Local diversity of heathland Cercozoa explored by in-depth sequencing
(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
- Harder, Christoffer Bugge LU ; Rønn, Regin ; Brejnrod, Asker ; Bass, David ; Al-Soud, Waleed Abu LU and Ekelund, Flemming
- publishing date
- 2016-10
- 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 >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.</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}}, }