Shotgun metagenomic data reveals significant abundance but low diversity of “Candidatus Scalindua” marine anammox bacteria in the Arabian Sea oxygen minimum zone

Laura Villanueva,Theo Van Alen,Daan R Speth,Alexander Hoischen,Mike S M Jetten

doi:10.3389/fmicb.2014.00031

Abstract

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 (OMZs). Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the OMZ 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.

Highlights

Anaerobic ammonium oxidation is mediated by a specialized group of bacteria that have many unique properties including the synthesis of ladderane lipids (Damsté et al, 2002), the presence of a prokaryotic cell organelle (van Niftrik and Jetten, 2012), and a metabolism using reactive intermediates hydrazine and nitric oxide (Kartal et al, 2011, 2013)
First studies on anammox bacteria diversity based on 16S rRNA gene sequences in suboxic waters, as well as marine and freshwater sediments, concluded that all environmental sequences were closely related to the “Candidatus Scalindua” genus and that the diversity was generally low in comparison with other systems, such as wastewater treatment plants (Woebken et al, 2007; Hu et al, 2010)
SAMPLING SITES AND OVERVIEW OF SEQUENCING RESULTS The Arabian Sea is one of the most expansive and intense oxygen minimum zones (OMZs) in the global ocean, and presence of anammox bacteria through activity tests and molecular surveys has been documented previously (Jensen et al, 2011; Pitcher et al, 2011) We used genomic DNA (gDNA) from suspended particulate matter obtained at 170 m, at the upper limit of the OMZ, and at 600 m depth, at the core of the OMZ, that was collected during a sampling campaign in January 2009

Summary

Introduction

Anaerobic ammonium oxidation (anammox) is mediated by a specialized group of bacteria that have many unique properties including the synthesis of ladderane lipids (Damsté et al, 2002), the presence of a prokaryotic cell organelle (van Niftrik and Jetten, 2012), and a metabolism using reactive intermediates hydrazine and nitric oxide (Kartal et al, 2011, 2013). First studies on anammox bacteria diversity based on 16S rRNA gene sequences in suboxic waters, as well as marine and freshwater sediments, concluded that all environmental sequences were closely related to the “Candidatus Scalindua” genus and that the diversity was generally low in comparison with other systems, such as wastewater treatment plants (Woebken et al, 2007; Hu et al, 2010).

Results

Conclusion