Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters

Yan, Zhenguang; Zhu, Xiaoyan; Zhang, Shouwen; Jiang, Hua; Wang, Shuping; Wei, Chao; Wang, Jie; Shao, Yun; Liu, Chen; Wang, Hui

doi:10.3389/fmicb.2023.1132925

Cited by 3 publications

(2 citation statements)

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“…The total alkalinity and distance of settlements from coastal areas constitute Environmental actors that have a significant influence on plankton diversity. Overall, the main pattern of community formation is the limitation of dispersal where about 83% of the community formation process is the assembly of eukaryotic plankton communities in coastal areas [25].…”

Section: Plankton Compositionmentioning

confidence: 99%

Effect of hatchery and mariculture activity at the northwest coastal area of Bali on water quality and plankton community

Slamet,

Kardi

2023

IOP Conf. Ser.: Earth Environ. Sci.

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The northwest coastal area of Bali is currently for the development of marine fish hatcheries and cage farming. This study aims to influence the hatchery and aquaculture activities of marine fish cages in the northwest coastal area of Bali on seawater quality and plankton community. The parameters observed on water quality were total suspended solids, temperature, transparency, pH, dissolved oxygen, Salinity, ammonia, nitrite, nitrate, phosphate, C-organic, total organic matter, and plankton community on diversity, similarity, and dominancy index. The results of water quality observations found that water temperature was 27.5-29.1°C, TSS 0.028-0.046 ppm, transparency 7.4-12.8 m, pH 8.1-8.3, DO 5.4-6.9, Salinity 33.2-34.1, ammonia, 0.01-0.04 ppm, nitrite 0.028-0.041 ppm, nitrate 0.018-0.036 ppm phosphate 0.026-0.038 ppm, C-Organic 0.65-0.74 ppm, TOM 0.75-1.23 ppm. Found 38 genera and 10 phyla of plankton, with an abundance was 258-26,546 ind/L, an index of the diversity of 0.89-2.15, an index of similarity of 0.22-0.64, and an index of dominancy 0.18-0.43. From these results, it can be concluded that the coastal waters of northwest Bali are in the criteria that have not been polluted and are good for marine fish farming. The northwest coastal area of Bali must be managed properly so that marine fish farming can be sustainable.

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Section: Plankton Compositionmentioning

confidence: 99%

Effect of hatchery and mariculture activity at the northwest coastal area of Bali on water quality and plankton community

Slamet,

Kardi

2023

IOP Conf. Ser.: Earth Environ. Sci.

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“…metagenomics) have provided novel opportunities for the description and monitoring of biodiversity (e.g. [3]), and the analyses of population dynamics, patterns of adaptation and the demographic history of organisms profit from extensive genome re-sequencing (e.g. [4]) (Fig.…”

Section: Introductionmentioning

confidence: 99%

De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide

Jackson,

Cerveau,

Posnien

2024

Front Zool

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Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the ‘scientific status’ of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.

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Environmental DNA in different media reveals distribution characteristics and assembly mechanisms of fish assemblages in a complex river–lake system

Shao,

Wang,

Wang

et al. 2024

Web Ecol.

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Abstract. Capture-based methods are commonly used for biomonitoring fish assemblages in freshwater. The recent advancement in environmental DNA (eDNA) metabarcoding provides a sensitive, cost-effective, and non-intrusive alternative to traditional methods. Nevertheless, the effectiveness of this approach in river–lake systems has yet to be assessed, and there is ongoing debate regarding the selection of sampling media. In this study, we investigated fish assemblages based on traditional approaches and the eDNA metabarcoding method by analyzing water and sediment from 30 locations along the Baiyang Lake and its inflow rivers (China). The results showed that 21 species were identified based on traditional methods, and a total of 29 species were detected using eDNA, with 22 species found in river water eDNA, 25 species in lake water eDNA, and 27 species in surface sediment samples. Nine benthic fish species were detected exclusively in sediment. The community composition of rivers and lakes revealed by water eDNA is similar, reflecting the biotic homogenization in this river–lake system. A neutral community model (NCM) analysis based on lake water and river water eDNA showed that fish assemblages were not dominated by random processes (5.3 % and 2.7 % concordance with the neutral model, respectively), while analysis of surface sediment eDNA showed more support for random processes (50.2 %). Temperature was the main environmental factor correlated with water eDNA, while NH3–N and TP were the main factors correlating with sediment eDNA.

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Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters

Cited by 3 publications

References 50 publications

Effect of hatchery and mariculture activity at the northwest coastal area of Bali on water quality and plankton community

Effect of hatchery and mariculture activity at the northwest coastal area of Bali on water quality and plankton community

De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide

Environmental DNA in different media reveals distribution characteristics and assembly mechanisms of fish assemblages in a complex river–lake system

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