Metagenome Analysis of a Complex Community Reveals the Metabolic Blueprint of Anammox Bacterium “Candidatus Jettenia asiatica”

Abstract

Anaerobic ammonium-oxidizing (anammox) bacteria are key players in the global nitrogen cycle and responsible for significant global nitrogen loss. Moreover, the anammox process is widely implemented for nitrogen removal from wastewaters as a cost-effective and environment-friendly alternative to conventional nitrification-denitrification systems. Currently, five genera of anammox bacteria have been identified, together forming a deep-branching order in the Planctomycetes-Verrucomicrobium-Chlamydiae superphylum. Members of all genera have been detected in wastewater treatment plants and have been enriched in lab-scale bioreactors, but genome information is not yet available for all genera. Here we report the metagenomic analysis of a granular sludge anammox reactor dominated (∼50%) by “Candidatus Jettenia asiatica.” The metagenome was sequenced using both Illumina and 454 pyrosequencing. After de novo assembly 37,432 contigs with an average length of 571 nt were obtained. The contigs were then analyzed by BLASTx searches against the protein sequences of “Candidatus Kuenenia stuttgartiensis” and a set of 25 genes essential in anammox metabolism were detected. Additionally all reads were mapped to the genome of an anammox strain KSU-1 and de novo assembly was performed again using the reads that could be mapped on KSU-1. Using this approach, a gene encoding copper-containing nitrite reductase NirK was identified in the genome, instead of cytochrome cd1-type nitrite reductase (NirS, present in “Ca. Kuenenia stuttgartiensis” and “Ca. Scalindua profunda”). Finally, the community composition was investigated through MetaCluster analysis, 16S rRNA gene analysis and read mapping, which showed the presence of other important community members such as aerobic ammonia-oxidizing bacteria, methanogens, and the denitrifying methanotroph “Ca. Methylomirabilis oxyfera”, indicating a possible active methane and nitrogen cycle in the bioreactor under the prevailing operational conditions.

Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils

“…The qPCR results further confirmed the occurrence of anammox bacteria in the collected samples. On the basis of the estimation of only one copy of the hzsA gene per anammox bacterium, as found in the genomes of "Candidatus Kuenenia stuttgartiensis" (35,36), "Candidatus Brocadia fulgida" (40), "Candidatus Jettenia asiatica" (15), "Candidatus Scalindua profunda" (12), and strain KSU-1 (41), the copy numbers of the anammox bacteria in the collected soil samples ranged from 6.38 ϫ 10 4 Ϯ 0.42 ϫ 10 4 to 3.69 ϫ 10 4 Ϯ 0.25 ϫ 10 6 copies per gram of dry weight ( Fig. 2b; see Table S1 in the supplemental material).…”

“…The anammox process is performed by a monophyletic order of bacteria, the Brocadiales (4). There are five described genera of anammox bacteria to date: "Candidatus Brocadia" (5-7), "Candidatus Kuenenia" (8), "Candidatus Scalindua" (9)(10)(11)(12), "Candidatus Anammoxoglobus" (13), and "Candidatus Jettenia" (14,15). Growing evidence shows that anammox bacteria are broadly distributed in various marine (11,16,17) and freshwater habitats (18)(19)(20).…”

Depth-specific distribution and importance of nitrite-dependent anaerobic ammonium and methane-oxidising bacteria in an urban wetland

“…The anammox process has been recognised as an important pathway for the production of dinitrogen gas (N 2 ) in the marine nitrogen cycle, which is estimated to be responsible for approximately 50% of the nitrogen loss in marine ecosystems (Arrigo, 2005;Brandes et al, 2007;Hu et al, 2011a). So far, there are five genera of anammox bacteria have been described, including Candidatus Brocadia (Strous et al, 1999;Kartal et al, 2008;Hu et al, 2010), Candidatus Kuenenia (Schmid et al, 2000), Candidatus Scalindua (Kuypers et al, 2003;Schmid et al, 2003;Woebken et al, 2008;van de Vossenberg et al, 2013), Candidatus Anammoxoglobus (Kartal et al, 2007) and Candidatus Jettenia (Quan et al, 2008;Hu et al, 2012). Until now, anammox bacteria have been found in various marine ecosystems Hu et al, 2012a;Shao et al, 2014), freshwater ecosystems (Hu et al, 2012b;Wenk et al, 2013;Ding et al, 2014) and terrestrial ecosystems (Humbert et al, 2010;Shen et al, 2013).…”

Occurrence and importance of anaerobic ammonium-oxidising bacteria in vegetable soils

“…The anammox process is performed by a monophyletic order of bacteria, the Brocadiales (Jetten et al 2010), and currently, there are five genera of anammox bacteria that have been described, including Candidatus Brocadia (Strous et al 1999;Kartal et al 2008), Candidatus Kuenenia (Schmid et al 2000), Candidatus Scalindua (Schmid et al 2003;Woebken et al 2008;van de Vossenberg et al 2013), Candidatus Anammoxoglobus (Kartal et al 2007) and Candidatus Jettenia (Quan et al 2008;Hu et al 2012c).…”