Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone
Anaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost excl...
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doaj-12f6d892b7384dde801442bd9537af3d2020-11-24T21:36:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2014-02-01510.3389/fmicb.2014.0003165580Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zonelaura eVillanueva0Daan R Speth1theo evanalen2alex ehoischen3Mike eJetten4Mike eJetten5Royal NIOZRadboud University NijmegenRadboud University NijmegenUMC St RadboudRadboud University NijmegenTU DelftAnaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to Candidatus Scalindua species. Recently the genome assembly of a marine anammox enrichment culture dominated by Candidatus Scalindua profunda became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones. Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the oxygen minimum zone in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of Candidatus Scalindua profunda served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the Candidatus Scalindua populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA and ACS) had a lower coverage but could still be assembled and analyzed. The results show that Candidatus Scalindua is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00031/fullMetagenomeMicrobial DiversityAnammoxArabian Seahydrazine synthaseion torrent sequencing |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
laura eVillanueva Daan R Speth theo evanalen alex ehoischen Mike eJetten Mike eJetten |
spellingShingle |
laura eVillanueva Daan R Speth theo evanalen alex ehoischen Mike eJetten Mike eJetten Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone Frontiers in Microbiology Metagenome Microbial Diversity Anammox Arabian Sea hydrazine synthase ion torrent sequencing |
author_facet |
laura eVillanueva Daan R Speth theo evanalen alex ehoischen Mike eJetten Mike eJetten |
author_sort |
laura eVillanueva |
title |
Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone |
title_short |
Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone |
title_full |
Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone |
title_fullStr |
Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone |
title_full_unstemmed |
Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone |
title_sort |
shotgun metagenomic data reveals signifcant abundance but low diversity of candidatus scalindua marine anammox bacteria in the arabian sea oxygen minimum zone |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2014-02-01 |
description |
Anaerobic ammonium oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to Candidatus Scalindua species. Recently the genome assembly of a marine anammox enrichment culture dominated by Candidatus Scalindua profunda became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones. Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the oxygen minimum zone in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of Candidatus Scalindua profunda served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the Candidatus Scalindua populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA and ACS) had a lower coverage but could still be assembled and analyzed. The results show that Candidatus Scalindua is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low. |
topic |
Metagenome Microbial Diversity Anammox Arabian Sea hydrazine synthase ion torrent sequencing |
url |
http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00031/full |
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