundant protistan parasites in productive systems, such as deep-sea hydrothermal vents (Moreira and López-García, 2003 ), neritic oceans (Gong et al, 2015 ), and polar marine environments (Liu et al, 2021 ). Given the cryptic nature of these microparasites and the general importance of parasites in trophic interactions affecting food web structure, keystone species, and ecosystem processes (Preston and Johnson, 2010 ; Fischhoff et al, 2020 ), the identities of microeukaryotic parasites and their hosts in sedimentary systems remain to be revealed and hypotheses regarding distributional patterns and regulating factors (such as the relationship with local primary productivity) have yet to be tested.…”

Section: Introductionmentioning

confidence: 99%

Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes

Pan

et al. 2022

Front. Microbiol.

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Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration of NH4+ in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.

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Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing

Cited by 38 publications

References 68 publications

The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments

The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments

Research on Cancer Molecular Typing Based on High-Throughput Sequencing Technology

Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes

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