Diversity of Heterolobosea

Pánek, Tomáš; Čepička, Ivan

doi:10.5772/35333

Cited by 13 publications

(20 citation statements)

References 92 publications

(144 reference statements)

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“…Similarly, in early successional networks, we found relationships between a predatory nematode in the Nygolaimidae (Yeates et al, 1993) and 31 different eukaryotes, bacteria, and fungi. We also found positive correlations in mid succession communities between a bacterial feeding Heterolobosean amoeba (Brown et al, 2012;Pánek and Cepicka, 2012) and 15 bacterial taxa. And in early successional communities, we found correlations among two filter-feeding (subclass Scuticociliatia and Hypotrichia) ciliates and 41 different bacteria, which likely indicate feeding relationships (Lee and Capriulo, 1990;Jurgens and Simek, 2000).…”

Section: Network Interactionssupporting

confidence: 56%

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

et al. 2019

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While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities.

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Section: Network Interactionssupporting

confidence: 56%

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

et al. 2019

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“…single nucleus with a central nucleolus, mitochondria with discoidal/flattened cristae surrounded by cisternae of RER). Moreover, surprising details of the ultrastructure of microaerophilic or anaerobic heteroloboseans (Pánek and Cepicka ; Pánek et al. ,b) advocate revision of heterolobosean characteristics.…”

Section: Discussionmentioning

confidence: 99%

“…), which includes about 150 nominal species (Geisen et al. ) of immensely diverse protists (Pánek and Cepicka ; Pánek et al. , ).…”

mentioning

confidence: 99%

Neovahlkampfia nana n. sp. Reinforcing an Underrepresented Subclade of Tetramitia, Heterolobosea

Tyml

Lares-Jiménez

Kostka

et al. 2016

J Eukaryotic Microbiology

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The study provides robust genetic evidence that a newly isolated naked ameba with morphological and ultrastructural features indicative of Heterolobosea is a new species. Neovahlkampfia nana n. sp. associates with the yet underrepresented subclade of Tetramitia I. Considerable differences found in 18S rRNA gene sequences of individual molecular clones derived from DNA of five clonal cultures, using a low fidelity DNA polymerase, raised the issue of intragenomic sequence variation, a phenomenon that has not been previously studied in Heterolobosea. However, as proved using a higher fidelity DNA polymerase, the sequence variability observed was introduced by PCR mediated by the low fidelity polymerase and fixed by molecular cloning. This points to the potentially dubious validity of some current nominal species of Heterolobosea that differ from one another in just one or two base positions.

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“…Furthermore, Heterolobosea was revealed to be the second most abundant group www.nature.com/scientificreports www.nature.com/scientificreports/ (38.6% of total read counts) in the supergroup 'Excavata' using the V9 region, but this group was not detected using the V4 region. Heterolobosea, including amoeba, amoeboflagellate, and flagellate forms, represents one of rare taxa in environmental surveys 17,30,35 , but were commonly isolated from freshwater, marine, soil, and extreme environments [36][37][38][39][40][41][42][43][44][45][46] . Pawlowski et al 17 reported that Heterolobosea comprises <1% of total reads using NGS technology with only the V9 region.…”

Section: Scientific Reports |mentioning

confidence: 99%

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Choi

Park

2020

Sci Rep

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Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems. Here, we investigated the eukaryotic community in a pond (salinity of 2-4) on Dokdo (island) in the East Sea, Korea, using Illumina sequencing with primer sets for the V4 and V9 regions of 18S rDNA from 2016 to 2018 for the first time. Totally, 1,413 operational taxonomic units (OTUs) and 915 OTUs were detected using the V9 and V4 primer sets, respectively. Taxonomic analyses of these OTUs revealed that although the V4 primer set failed to describe the extant diversity for some major sub-division groups, the V9 primer set represented their diversity. Moreover, the rare taxa with <1% of total reads were exclusively detected using V9 primer set. Hence, the diversity of the eukaryotic community can vary depending on the choice of primers. The Illumina sequencing data of the V9 region of 18S rDNA may be advantageous for estimating the richness of the eukaryotic community including a rare biosphere, whereas the simultaneous application of two biomarkers may be suitable for understanding the molecular phylogenetic relationships. We strongly recommend both biomarkers be used to assess the diversity and phylogenetic relationship within the eukaryotic community in natural samples.The advent of next-generation sequencing (NGS) led to a substantial change in the previous knowledge about the microbial diversity in natural ecosystems 1,2 . NGS targeting the 18S rDNA is usually used to evaluate the diversity within all domains of life and provides large quantities of sequencing data for individual investigators. The 454 platform is hardly used anymore and a lot of other platforms are currently used far more widely. The Illumina platforms are representative tools for the investigation of the microbial community although this method can read a relatively short fragment of sequence (200 bp-500 bp) due to the technical limitations 3,4 . Illumina platform is a cost-effective tool per base (priced ~100 times lower than the 454 platform) and can now read longer sequences (200 bp-300 bp) than the initial platform 5,6 . Furthermore, the error rate of the Illumina platform is lower than that of the 454 platform 7 . However, considering the revolutionary application of the Illumina platform, our knowledge about the diversity and phylogenetic relationship of eukaryotes remains poor in field surveys such as those for brackish water 8 .Several studies on the diversity of eukaryotes noted that the V1-V2, V3, V4, and V9 regions of 18S rDNA have been used for better understanding the massive diversity of microbial community 9-11 . The V4 (expected amplicon size, 270 bp-387 bp) and V9 (expected amplicon size, 96 bp-134 bp) regions are considered to be the popular for metabarcoding 12,13 . Based on an in silico analysis, the V9 region of 18S rDNA offers the advantage to reveal the extant diversity of eukaryotes, whereas the V4 region of 18S rDNA is commonly used for studying the phylogenetic relationship of eukaryot...

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Diversity of Heterolobosea

Cited by 13 publications

References 92 publications

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

Neovahlkampfia nana n. sp. Reinforcing an Underrepresented Subclade of Tetramitia, Heterolobosea

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

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