Aerobic Ammonia-oxidizing Archaea Research Articles

Deep-Sea Carbonates Are a Reservoir of Fossil Microbes Previously Inhabiting Cold Seeps

Carbonates are globally distributed particularly around deep-sea cold seeps. The embedded microbes are fossil records of the past bioprocess but metagenomes of the carbonates have not been fully studied. In this study, we report microbial community structures and genomes of dominant species in cold-seep carbonates from the South China Sea (SCS) and Gulf of Mexico (GoM). The carbonates contained both anaerobic microbes represented by methane oxidizing archaea (ANME) and aerobic ammonia-oxidizing archaea (AOA). The samples from GoM were mostly composed of small microbial groups, indicating heavy degradation of the fossil microbes. The composition of the carbonate communities differed from that of cold seep sediments, suggesting alteration of cold-seep microbial structures during formation and weathering of carbonates. Extraction of 18S rRNA genes from metagenomic reads revealed prevalence of fungal species in the carbonates of the GoM. Genome binning resulted in 10 genomes for dominant prokaryotic species. The ANME genomes showed a short genetic distance to the relatives from the current cold seep sediments; the AOA genomes were affiliated with alpha ecotype dominating deep-sea sediments. Our study reports the genomes in ancient carbonates and sheds lights on microbial role in formation and bioweathering of carbonates.

Evaluation of the key factors to dominate aerobic ammonia-oxidizing archaea in wastewater treatment plant

Wastewater treatment plants (WWTPs) face great challenges globally, especially in China, for increasingly strict discharge standard. Abundance of AOA was found dramatically higher in a SBR WWTP in South China (ZSH) recently, which achieved extremely low ammonium concentration in effluents. Moreover, AOA equips lower half-saturation constant (Km) for dissolved oxygen (DO) and ammonia in comparison with AOB, which indicate AOA can oxidize ammonia to nitrite more thoroughly than AOB. Thus, AOA may play an important role for nitrogen removal in SBR WWTP. To understand the key factors for AOA dominance in SBR WWTP is of importance for designing and operating WWTP in future. In this study, a Nitrosocosmicus sp. AOA was enriched from the ZSH SBR WWTP. Growth, pH, temperature, ammonium and oxygen tolerance of AOA enrichments were explored. Moreover, ammonia-oxidizing pathway was investigated with presence of PTIO as inhibitor, and the production of middle products (NH2OH and N2O) during ammonia oxidation were monitored over time. Growth of Nitrosocosmicus sp. AOA was observed with a doubling time of 4.5 days, which was active under a wide pH range (6.0–9.0), with optimal pH of 7.5. Activity of Nitrosocosmicus sp. AOA increased with increasing of ammonium concentration below 40 mM, which was suppressed above 40 mM ammonium. Moreover, Km for ammonia and oxygen were 0.14 μM and 4.1 μM, respectively, which suggested the enriched AOA could thoroughly oxidize ammonia under low dissolved oxygen conditions. Activity of Nitrosocosmicus sp. AOA was completely inhibited by PTIO. Emission of N2O by AOA (0.05%) was lower than most reported AOB and Comammox bacteria. Our results demonstrated that the long sludge retention time, intermittent aeration, high ammonium and pH resistance were most probably the controlling factors for AOA dominance in WWTPs, which benefitted to lowing ammonium in effluents, saving energy and reducing greenhouse gas in future.

Nitric Oxide Production from Nitrite Reduction and Hydroxylamine Oxidation by Copper-containing Dissimilatory Nitrite Reductase (NirK) from the Aerobic Ammonia-oxidizing Archaeon, Nitrososphaera viennensis.

Aerobic ammonia-oxidizing archaea (AOA) play a crucial role in the global nitrogen cycle by oxidizing ammonia to nitrite, and nitric oxide (NO) is a key intermediate in AOA for sustaining aerobic ammonia oxidation activity. We herein heterologously expressed the NO-forming, copper-containing, dissimilatory nitrite reductase (NirK) from Nitrososphaera viennensis and investigated its enzymatic properties. The recombinant protein catalyzed the reduction of 15NO2− to 15NO, the oxidation of hydroxylamine (15NH2OH) to 15NO, and the production of 14–15N2O from 15NH2OH and 14NO2−. To the best of our knowledge, the present study is the first to document the enzymatic properties of AOA NirK.

Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments.

In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH4+ but lower concentrations of both NO2- and NO3-, and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH4+ and NO2- were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

Abundance and Diversity of Aerobic/Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms in an Ammonium-Rich Aquitard in the Pearl River Delta of South China

Natural occurring groundwater with abnormally high ammonium concentrations was discovered in the aquifer-aquitard system in the Pearl River Delta, South China. The community composition and abundance of aerobic/anaerobic ammonia/ammonium-oxidizing microorganisms (AOM) in the aquitard were investigated in this study. The alpha subunit of ammonia monooxygenase gene (amoA) was used as the biomarker for the detection of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), and also partial 16S rRNA gene for Plantomycetes and anaerobic ammonium-oxidizing (anammox) bacteria. Phylogenetic analysis showed that AOA in this aquitard were affiliated with those from water columns and wastewater treatment plants; and AOB were dominated by sequences among the Nitrosomonas marina/Nitrosomonas oligotropha lineage, which were affiliated with environmental sequences from coastal eutrophic bay and subtropical estuary. The richness and diversity of both AOA and AOB communities had very little variations with the depth. Candidatus Scalindua-related sequences dominated the anammox bacterial community. AOB amoA gene abundances were always higher than those of AOA at different depths in this aquitard. The Pearson moment correlation analysis showed that AOA amoA gene abundance positively correlated with pH and ammonium concentration, whereas AOB amoA gene abundance negatively correlated with C/N ratio. This is the first report that highlights the presence with low diversity of AOM communities in natural aquitard of rich ammonium.

Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms

Anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB) are three groups of ammonia/ammonium-oxidizing prokaryotes (AOPs) involved in the biochemical nitrogen cycling. In this study, the effects of allylthiourea (ATU), pH, and salinity on these three groups from mangrove sediment were investigated through microcosm incubation in laboratory. ATU treatments (50, 100, and 500 mg L(-1)) obviously affected the community structure of anammox bacteria and AOB, but only slightly for AOA. ATU began to inhibit anammox bacteria growth slightly from day 10, but had an obvious inhibition on AOA growth from the starting of the study. At 100 mg L(-1) of ATU or higher, AOB growth was inhibited, but only lasted for 5 days. The pH treatments showed that acidic condition (pH 5) had a slight effect on the community structure of anammox bacteria and AOA, but an obvious effect on AOB. Acidic condition promoted the growth of all groups of AOPs in different extent, but alkaline condition (pH 9) had a weak effect on AOB community structure and a strong effect on both anammox bacteria and AOA. Alkaline condition obviously inhibited anammox bacteria growth, slightly promoted AOA, and slightly promoted AOB in the first 20 days, but inhibited afterward. Salinity treatment showed that higher salinity (20 and 40 ‰) resulted in higher anammox bacteria diversity, and both AOA and AOB might have species specificity to salinity. High salinity promoted the growth of both anammox bacteria and AOB, inhibited AOA between 5 and 10 days, but promoted afterward. The results help to understand the role of these microbial groups in biogeochemical nitrogen cycling and their responses to the changing environments.

Higher diversity of ammonia/ammonium-oxidizing prokaryotes in constructed freshwater wetland than natural coastal marine wetland

Anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) are three groups of ammonium/ammonia-oxidizing prokaryotes (AOPs) that are involved in the nitrogen cycle. This research compared the AOP communities in a constructed freshwater wetland with a natural coastal marine wetland in the subtropical Hong Kong. Both vegetated/rhizosphere and nonvegetated sediments were investigated to identify the effects of different macrophytes on the AOP communities. The polymerase chain reaction (PCR)-amplified gene fragments of 16S rRNA and archaeal and bacterial amoA (encoding the ammonia monooxygenase alpha subunit) were applied as molecular biomarkers to analyze the AOPs’ phylogeny and diversity. Quantitative PCR was used to determine the abundances of AOPs in the sediments. The results showed that the relatively more heterogeneous freshwater wetland contained a broader range of phylotypes, higher diversity, more complex community structures, and more unevenly distributed abundances of AOPs than the coastal wetland. The effects of vegetation on the community structures of AOPs were plant-specific. The exotic Typha angustifolia affected the community structures of all AOPs and enhanced their abundances in the rhizosphere region. Both Phragmites australis and Cyperus malaccensis showed some effects on the community structures of AOB, but minimal effects on those of anammox bacteria or AOA. Kandelia obovata had almost no detectable effect on all AOPs due to their smaller size. This study suggested that the freshwater and coastal marine wetlands may have different contributions to the inorganic N removal due to the variations in AOP communities and plant types.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-012-4430-4) contains supplementary material, which is available to authorized users.

High diversity of ammonia‐oxidizing archaea in permanent and seasonal oxygen‐deficient waters of the eastern South Pacific

The community structure of putative aerobic ammonia-oxidizing archaea (AOA) was explored in two oxygen-deficient ecosystems of the eastern South Pacific: the oxygen minimum zone off Peru and northern Chile (11°S-20°S), where permanent suboxic and low-ammonium conditions are found at intermediate depths, and the continental shelf off central Chile (36°S), where seasonal oxygen-deficient and relatively high-ammonium conditions develop in the water column, particularly during the upwelling season. The AOA community composition based on the ammonia monooxygenase subunit A (amoA) genes changed according to the oxygen concentration in the water column and the ecosystem studied, showing a higher diversity in the seasonal low-oxygen waters. The majority of the archaeal amoA genotypes was affiliated to the uncultured clusters A (64%) and B (35%), with Cluster A AOA being mainly associated with higher oxygen and ammonium concentrations and Cluster B AOA with permanent oxygen- and ammonium-poor waters. Q-PCR assays revealed that AOA are an abundant community (up to 10(5) amoA copies ml(-1) ), while bacterial amoA genes from β proteobacteria were undetected. Our results thus suggest that a diverse uncultured AOA community, for which, therefore, we do not have any physiological information, to date, is an important component of the nitrifying community in oxygen-deficient marine ecosystems, and particularly in rich coastal upwelling ones.

RNA-Based Investigation of Ammonia-Oxidizing Archaea in Hot Springs of Yunnan Province, China

Using RNA-based techniques and hot spring samples collected from Yunnan Province, China, we show that the amoA gene of aerobic ammonia-oxidizing archaea can be transcribed at temperatures higher than 74 degrees C and up to 94 degrees C, suggesting that archaeal nitrification can potentially occur at near boiling temperatures.