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Local diversity of heathland Cercozoa explored by in-depth sequencing

Harder, Christoffer Bugge LU ; Rønn, Regin ; Brejnrod, Asker ; Bass, David ; Al-Soud, Waleed Abu LU and Ekelund, Flemming (2016) In The Isme Journal 10(10). p.2488-2497
Abstract

Cercozoa are abundant free-living soil protozoa and quantitatively important in soil food webs; yet, targeted high-throughput sequencing (HTS) has not yet been applied to this group. Here we describe the development of a targeted assay to explore Cercozoa using HTS, and we apply this assay to measure Cercozoan community response to drought in a Danish climate manipulation experiment (two sites exposed to artificial drought, two unexposed). Based on a comparison of the hypervariable regions of the 18S ribosomal DNA of 193 named Cercozoa, we concluded that the V4 region is the most suitable for group-specific diversity analysis. We then designed a set of highly specific primers (encompassing ~270 bp) for 454 sequencing. The primers... (More)

Cercozoa are abundant free-living soil protozoa and quantitatively important in soil food webs; yet, targeted high-throughput sequencing (HTS) has not yet been applied to this group. Here we describe the development of a targeted assay to explore Cercozoa using HTS, and we apply this assay to measure Cercozoan community response to drought in a Danish climate manipulation experiment (two sites exposed to artificial drought, two unexposed). Based on a comparison of the hypervariable regions of the 18S ribosomal DNA of 193 named Cercozoa, we concluded that the V4 region is the most suitable for group-specific diversity analysis. We then designed a set of highly specific primers (encompassing ~270 bp) for 454 sequencing. The primers captured all major cercozoan groups; and >95% of the obtained sequences were from Cercozoa. From 443 350 high-quality short reads (>300 bp), we recovered 1585 operational taxonomic units defined by >95% V4 sequence similarity. Taxonomic annotation by phylogeny enabled us to assign >95% of our reads to order level and ~85% to genus level despite the presence of a large, hitherto unknown diversity. Over 40% of the annotated sequences were assigned to Glissomonad genera, whereas the most common individually named genus was the euglyphid Trinema. Cercozoan diversity was largely resilient to drought, although we observed a community composition shift towards fewer testate amoebae.

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author
; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Biodiversity, Cercozoa/classification, DNA Primers/genetics, DNA, Ribosomal/genetics, High-Throughput Nucleotide Sequencing, Phylogeny, Soil/parasitology
in
The Isme Journal
volume
10
issue
10
pages
2488 - 2497
publisher
Nature Publishing Group
external identifiers
  • scopus:84960172219
  • pmid:26953604
ISSN
1751-7362
DOI
10.1038/ismej.2016.31
language
English
LU publication?
no
id
5b1e940b-7b71-437d-b2e0-e7a0f9445f3c
date added to LUP
2020-09-09 11:16:02
date last changed
2024-03-20 17:05:31
@article{5b1e940b-7b71-437d-b2e0-e7a0f9445f3c,
  abstract     = {{<p>Cercozoa are abundant free-living soil protozoa and quantitatively important in soil food webs; yet, targeted high-throughput sequencing (HTS) has not yet been applied to this group. Here we describe the development of a targeted assay to explore Cercozoa using HTS, and we apply this assay to measure Cercozoan community response to drought in a Danish climate manipulation experiment (two sites exposed to artificial drought, two unexposed). Based on a comparison of the hypervariable regions of the 18S ribosomal DNA of 193 named Cercozoa, we concluded that the V4 region is the most suitable for group-specific diversity analysis. We then designed a set of highly specific primers (encompassing ~270 bp) for 454 sequencing. The primers captured all major cercozoan groups; and &gt;95% of the obtained sequences were from Cercozoa. From 443 350 high-quality short reads (&gt;300 bp), we recovered 1585 operational taxonomic units defined by &gt;95% V4 sequence similarity. Taxonomic annotation by phylogeny enabled us to assign &gt;95% of our reads to order level and ~85% to genus level despite the presence of a large, hitherto unknown diversity. Over 40% of the annotated sequences were assigned to Glissomonad genera, whereas the most common individually named genus was the euglyphid Trinema. Cercozoan diversity was largely resilient to drought, although we observed a community composition shift towards fewer testate amoebae.</p>}},
  author       = {{Harder, Christoffer Bugge and Rønn, Regin and Brejnrod, Asker and Bass, David and Al-Soud, Waleed Abu and Ekelund, Flemming}},
  issn         = {{1751-7362}},
  keywords     = {{Biodiversity; Cercozoa/classification; DNA Primers/genetics; DNA, Ribosomal/genetics; High-Throughput Nucleotide Sequencing; Phylogeny; Soil/parasitology}},
  language     = {{eng}},
  number       = {{10}},
  pages        = {{2488--2497}},
  publisher    = {{Nature Publishing Group}},
  series       = {{The Isme Journal}},
  title        = {{Local diversity of heathland Cercozoa explored by in-depth sequencing}},
  url          = {{http://dx.doi.org/10.1038/ismej.2016.31}},
  doi          = {{10.1038/ismej.2016.31}},
  volume       = {{10}},
  year         = {{2016}},
}