Global Ecological Pattern of Ammonia-Oxidizing Archaea

Abstract

BackgroundThe global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent.Methodology and ResultsWe conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats.Conclusion and SignificanceBased on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.

Detection of Ammonia-Oxidizing Archaea in Fish Processing Effluent Treatment Plants

“…More recently, the role of AOA is being increasingly recognized in AO in the environment [6,18] and comparative genomics has enabled AOA to be placed in a newly assigned phylum Thaumarchaeota [6,18]. Recent meta-analysis of 6,200 AOA-amoA gene sequences showed unique AOA community distribution patterns along a wide spectrum of physicochemical conditions and habitat types such as soil, freshwater and the sediment therein, estuarine sediment, marine water and the sediment therein, and geothermal system [19]. These results suggest the existence of AOA populations with different evolutionary history in the varied habitats.…”

Coastal and marine pollution and ecotoxicology

“…This is evident by the observations of hypoxia in coastal ocean and also by decrease in biodiversity. As industrialization and urbanization in the developing countries including China, India and Brazil intensify further, more serious deterioration and pollution of the natural ecosystems can be more strongly pronounced than before for air, soil, water and also the biodiversity (Cao et al 2012(Cao et al , 2013Han and Gu 2015) . Relevant results from different directions of research focus are reported before on chemical pollutants and ecotoxicological data (Ford and Cheng 2009; Ford et al 2012; Wang 2012, 2013a;Zhao et al 2013), continuous investigations with new research tools available are also necessary to further document the changes for better understanding, and also forecasting the changes and trends in the future to better serve our society for regulation and legislative action.…”

“…However, it is undeniable that ecological analysis coupling with chemical data can provide more meaningful insights to the environmental status of the ecosystems and the changes that have been taking place. In a similar but different approach, microbial community structure composition of selective biochemical process can be used as reliable environmental quality indicators, anammox bacteria as one has been proposed as selective species of this group are only detected in contaminated environments while others are only in pristine ecosystems (Cao et al 2012(Cao et al , 2013Li et al 2011a, b;Han and Gu 2015).…”

“…Similarly, phytoremediation is a specific subject where scientific investigation should be focused on removal of metals and metalloid or organics from the polluted niches (Yu and Gu 2006;Yu et al 2008;Mitchell and Gu 2010) and alleochemicals may also facilitate the inhibition of pollution-induce bloom of algae ). The problems we are facing are the anthropogenic sources of pollutants, high population and growth, and related activities (Cao et al 2012(Cao et al , 2013Li et al 2011a;Han and Gu 2015).…”

“…Because of our thirst for energy, petroleum is widely and increasing consumed as the major energy source, but pollution and oil spills are notable widely. Similarly, wastewater is also part of life style, it contaminates the rivers and streams and also coastal ecosystems, resulting in serious eutrophication and harmful algal bloom, killing fishes and other organisms (Cao et al 2013;Jiang et al 2015). Drinking water quality is a much wide issue of common interest and contamination of food and beverages by plasticizers are still facing the public and the developing countries (Gu and Wang 2013b).…”