Bacterial amoA Gene Abundance Research Articles

Community structure and abundance of ammonia-oxidizing archaea and bacteria after conversion from soybean to rice paddy in albic soils of Northeast China

Community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the albic soil grown with soybean and rice for different years was investigated by construction of clone libraries, denaturing gradient gel electrophoresis (DGGE), and quantitative polymerase chain reaction (q-PCR) by PCR amplification of the ammonia monooxygenase subunit A (amoA) gene. Soil samples were collected at two layers (0-5 and 20-25 cm) from a soybean field and four rice paddy fields with 1, 5, 9, and 17 years of continuous rice cultivation. Both the community structures and abundances of AOA and AOB showed detectable changes after conversion from soybean to rice paddy judged by clone library, DGGE, and q-PCR analyses. In general, the archaeal amoA gene abundance increased after conversion to rice cultivation, while bacterial amoA gene abundance decreased. The abundances of both AOA and AOB were higher in the surface layer than the bottom one in the soybean field, but a reverse trend was observed for AOB in all paddy samples regardless of the duration of paddy cultivation. Phylogenetic analysis identified nine subclusters of AOA and seven subclusters of AOB. Community composition of both AOA and AOB was correlated with available ammonium and increased pH value caused by flooding in multiple variance analysis. Community shift of AOB was also observed in different paddy fields, but the two layers did not show any detectable changes in DGGE analysis. Conversion from soybean to rice cultivation changed the community structure and abundance of AOA and AOB in albic agricultural soil, which requires that necessary cultivation practice be followed to manage the N utilization more effectively.

Response of an Arctic Sediment Nitrogen Cycling Community to Increased CO2

Ocean acidification influences sediment/water nitrogen fluxes, possibly by impacting on the microbial process of ammonia oxidation. To investigate this further, undisturbed sediment cores collected from Ny Alesund harbour (Svalbard) were incubated with seawater adjusted to CO2 concentrations of 380, 540, 760, 1,120 and 3,000 µatm. DNA and RNA were extracted from the sediment surface after 14 days' exposure and the abundance of bacterial and archaeal ammonia oxidising (amoA) genes and transcripts quantified using quantitative polymerase chain reaction. While there was no change to the abundance of bacterial amoA genes, an increase to 760 µatm pCO2 reduced the abundance of bacterial amoA transcripts by 65 %, and this was accompanied by a shift in the composition of the active community. In contrast, archaeal amoA gene and transcript abundance both doubled at 3,000 µatm, with an increase in species richness also apparent. This suggests that ammonia oxidising bacteria and archaea in marine sediments have different pH optima, and the impact of elevated CO2 on N cycling may be dependent on the relative abundances of these two major microbial groups. Further evidence of a shift in the balance of key N cycling groups was also evident: the abundance of nirS-type denitrifier transcripts decreased alongside bacterial amoA transcripts, indicating that NO3− produced by bacterial nitrification fuelled denitrification. An increase in the abundance of Planctomycete-specific 16S rRNA, the vast majority of which grouped with known anammox bacteria, was also apparent at 3,000 µatm pCO2. This could indicate a possible shift from coupled nitrification–denitrification to anammox activity at elevated CO2.

Short-Term Effect of Elevated Temperature on the Abundance and Diversity of Bacterial and Archaeal amoA Genes in Antarctic Soils

Global warming will have far-reaching effects on our ecosystem. However, its effects on Antarctic soils have been poorly explored. To assess the effects of warming on microbial abundance and community composition, we sampled Antarctic soils from the King George Island in the Antarctic Peninsula and incubated these soils at elevated temperatures of 5°C and 8°C for 14 days. The reduction in total organic carbon and increase in soil respiration were attributed to the increased proliferation of Bacteria, Fungi, and Archaea. Interestingly, bacterial ammonia monooxygenase (amoA) genes were predominant over archaeal amoA, unlike in many other environments reported previously. Phylogenetic analyses of bacterial and archaeal amoA communities via clone libraries revealed that the diversity of amoA genes in Antarctic ammonia-oxidizing prokaryotic communities were temperature-insensitive. Interestingly, our data also showed that the amoA of Antarctic ammonia-oxidizing bacteria (AOB) communities differed from previously described amoA sequences of cultured isolates and clone library sequences, suggesting the presence of novel Antarctic-specific AOB communities. Denitrification-related genes were significantly reduced under warming conditions, whereas the abundance of amoA and nifH increased. Barcoded pyrosequencing of the bacterial 16S rRNA gene revealed that Proteobacteria, Acidobacteria, and Actinobacteria were the major phyla in Antarctic soils and the effect of short-term warming on the bacterial community was not apparent.

Biases in community structures of ammonia/ammonium-oxidizing microorganisms caused by insufficient DNA extractions from Baijiang soil revealed by comparative analysis of coastal wetland sediment and rice paddy soil

Repetitive extraction of DNAs from surface sediments of a coastal wetland in Mai Po Nature Reserve (MP) of Hong Kong and surface Baijiang soils from a rice paddy (RP) in Northeast China was conducted to compare the microbial diversity in this study. Community structures of ammonia/ammonium-oxidizing microorganisms in these samples were analyzed by PCR-DGGE technique. The diversity and abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonium-oxidizing (anammox) bacteria were also analyzed based on archaeal and bacterial ammonia monooxygenase subunit A encoding (amoA) and anammox bacterial 16S rRNA genes, respectively. DGGE profiles of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes showed a similar pattern among all five repetitively extracted DNA fractions from both MP and RP, except the anammox bacteria in RP, indicating a more diverse anammox community retrieved in the second to the fifth fractions than the first one. Both soil and marine group AOA were detected while soil and coastal group AOB and Scalindua-anammox bacteria were dominant in MP. Soil group AOA and marine group AOB were dominant in RP, while both Scalindua and Kuenenia species were detected in RP. Pearson correlation analysis showed that the abundance of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes was significantly correlated with the DNA concentrations of the five DNA fractions from MP, but not from RP (except the archaeal amoA gene). Results suggest that anammox bacteria diversity may be biased by insufficient DNA extraction of rice paddy soil samples.

Effects of submerged macrophytes on the abundance and community composition of ammonia-oxidizing prokaryotes in a eutrophic lake

Abundances and community compositions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in unvegetated sediment and the rhizosphere sediments of three submerged macrophytes (Ceratophyllum demersum, Vallisneria spinulosa, and Potamogeton crispus) were investigated in a large, eutrophic freshwater lake, Lake Taihu. Abundances of archaeal ammonia monooxygenase alpha-subunit (amoA) gene (from 6.56 × 10(6) copies to 1.06 × 10(7) copies per gram of dry sediment) were higher than those of bacterial amoA (from 6.13 × 10(5) to 3.21 × 10(6) copies per gram of dry sediment) in all samples. Submerged macrophytes exhibited no significant effect on the abundance and diversity of archaeal amoA gene. C. demersum and V. spinulosa increased the abundance and diversity of bacterial amoA gene in their rhizosphere sediment. However, the diversity of bacterial amoA gene in the rhizosphere sediments of P. crispus was decreased. The data obtained in this study would be helpful to elucidate the roles of submerged macrophytes involved in the nitrogen cycling of eutrophic lake ecosystems.

Manure fertilization alters the population of ammonia‐oxidizing bacteria rather than ammonia‐oxidizing archaea in a paddy soil

Manure fertilizers are widely used in agriculture and highly impacted the soil microbial communities such as ammonia oxidizers. However, the knowledge on the communities of archaeal versus bacterial ammonia oxidizers in paddy soil affected by manure fertilization remains largely unknown, especially for a long-term influence. In present work, the impact of manure fertilization on the population of ammonia oxidizers, related potential nitrification rates (PNRs) and the key factors manipulating the impact were investigated through studying two composite soil cores (long-term fed with manure fertilization versus undisturbed). Moreover, soil incubated with NH(4)(+) for 5 weeks was designed to verify the field research. The results showed that the copy numbers of bacterial amoA gene in the manure fed soil were significant higher than those in the unfed soil (p < 0.05), suggesting a clear stimulating effect of long-term manure fertilization on the population of ammonia-oxidizing bacteria (AOB). The detected PNRs in the manure fed soil core (14-218 nmol L(-1) N g(-1) h(-1)) were significant higher than those in the unfed soil core (5-72 nmol L(-1) N g(-1) h(-1) ; p < 0.05). Highly correlations between the PNRs and the bacterial amoA gene copies rather than archaeal amoA gene were observed, indicating strong nitrification capacity related to bacterial ammonia oxidizers. The NH(4)(+) -N significantly correlated to the abundance of AOB (p < 0.01) and explained 96.1% of the environmental variation, showing the NH(4)(+) -N was the main factor impacting the population of AOB. The incubation experiment demonstrated a clear increase of the bacterial amoA gene abundance (2.0 × 10(6) to 8.4 × 10(6) g(-1) d.w.s. and 1.6 × 10(4) to 4.8 × 10(5) g(-1) d.w.s.) in both soil but not for the archaeal amoA gene, in agreement with the field observation. Overall, our results suggested that manure fertilization promoted the population size of bacterial ammonia oxidizers rather than their archaeal counterparts whether in long-term or short-term usage and the NH(4)(+) -N was the key impact factor.

Effect of agricultural land use change on community composition of bacteria and ammonia oxidizers

Soil microbial communities can be strongly influenced by agricultural practices, but little is known about bacterial community successions as land use changes. The objective of this study was to determine microbial community shifts following major land use changes in order to improve our understanding of land use impacts on microbial community composition and functions. Four agricultural land use patterns were selected for the study, including old rice paddy fields (ORP), Magnolia nursery planting (MNP), short-term vegetable (STV), and long-term vegetable (LTV) cultivation. All four systems are located in the same region with same soil parent material (alluvium), and the MNP, STV, and LTV systems had been converted from ORP for 10, 3, and 30 years, respectively. Soil bacteria and ammonia oxidizer community compositions were analyzed by 454 pyrosequencing and terminal restriction fragment length polymorphism, respectively. Quantitative PCR was used to determine 16S rRNA and amoA gene copy numbers. The results showed that when land use was changed from rice paddy to upland systems, the relative abundance of Chloroflexi increased whereas Acidobacteria decreased significantly. While LTV induced significant shifts of bacterial composition, MNP had the highest relative abundance of genera GP1, GP2, and GP3, which were mainly related to the development of soil acidity. The community composition of ammonia-oxidizing bacteria (AOB) but not ammonia-oxidizing archaea was strongly impacted by the agricultural land use patterns, with LTV inducing the growth of a single super predominant AOB group. The land use changes also induced significant shifts in the abundance of 16S rRNA and bacterial amoA genes, but no significant differences in the abundance of archaea amoA was detected among the four land use patterns. Soil total phosphorous, available phosphorous, NO3 −, and soil organic carbon contents and pH were the main determinants in driving the composition of both bacteria and AOB communities. These results clearly show the significant impact of land use change on soil microbial community composition and abundance and this will have major implications on the microbial ecology and nutrient cycling in these systems, some of which is unknown. Further research should be directed to studying the impacts of these microbial community shifts on nutrient dynamics in these agroecosystems so that improved nutrient management systems can be developed.

Emissions of nitrous oxide from casts of tropical earthworms belonging to different ecological categories

Abstract While earthworms’ feeding behavior has been shown to be a key driver of greenhouse gas like nitrous oxide (N 2 O) emissions for temperate species, this assessment remains to be demonstrated for tropical ones. This study constitutes a comparative assessment of the impact of different feeding strategies of tropical earthworms on their cast emissions of N 2 O and the characterization of microbial communities associated with these emission dynamics. N 2 O flux was determined in vitro from casts of 2 epigeic ( Dichogaster annae and Eisenia andrei ) and 4 endogeic/epiendogeic ( Metaphire houlleti , Octolasion tyrtaeum , Pontoscolex corethrurus and Amynthas corticis ) earthworm species in the presence or absence of acetylene. Casts of epigeic earthworms, fed on fresh coffee pulp, emitted about 392-fold higher amounts of N 2 O than those of endogeic ones, fed on a tropical soil. Acetylene exposure significantly increased the cast emission rates indicating that (i) apart from N 2 O, dinitrogen (N 2 ) is also emitted by earthworm casts, particularly by the epigeic guild (45%) and (ii) denitrification is the major microbial process responsible for these N-gas emissions from casts. Total bacteria were 10-fold higher in epigeic casts than endogeic but the relative abundance of nitrifier (AOB) and denitrifiers (nirK and nirS) was many times higher in endogeic casts than epigeic ones. The relative gene density of nosZ to (nirK + nirS) was 4-fold higher in epigeic casts than endogeic ones. Moreover, bacterial amoA gene abundance was higher in casts of all species than for their archaeal counterparts. Cast N 2 O emission was positively correlated with nitrifier as well as denitrifier gene abundance, while it was positively correlated with epigeic nitrate and negatively with endogeic nitrate contents. Ammonium contents did not show any relationship with cast emissions. Mean ammonium and nitrate contents were many times higher in casts than food substrates except nitrate in endogeic casts which was 4-fold less than parent food substrate.

Production of oceanic nitrous oxide by ammonia-oxidizing archaea

Abstract. The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA) were detectable throughout the water column of the eastern tropical North Atlantic (ETNA) and eastern tropical South Pacific (ETSP) Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen in the ocean.

Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska

Nitrification and denitrification processes are crucial to plant nutrient availability, eutrophication and greenhouse gas production both locally and globally. Unravelling the major environmental predictors for nitrification and denitrification is thus pivotal in order to understand and model environmental nitrogen (N) cycling. Here, we sampled five plant community types characteristic of interior Alaska, including black spruce, bog birch, tussock grass and two fens. We assessed abundance of functional genes affiliated with nitrification (bacterial and archaeal amoA) and denitrification (nirK/S and nosZ) using qPCR, soil characteristics, potential nitrification and denitrification rates (PNR and PDR) and gross mineralization rates. The main chemical and biological predictors for PNR and PDR were assigned through path analysis. The potential N cycling rates varied dramatically between sites, from some of the highest (in fens) to some of the lowest (in black spruce) measured globally. Based on path analysis, functional gene abundances were the most important variables to predict potential rates. PNR was best explained by bacterial amoA gene abundance followed by ammonium content, whereas PDR was best explained directly by nosZ gene abundance and indirectly by nirK/S gene abundance and nitrate. Hence, functional gene abundance is a valuable index that integrates recent environmental history and recent process activity, and therefore is a good predictor of potential rates. The results of this study contribute to our understanding of the relative importance of different biological and chemical factors in driving the potential for nitrification and denitrification across terrestrial ecosystems.

Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO 2

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global nitrogen (N) biogeochemical cycling. Responses of the associated microorganisms to global changes remain unclear. This study was to determine if there was a shift in soil AOB and AOA abundances and community structures under free-air carbon dioxide (CO 2) enrichment (FACE) and N fertilization in Duke Forest of North Carolina, by using DNA-based molecular techniques, i.e., quantitative PCR, restriction fragment length polymorphism (RFLP) and clone library. The N fertilization alone increased the abundance of bacterial amoA gene, but this effect was not observed under elevated CO 2 condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO 2 treatments, while such effect increased significantly under elevated CO 2. A total of 690 positive clones for AOA and 607 for AOB were selected for RFLP analysis. Analysis of molecular variance (AMOVA) indicated that effects of CO 2 enrichment and N fertilization on the community structure of AOA and AOB were not significant. Canonical correspondence analysis also showed that soil pH rather than elevated CO 2 or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ 13C and archaeal amoA gene abundance indicated a positive effect of elevated CO 2 on the growth ammonia oxidizing archaea. On the other hand, the community structures of AOB and AOA are determined by the soil niche properties rather than elevated CO 2 and N fertilization.

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses

Ammonia-oxidizing bacteria and ammonia-oxidizing archaea are commonly found together in soils, yet the factors influencing their relative distribution and activity remain unclear. We examined archaeal and bacterial amoA gene distribution, and used a novel bioassay to assess archaeal and bacterial contributions to nitrification potentials in soils spanning a range of land uses (forest, pasture, cultivated and long-term fallowed cropland) along a 10 km transect. The assay, which quantifies the extent to which acetylene-inactivated soil nitrification potential recovers (RNP) in the presence of bacterial protein synthesis inhibitors, indicated a significant archaeal contribution to the nitrification potentials of the pasture and long-term fallowed soils. Archaeal amoA gene abundance did not vary significantly among the soils, but bacterial amoA gene abundance did, resulting in archaeal : bacterial amoA abundance ratios ranging from 1.1 ± 0.8 in cultivated soils to 396 ± 176 in pasture soils. Both archaeal and bacterial amoA gene compositions were heterogeneous across the landscape, but differed in their patterns of variability. Archaeal amoA gene distributions were distinct among each of the three main land-use types: forest, pasture and cropland soils. In contrast, bacterial amoA gene composition was distinct in forest and in cultivated cropland, while pasture and long-term fallowed cropland soils were similar. In both pasture and long-term fallowed cropland soils, one phylotype of Nitrosospira cluster 3a was highly abundant. This distinct bacterial amoA gene fingerprint correlated with significant contributions of archaea to RNP of both soils, despite differences in archaeal amoA gene composition between the pasture and fallowed soils. This observation suggests that the factors driving the development of ammonia-oxidizing bacteria community composition might influence the extent of archaeal contribution to soil nitrification.

Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting

The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R2=0.554; P<0.001), indicating that archaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R2=0.503; P=0.03) especially during the mesophilic and maturation stages.

Impacts of Spartina alterniflora invasion on abundance and composition of ammonia oxidizers in estuarine sediment

Spartina alterniflora widely invades coastal wetland in China and might change nitrification in sediment. Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are involved in nitrification in this environment. The objective of this study was to examine the effect of S. alterniflora invasion on abundance and composition of AOA and AOB. The abundance and composition of AOA, AOB, and total bacteria in the sediments from S. alterniflora-invaded native mangrove vegetated and unvegetated zones at two depths of 0–5 cm (O) and 5–20 cm (R) were investigated using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis. Relationships were also determined between sediment properties and the AOB and AOA population sizes. Compared with native mangrove vegetated zone, the archaeal amoA gene abundance was reduced by 11.3-fold (O) and 46.1-fold (R), but the bacterial amoA gene abundance was increased by 9.8-fold (O) and 1.8-fold (R), respectively, in the S. alterniflora-invaded zone. The AOA abundance was always higher than AOB, especially in the native mangrove zone. Both AOA and AOB population sizes in the upper layer (O) were bigger than those in the deeper layer (R). Little difference was found in the AOB community composition among different zones, while diversity of AOA community was increased by the presence of S. alterniflora. This study demonstrated that the S. alterniflora invasion affects the abundance of both AOA and AOB, but only affects the community composition of AOA in the tidal sediments.

Nitrous Oxide Emissions from Ephemeral Wetland Soils are Correlated with Microbial Community Composition

Nitrous oxide (N2O) is a greenhouse gas with a global warming potential far exceeding that of CO2. Soil N2O emissions are a product of two microbially mediated processes: nitrification and denitrification. Understanding the effects of landscape on microbial communities, and the subsequent influences of microbial abundance and composition on the processes of nitrification and denitrification are key to predicting future N2O emissions. The objective of this study was to examine microbial abundance and community composition in relation to N2O associated with nitrification and denitrification processes over the course of a growing season in soils from cultivated and uncultivated wetlands. The denitrifying enzyme assay and pool dilution methods were used to compare the rates of denitrification and nitrification and their associated N2O emissions. Functional gene composition was measured with restriction fragment length polymorphism profiles and abundance was measured with quantitative polymerase chain reaction. The change in denitrifier nitrous oxide reductase gene (nosZ) abundance and community composition was a good predictor of net soil N2O emission. However, neither ammonia oxidizing bacteria ammonia monooxygenase (bacterial amoA) gene abundance nor composition predicted nitrification-associated-N2O emissions. Alternative strategies might be necessary if bacterial amoA are to be used as predictive in situ indicators of nitrification rate and nitrification-associated-N2O emission.

Response of Archaeal Communities in the Rhizosphere of Maize and Soybean to Elevated Atmospheric CO2 Concentrations

BackgroundArchaea are important to the carbon and nitrogen cycles, but it remains uncertain how rising atmospheric carbon dioxide concentrations ([CO2]) will influence the structure and function of soil archaeal communities.Methodology/Principal FindingsWe measured abundances of archaeal and bacterial 16S rRNA and amoA genes, phylogenies of archaeal 16S rRNA and amoA genes, concentrations of KCl-extractable soil ammonium and nitrite, and potential ammonia oxidation rates in rhizosphere soil samples from maize and soybean exposed to ambient (∼385 ppm) and elevated (550 ppm) [CO2] in a replicated and field-based study. There was no influence of elevated [CO2] on copy numbers of archaeal or bacterial 16S rRNA or amoA genes, archaeal community composition, KCl-extractable soil ammonium or nitrite, or potential ammonia oxidation rates for samples from maize, a model C4 plant. Phylogenetic evidence indicated decreased relative abundance of crenarchaeal sequences in the rhizosphere of soybean, a model leguminous-C3 plant, at elevated [CO2], whereas quantitative PCR data indicated no changes in the absolute abundance of archaea. There were no changes in potential ammonia oxidation rates at elevated [CO2] for soybean. Ammonia oxidation rates were lower in the rhizosphere of maize than soybean, likely because of lower soil pH and/or abundance of archaea. KCl-extractable ammonium and nitrite concentrations were lower at elevated than ambient [CO2] for soybean.ConclusionPlant-driven shifts in soil biogeochemical processes in response to elevated [CO2] affected archaeal community composition, but not copy numbers of archaeal genes, in the rhizosphere of soybean. The lack of a treatment effect for maize is consistent with the fact that the photosynthesis and productivity of maize are not stimulated by elevated [CO2] in the absence of drought.

Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification. The spatial distribution showed that AOA had higher diversity and abundance in the surface layer sediments near the mangrove trees (0 and 10 m) but lower away from the mangrove trees (1,000 m), and communities of AOA could be clustered into surface and bottom sediment layer groups. In contrast, AOB showed a reverse distributed pattern, and its communities were grouped by the distances between sites and mangrove trees, indicating mangrove trees might have different influences on AOA and AOB community structures. Furthermore, the strong correlations among archaeal and bacterial amoA gene abundances and their ratio with NH4+, salinity, and pH of sediments indicated that these environmental factors have strong influences on AOA and AOB distributions in mangrove sediments. In addition, AOA diversity and abundances were significantly correlated with hzo gene abundances, which encodes the key enzyme for transformation of hydrazine into N2 in anaerobic ammonium-oxidizing (anammox) bacteria, indicating AOA and anammox bacteria may interact with each other or they are influenced by the same controlling factors, such as NH4+. The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-010-2929-0) contains supplementary material, which is available to authorized users.

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.

Do ammonia-oxidizing archaea respond to soil Cu contamination similarly asammonia-oxidizing bacteria?

Inhibitory experiments were conducted to investigate the responses of the population sizes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and the potential nitrification rates (PNRs) to Cu contamination in four Chinese soils. PNR was determined using a substrate-induced nitrification (SIN) assay, and the population size of the nitrifiers represented by amoA gene abundances was quantified using a real-time polymerase chain reaction (qPCR) assay. Both population size and PNR of the ammonia oxidizers reduced considerably at high Cu concentrations in all the soils. Bacterial amoA gene abundance was reduced by from 107-fold (Hailun soil) to more than 232-fold (Hangzhou soil) at the highest Cu concentrations (2,400 mg kg−1 Cu for Hailun, Langfang and Guangzhou soils and 1,600 mg kg−1 Cu for Hangzhou soil), while reduction in archaeal amoA gene abundance was from 10-fold (Langfang soil) to 89-fold (Hangzhou soil). AOA seemed more tolerant to Cu contamination than AOB. Nitrification rates were inhibited by more than 50% at a Cu concentration of 600 mg kg−1, and by more than 90% at the highest Cu concentrations in all soils. These results indicated that both AOA and AOB can be inhibited by toxic metals, highlighting the need to consider the role of AOA in nitrification in soils.