Presence Of Ammonia-oxidizing Archaea Research Articles

Annual nitrification dynamics in a seasonally ice-covered lake.

We investigated the variability in ammonia oxidation (AO) rates and the presence of ammonia-oxidizing archaea and bacteria (AOB and AOA) over an annual cycle in the water column of a small, seasonnally ice covered, temperate shield lake. AO, the first step of nitrification, was measured in situ using 15N-labelled ammonium (NH4+) at 1% and 10% of photosynthetic active radiation during day and at the same depths during night. AO was active across seasons and light levels, ranging from undetectable to 333 nmol L-1 d-1 with peak activity in winter under ice cover. NH4+ concentration was the single most important positive predictor of AO rates. High NH4+ concentrations and reduced chlorophyll a concentrations under ice, which favoured AO, were coherent with high nitrate concentrations and super saturation in nitrous oxide. When targeting the ammonia monooxygenase (amoA) gene in samples from the photic zone, we found AOA to be omnipresent throughout the year while AOB were observed predominantly during winter. Our results demonstrate that AO is an ongoing process in sunlit surface waters of temperate lakes and at all seasons with pronounced nitrification activity observed during winter under ice. The combination of high NH4+ concentrations due to fall overturn, reduced light availability that limited phytoplankton competition, and the presence of AOB together with AOA apparently favoured these elevated rates under ice. We suggest that lake ice could be a control point for nitrification in oligotrophic temperate shield lakes, characterized as a moment and place that exerts disproportionate influence on the biogeochemical behaviour of ecosystems.

Detection of ammonia-oxidizing archaea in fish processing effluent treatment plants.

Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of thaumarchaeal ammonia monooxygenase subunit A (AOA-amoA) gene. Different primer sets targeting 16S rRNA and AOA-amoA gene were used for the detection of AOA in FPETPs. Phylogenetic analysis of the gene revealed that the AOA was affiliated with thaumarchaeal group 1.1a lineage (marine cluster). Quantitative real time PCR of amoA gene was used to study the copy number of AOA and AOB in FPETPs. The AOA-amoA and AOB-amoA gene copy numbers of sludge samples ranged from 2.2×10(6) to 4.2×10(8) and 1.1×10(7) to 8.5×10(8)mg(-1) sludge respectively. Primer sets Arch-amoAF/Arch-amoAR and 340F/1000R were found to be useful for the sensitive detection of AOA-amoA and Archaeal 16S rRNA genes respectively in FPETPs. Their presence suggests the widespread occurrence and possible usefulness in removing ammonia from FPETPs which is in line with reports from other waste water treatment plants.

Aerobic and Anaerobic Ammonia-Oxidizing Microorganisms in Low-Temperature Hydrothermal Fe-Si-rich Precipitates of the Southwestern Pacific Ocean

Fe-Si-rich hydrothermal precipitates are distributed widely in low-temperature diffusing hydrothermal fields. Due to the significant contribution of Fe-oxidizing bacteria (FeOB) to the formation of this type of hydrothermal precipitates, previous studies focus mostly on investigating FeOB-related microbial populations, albeit these precipitates actually accommodate abundant other microbial communities, particularly those involved in marine nitrogen cycle. In this study, we investigated the composition, diversity, and abundance of aerobic and anaerobic ammonia-oxidizing microorganisms dwelling in low-temperature Fe-Si-rich hydrothermal precipitates of the Lau Integrated Study Site based on ammonia monooxygenase (amoA) gene and 16S rRNA gene. Phylogenetic analysis revealed the common presence of ammonia-oxidizing archaea (AOA), Nitrosospira-like ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing anammox (bacteria) in the Fe-Si-rich hydrothermal precipitates. Quantitative PCR analysis showed that AOA dominated the whole microbial community and the abundance of archaeal amoA gene was 2–3 orders of magnitude higher than that of AOB and anammox bacteria. Result of glycerol dialkyl glycerol tetraether analysis confirmed the presence and abundance of AOA. Our results suggest that microbial ammonia oxidations, especially archaeal aerobic ammonia oxidation, are prevalent and pivotal processes in low-temperature diffusing hydrothermal fields. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.

Mathematical modeling of competition for ammonium among Bacteria, Archaea and cyanobacteria within cyanobacterial mats: Can ammonia-oxidizers force nitrogen fixation?

Molecular analysis of cyanobacterial mat communities indicated that cyanobacteria, ammonia-oxidizing Archaea (AOA), and ammonia-oxidizing bacteria (AOB) coexist in those systems, competing for ammonium; this situation would imply competitive exclusion. We attempted to model how ammonia utilization niche partitioning occurs, and how ammonium levels can influence the interaction between those groups in a one-dimensional diffusionlimited system using Michaelis-Menten kinetics to describe ammonium consumption by each of those three groups. In our model, AOAs were able to dominate ammonium uptake by the community under most circumstances, except for unrealistically high (millimolar) levels of ammonium, where AOBs gained advantage. Cyanobacteria were unable to effectively compete for ammonium with either AOBs or AOAs throughout the mat at all ammonium concentrations and cell counts, suggesting that the presence of AOAs or AOBs forces cyanobacteria into nitrogen fixation mode. Such interaction can make cyanobacterial mats a net nitrogen source, as well as provide a carbon-independent energy transfer pathway from primary producers to the rest of the ecosystem.

Microbial community changes at a terrestrial volcanic CO2vent induced by soil acidification and anaerobic microhabitats within the soil column

CO2 capture and storage (CCS) in deep geological formations is one option currently evaluated to reduce greenhouse gas emissions. Consequently, the impact of a possible CO2 leakage from a storage site into surface environments has to be evaluated. During such a hypothetical leakage event, the CO2 migrates upwards along fractures entering surface soils, a scenario similar to naturally occurring CO2 vents. Therefore, such a natural analogue site at the Laacher See was chosen for an ecosystem study on the effects of high CO2 concentrations on soil chemistry and microbiology. The microbial activities revealed differences in their spatial distribution and temporal variability for CO2 -rich and reference soils. Furthermore, the abundance of several functional and group-specific gene markers revealed further differences, for example, a decrease in Geobacteraceae and an increase in sulphate-reducing prokaryotes in the vent centre. Molecular-biological fingerprinting of the microbial communities with DGGE indicated a shift in the environmental conditions within the Laacher See soil column leading to anaerobic and potentially acidic microenvironments. Furthermore, the distribution and phylogenetic affiliation of the archaeal 16S rRNA genes, the presence of ammonia-oxidizing Archaea and the biomarker analysis revealed a predominance of Thaumarchaeota as possible indicator organisms for elevated CO2 concentrations in soils.

Diversity and abundance of ammonia-oxidizing archaea in the Dongjiang River, China

Nitrification in aquatic ecosystems plays a crucial role in the global nitrogen cycling. It has been widely accepted that ammonia-oxidizing bacteria (AOB) are responsible for nitrification. However, this concept is currently challenged by the ubiquity of ammonia-oxidizing archaea (AOA) in various environments, such as in aquatic and terrestrial ecosystems. In this study, the presence of AOA in the Dongjiang River was documented via archaeal amoA amplification; the abundance of archaeal and bacterial amoA genes were estimated by quantitative polymerase chain reaction (qPCR), and the diversity was investigated by sequencing of archaeal amoA gene. Based on retrieved sequences and phylogenetic analysis, the majority of sequences obtained were different from Crenarchaeota phylum of marine and soil, affiliated with Freshwater Cluster 1 crenarchaeota. The results showed that the AOA detected fell into clusters which are specifically associated with freshwater habitats, and AOA was more abundance than AOB by around 2-4 orders of magnitude. Furthermore, it was found that AOA was more prefer to aerobic and relative low-ammonia concentrations in fresh water. Our finding provides a vital supplement to the distribution of AOA in global pattern, and offers implications for further understanding of the potential role of ammonia oxidizers in river ecosystems.

Diversity and mode of transmission of ammonia‐oxidizing archaea in marine sponges

The model marine crenarchaeote 'Cenarchaeum symbiosum' is until now the only ammonia-oxidizing archaeon known from a marine sponge. Here, phylogenetic analyses based on the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes revealed the presence of putative ammonia-oxidizing archaea (AOA) in a diverse range of sponges from the western Pacific, Caribbean and Mediterranean. amoA diversity was limited even between different oceans, with many of the obtained sequences (75.9%; n(total) = 83) forming a monophyletic, apparently sponge- (and coral-) specific lineage, analogous to those previously inferred from comparative 16S rRNA gene studies of sponge-associated microbes. The presence of AOA in sponge larvae, as detected by 16S rRNA and amoA PCR assays as well as by fluorescence in situ hybridization, suggests they are vertically transmitted and thus might be of importance for ammonia detoxification within the sponge.