Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

Abstract

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.

Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities

“…Anammox also requires a hydrazine synthase, not identified in the BOGUAY genome. Hydroxylamine oxidases are involved in aerobic ammonia oxidation, which likewise is known to be carried out by only a few microbial groups (33). No BOGUAY homolog for the ammonia monooxygenase (AmoA) required by all identified ammonia oxidizers could be found in the genome.…”

Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria

“…Since certain microorganisms performing a common physiological function may not be numerically dominant, the use of functional gene markers provides a good alternative. In a recent review, Junier et al (15) summarized the state of the art for aerobic ammonium-oxidizing organisms from the domains Bacteria and Archaea and for anammox bacteria. Genes encoding hydroxylamine/hydrazine oxidoreductase (HAO/HZO) proteins are potential targets for molecular ecological studies of both aerobic and anaerobic ammonium-oxidizing bacteria (7,24,30,38).…”

“…As mentioned above, several methods are being used to detect the presence and activity of anammox bacteria in the environment and wastewater treatment systems, such as fluorescence in situ hybridization (FISH) (29,33,34,36), real-time PCR (46), tracer experiments with 15 N-labeled NH 4 ϩ , which reacts with 14 NO 2 Ϫ to form 29 N 2 (31), and the use of the unique ladderane lipids as a biomarker (40,41). However, when using a 16S rRNA gene-based approach on environmental samples, anammox bacteria may be underrepresented in general 16S rRNA clone libraries since the widely used "universal" primer set for 16S rRNA gene amplification has several mismatches.…”

Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

“…AOB and AOA belong to the phyla proteobacteria and thaumarchaeota, respectively (6,24). Phylogenetic studies on ammonia oxidizers are mainly based on the analysis of the amoA gene, coding for the ␣ subunit of the ammonia monooxygenase (20,44). The ammonia oxidizers are present in marine environments either as planktonic populations (21,34) or on host-associated marine microbial communities of corals (3) and sponges (35,48).…”