Relative Abundance Of Ammonia-oxidizing Archaea Research Articles

Exploring the mechanism of a novel recirculating aquaculture system based on water quality parameters and bacterial communities.

To mitigate the serious environmental problems caused by aquaculture wastewater discharge, the development of improved aquaculture systems with more self-purification capacity and less environmental impact has become essential. A novel recirculating aquaculture system (RAS) with ecological ponds was introduced. However, the mechanism of how the ecological ponds decompose the nutrients from the residual feed and excrement of fish is still unclear. Therefore, we designed a seven-week field experiment to explore the dynamic of water quality and the shift of bacterial communities during the initial stage of the RAS ecosystem to maintain the stability of the system. According to the result, the dissolved oxygen concentration maintained at 5.63 to 10.22mg·L-1 in aquaculture water, and electrical conductivity increased by 100% to over 800μs·cm-1. High-throughput sequencing showed that the abundance and diversity of the bacterial communities in sediment samples were significantly higher than in water samples, and the Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were dominant phyla in all samples. The relative abundance of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and nitrite-oxidizing bacteria was lower than 0.10, but rising. Redundancy analysis suggested that TOC, EC, NO3-, and NO2- were the most important factors shaping the bacterial communities in aquaculture water. Our studies assessed the RAS with ecological ponds for the first time based on water quality parameters and bacterial communities, which indicates that decomposition capacity is insufficient but improved at the initial stage of the operation, and potential risks like eutrophication require attention.

Response of microbial communities based on full-scale classification and antibiotic resistance genes to azithromycin and copper combined pollution in activated sludge nitrification laboratory mesocosms at low temperature

This study aimed to investigate the short-term response of abundant-rare genera and antibiotic resistance genes (ARGs) to azithromycin (AZM, 0.05–40 mg/L) and copper (1 mg/L) combined pollution in activated sludge nitrification system at low temperature. Nitrification was as expected inhibited in stress- and post-effects periods under AZM concentration higher than 5 mg/L. Abundant and rare taxa presented dissimilar responses based on full-scale classification. Conditionally rare or abundant taxa (CRAT) were keystone taxa. Relative abundance of ammonia-oxidizing archaea increased, and three aerobic denitrifying bacteria (Brevundimonas, Comamonas and Trichococcus) were enriched (from 9.83% to 68.91% in total). Ammonia nitrogen assimilating into Org-N and denitrification may be nitrogen pathways based on predict analysis. 29 ARGs were found with more co-occurrence patterns and high concentration of AZM (greater than 5 mg/L) caused their proliferation. Importantly, expect for some abundant taxa, rare taxa, potential pathogens and nitrogen-removal functional genera were the main potential hosts of ARGs.

Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin

Tropical peatlands are hotspots of methane (CH4) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NOx) on methanogenic activity are known from pure culture studies, the role of NOx in the methane cycling of peatlands remains unexplored. Here, we investigated the CH4 content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NOx and nitrous oxide (N2O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and 13C enrichment in dissolved inorganic carbon and CH4 pools, which are primarily contingent on H2-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NOx cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NOx. Experiments testing the interaction of NOx species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N2O (complete inhibition), which would act as an unaccounted CH4 control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH4 fluxes.

Diversity and community structure of ammonia-oxidizing archaea in rhizosphere soil of four plant groups in Ebinur Lake wetland.

The aim of this study was to reveal the differences in the community structure of ammonia-oxidizing archaea (AOA) between rhizosphere and non-rhizosphere soil, to provide a theoretical basis for further study on the relationship between halophyte rhizosphere soil microorganisms and salt tolerance. The results of diversity and community structure showed that the diversity of the AOA community in rhizosphere soil of Reeds was higher than that in non-rhizosphere soil in spring and lower than that in non-rhizosphere soil in summer and autumn. In summer, the diversity of rhizosphere soil of Karelinia caspica was higher than that of non-rhizosphere soil and lower than that of non-rhizosphere soil in spring and autumn. The diversity of rhizosphere soil of Halocnemum strobilaceum in 3 seasons was lower than that in non-rhizosphere soil. The diversity of rhizosphere soil of Salicornia was higher than that in non-rhizosphere soil in 3 seasons. In addition, the relative abundance of AOA in rhizosphere soil of 4 plants was higher than that in non-rhizosphere soil. The AOA community in all soil samples was mainly concentrated in Crenarchaeota and Thaumarchaeota. Redundancy analysis results showed salinity, soil water moisture, pH, and soil organic matter were important factors affecting the differentiation of AOA communities.

Structural and functional microbial diversity of sandy soil under cropland and grassland.

BackgroundLand use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties.MethodsWe investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests.ResultsIt was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.

Distribution characteristics of ammonia oxidizing microorganisms in rhizosphere sediments of cattail

The abundance, diversity and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated, using amoA gene as a molecular biomarker, to examine how cattail (Typha orientalis) growth affects the abundances and communities of AOB and AOA in the rhizosphere sediment. Clone libraries and qPCR (quantitative polymerase chain reaction) results indicated the amoA gene copies numbers, relative abundance of AOA and AOB amoA gene clone libraries were highest in rhizosphere sediment, followed by non-rhizosphere sediment and control, indicating that cattail growth has a remarkable effect on the abundance and community structure of ammonia oxidizing microorganisms. Diversity index (Chao1 and Shannon H) have an obvious variation in cattail rhizosphere, non-rhizosphere and control sediments. The average values of Shannon H of AOA and AOB in the rhizosphere sediment were higher than the non-rhizosphere sediment and control. The average value of Chao1 was highest in non-rhizosphere sediment for AOA, whereas, was highest in the rhizosphere sediment for AOB. The abundance, diversity and community structure of AOA and AOB were obvious different in the cattail's three developmental stages, and higher abundances and more complex community structure were obtained in the maturity stage, which may be attributable to the higher root exudation owing to fast growth rates and strong metabolisms in the maturity stage. In addition, despite higher abundant of AOA versus AOB was demonstrated in the cattail rhizosphere, non-rhizosphere sediment and control, bacteria, not archaeal, have more ecosystem functions and play a more important role in dominating ammonia oxidation under the conditions of this study according to the two findings from the present study. One is that AOB had a more diverse and more complex community structure than AOA; the other is that the average value of potential nitrification rates (PNRs) significantly decreased (by 49.08%, 53.69% and 10.39%, respectively) in rhizosphere, non-rhizosphere sediment and control, as compared to PNRs without the ampicillin, when ammonia-oxidizing bacteria were inhibited by ampicillin.

Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore.

Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

Diversity of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during composting of municipal sludge

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. The diversity and relative abundance of AOA and AOB in compost samples from four composting stages [initial (day 0), heating (day 3), thermophilic (day 12), and cooling (day 28) stage ] were analyzed using the amoA gene as a functional marker. The number of operational taxonomic units (OTUs) found in each stage during sewage sludge composting was 33.3 % to 66.6 % of the total OTUs for AOB and 43.8 % to 62.5 % for AOA, with OTUs defined on the basis of a 5 % difference in nucleotides. Phylogenetic analysis showed that the AOB amoA sequences related to the Nitrosomonas lineage were dominant throughout the entire composting process. Most of the AOA amoA sequences fell into a soil/sediment cluster containing “Candidatus Nitrososphaera gargensis”. These results indicate that different ammonia oxidizers were present in different stages during composting, but that the dominant phylogenetic types were stable.

Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.

In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.

Ammonia oxidizers in a pilot-scale multilayer rapid infiltration system for domestic wastewater treatment.

A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO3-N and NH3-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH3-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS.

First insights into the microbiome of a carnivorous sponge

Using 454 pyrosequencing, we characterized for the first time the associated microbial community of the deep-sea carnivorous Demosponge Asbestopluma hypogea (Cladorhizidae). Targeting the 16S rRNA gene V3 and V6 hypervariable regions, we compared the diversity and composition of associated microbes of two individual sponges of A.hypogea freshly collected in the cave with surrounding seawater and with one sponge sample maintained 1year in an aquarium after collection. With more than 22961 high quality sequences from sponge samples, representing c. 800 operational taxonomic units per sponge sample at 97% sequence similarities, the phylogenetic affiliation of A.hypogea-associated microbes was assigned to 20 bacterial and two archaeal phyla, distributed into 45 classes and 95 orders. Several differences between the sponge and seawater microbes were observed, highlighting a specific and stableA.hypogea microbial community dominated by Proteobacteria and Bacteroidetes and Thaumarchaeota phyla. A high relative abundance of ammonia-oxidizing archaea and a dominance of sulfate oxidizing/reducing bacteria were observed. Our findings shed lights on the potential roles of associated microbial community in the lifestyle of A.hypogea.

Experimental removal and addition of leaf litter inputs reduces nitrate production and loss in a lowland tropical forest

Environmental perturbations such as changes in land use, climate, and atmospheric carbon dioxide concentrations may alter organic matter inputs to surface soils. While the carbon (C) cycle response to such perturbations has received considerable attention, potential responses of the soil nitrogen (N) cycle to changing organic matter inputs have been less well characterized. Changing litter inputs to surface to soils may alter the soil N cycle directly, by controlling N substrate availability, or indirectly, via interactions with soil C biogeochemistry. We investigated soil N-cycling responses to a leaf litter manipulation in a lowland tropical forest using isotopic and molecular techniques. Both removing and doubling leaf litter inputs decreased the size of the soil nitrate pool, gross nitrification rates, and the relative abundance of ammonia-oxidizing microorganisms. Gross nitrification rates were correlated with the relative abundance of ammonia-oxidizing archaea, and shifts in the N-cycling microbial community composition correlated with concurrent changes in edaphic properties, notably pH and C:N ratios. These results highlight the importance of understanding coupled biogeochemical cycles in global change scenarios and suggest that environmental perturbations that alter organic matter inputs in tropical forests could reduce inorganic N losses to surface waters and the atmosphere by limiting nitrate production.

Drivers of archaeal ammonia-oxidizing communities in soil

Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.