title: High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.
abstract: Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.
authors.affiliation: CSIRO Marine and Atmospheric Research and Wealth from Oceans National Research Flagship, Hobart, Tasmania, Australia.
authors.forename: Guy C J
authors.initials: GC
authors.lastname: Abell
authors.forename: Stan S
authors.initials: SS
authors.lastname: Robert
authors.forename: Dion M F
authors.initials: DM
authors.lastname: Frampton
authors.forename: John K
authors.initials: JK
authors.lastname: Volkman
authors.forename: Farhan
authors.initials: F
authors.lastname: Rizwi
authors.forename: József
authors.initials: J
authors.lastname: Csontos
authors.forename: Levente
authors.initials: L
authors.lastname: Bodrossy
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019843:Archaeal Proteins / Q000235:genetics*; D052818:Autotrophic Processes / Q000502:physiology*; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics*; D015415:Biomarkers / Q000378:metabolism; D004784:Environmental Monitoring; D020869:Gene Expression Profiling; D057166:High-Throughput Screening Assays; D058465:Nitrification; D009573:Nitrites / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics* / Q000378:metabolism; D012988:Soil Microbiology
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D015415:Biomarkers; D009573:Nitrites; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase