Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters

Zhu, Changyu; Bass, David; Wang, Yutao; Shen, Zhuo; Song, Weibo; Yi, Zhenzhen

doi:10.3389/fmicb.2020.555795

Cited by 9 publications

(7 citation statements)

References 85 publications

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“…The location of sampling regions, modi ed from Zhu et al [11]. Sampling areas and their abbreviations are as follows: Daya Bay (DY1, DY2, DY5), the Pearl River Estuary (PRE1-PRE10), and the coast of Guangzhou (GZ1-GZ5), Shenzhen (SZ1-SZ4), Zhuhai (ZH1-ZH5) and Zhanjiang (ZJ1-ZJ4, ZJ6).…”

Section: Discussionmentioning

confidence: 99%

“…ciliates comprise two subclasses, Oligotrichia and Choreotrichia [30]. Environmental V4 region of SSU rDNA sequences were downloaded from GenBank under the accession number PRJNA646537, the geographic locations of sampling sites and the salinity of each site are shown in our previous study (Figure 1, Table 1 in [11]). In summary, PRE1-PRE11 were sampling sites along the ow direction of Pearl River Estuary (PRE), sampling sites DY1-DY5, GZ1-GZ5, SZ1-SZ6, ZH1-ZH5 and ZJ1-ZJ6 were in sampling area Daya Bay (DY), Guangzhou (GZ), Shenzhen (SZ), Zhuhai (ZH) and Zhanjiang (ZJ), respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Consequently, insu cient sampling dense of protists in studies using isolated cells might halt revealing their accurate patterns of diversity, phylogeny, transition and so on. Fortunately, a great number of sequences produced by high-throughput sequencing (HTS) without limitations of culturing and ignoring in observation that provide us a chance to investigate more accurate diversity and distribution patterns of protists [7][8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

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Diversity Patterns of Protists are Highly Affected by Methods Disentangling Inter-specific Variants: A Case Study in Oligotrich (s.l.) Ciliates

Han

et al. 2021

Preprint

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An enormous amount of environmental sequences produced by high-throughput sequencing (HTS) is popular for inferring diversity and distribution patterns of protists, which are widely distributed and playing important roles in energy flux and nutrient cycling. However, study testing whether methods disentangling inter-specific variants affect the diversity and distribution patterns of protists using field samples is insufficient. Using oligotrich (s.l.) ciliates, one group of abundant and dominate planktonic protists, in field samples as an example, the present study indicates that DADA2 performs better than UCLUST and UPARSE for inferring diversity patterns of oligotrich (s.l.) ciliates in Pearl River Estuary and surrounding regions. UPARSE, as an OTU-construction method might underestimate species richness and produce less reliable beta diversity pattern than DADA2. UCLUST with 97% and 99% clustering thresholds overestimate species richness, and the beta diversity pattern inferred by the former one is unreasonable. Salinity is shown to be one of the key factors responsible for variations in community distribution of ciliates, but infrequent marine-freshwater transitions occurred during evolutionary terms of this group.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Diversity Patterns of Protists are Highly Affected by Methods Disentangling Inter-specific Variants: A Case Study in Oligotrich (s.l.) Ciliates

Han

et al. 2021

Preprint

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“…Consequently, insufficient sampling of protists in studies using isolated cells might halt revealing their accurate patterns of diversity, phylogeny, and transition. Fortunately, rare and cryptic protists could be revealed by high-throughput sequencing (HTS) with large data output, which provides us a chance to investigate more accurate diversity and distribution patterns of protists [ 9 , 10 , 11 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Diversity Patterns of Protists Are Highly Affected by Methods Disentangling Biological Variants: A Case Study in Oligotrich (s.l.) Ciliates

Han

et al. 2022

Microorganisms

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Protists are a dominant group in marine microplankton communities and play important roles in energy flux and nutrient cycling in marine ecosystems. Environmental sequences produced by high-throughput sequencing (HTS) methods are increasingly used for inferring the diversity and distribution patterns of protists. However, studies testing whether methods disentangling biological variants affect the diversity and distribution patterns of protists using field samples are insufficient. Oligotrich (s.l.) ciliates are one group of the abundant and dominant planktonic protists in coastal waters and open oceans. Using oligotrich (s.l.) ciliates in field samples as an example, the present study indicates that DADA2 performs better than SWARM, UNOISE, UPARSE, and UCLUST for inferring diversity patterns of oligotrich (s.l.) ciliates in the Pearl River Estuary and surrounding regions. UPARSE and UNOISE might underestimate species richness. SWARM might not be suitable for the resolution of alpha diversity owing to its rigorous clustering and sensitivity to sequence variations. UCLUST with 99% clustering threshold overestimates species richness, and the beta diversity pattern inferred by DADA2 is more reasonable than that of the other methods. Additionally, salinity is shown to be one of the key factors responsible for variations in the community distribution of ciliates, but infrequent marine–freshwater transitions occurred during evolutionary terms of this group.

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“…et al, 2019Wang Y.R. et al, , 2020Zhang et al, 2020;Zhu et al, 2020). Peritrichia Stein, 1859 is probably the most speciose subclass in the class Oligohymenophorea de Puytorac et al, 1974 with more than 1,000 nominal species collected from a wide range of habitats (Kent, 1880(Kent, -1882Entz, 1884;Penard, 1922;Kahl, 1935;Foissner et al, 1992;Lu et al, 2019;Wang Z. et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

The Morphology, Taxonomy, and Phylogenetic Analyses of Five Freshwater Colonial Peritrich Ciliates (Alveolata, Ciliophora), Including the Descriptions of Two New Species

Wang

Duan

et al. 2021

Front. Microbiol.

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The morphology and phylogeny of two new sessilid species, Zoothamnium weishanicum n. sp. and Epicarchesium sinense n. sp., two insufficiently known species, Zoothamnium arbusculaEhrenberg, 1831 and Zoothamnium hentscheliKahl, 1935, and a well-known species, Carchesium polypinum (Linnaeus, 1767) Ehrenberg, 1838, collected from freshwater habitats of China, were investigated. Zoothamnium weishanicum n. sp. is characterized by its inverted bell-shaped zooids, double-layered peristomial lip, alternately branched stalk, and two different-length rows in infundibular polykinety 3 (P3). Epicarchesium sinense n. sp. is recognized by its asymmetric-pyriform zooids, single-layered peristomial lip, conspicuous cortical blisters on the pellicle, dichotomously branched stalk, and P3 containing one short inner row and two long outer rows. Based on previous and newly obtained data of the three known species, improved diagnoses and redescriptions are provided including, for the first time, data on the infraciliature of Z. arbuscula and Z. hentscheli. In addition, we analyzed the phylogeny of each species based on SSU rDNA sequence data.

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Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters

Cited by 9 publications

References 85 publications

Diversity Patterns of Protists are Highly Affected by Methods Disentangling Inter-specific Variants: A Case Study in Oligotrich (s.l.) Ciliates

Diversity Patterns of Protists are Highly Affected by Methods Disentangling Inter-specific Variants: A Case Study in Oligotrich (s.l.) Ciliates

Diversity Patterns of Protists Are Highly Affected by Methods Disentangling Biological Variants: A Case Study in Oligotrich (s.l.) Ciliates

The Morphology, Taxonomy, and Phylogenetic Analyses of Five Freshwater Colonial Peritrich Ciliates (Alveolata, Ciliophora), Including the Descriptions of Two New Species

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