Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon

This study determined nitrification activity and nitrifier community composition in soils under stands of red alder (Alnus rubra) and Douglas fir (Pseudotsuga menziesii) at two sites in Oregon. The H.J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon, has low net N mineralization and gross nitrification rates. Cascade Head Experimental Forest, in the Coast Range, has higher net N mineralization and nitrification rates and soil pH is lower. Communities of putative bacterial [ammonia-oxidizing bacteria (AOB)] and archaeal [ammonia-oxidizing archaea (AOA)] ammonia oxidizers were examined by targeting the gene amoA, which codes for subunit A of ammonia monooxygenase. Nitrification potential was significantly higher in red alder compared with Douglas-fir soil and greater at Cascade Head than H.J. Andrews. Ammonia-oxidizing bacteria amoA genes were amplified from all soils, but AOA amoA genes could only be amplified at Cascade Head. Gene copy numbers of AOB and AOA amoA were similar at Cascade Head regardless of tree type (2.3-6.0 x 10(6)amoA gene copies g(-1) of soil). DNA sequences of amoA revealed that AOB were members of Nitrosospira clusters 1, 2 and 4. Ammonia-oxidizing bacteria community composition, determined by terminal restriction fragment length polymorphism (T-RFLP) profiles, varied among sites and between tree types. Many of the AOA amoA sequences clustered with environmental clones previously obtained from soil; however, several sequences were more similar to clones previously recovered from marine and estuarine sediments. As with AOB, the AOA community composition differed between red alder and Douglas-fir soils.     

Comparative analysis of archaeal 16S rRNA and <Emphasis Type="Italic">amoA</Emphasis> genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments

Considering their abundance and broad distribution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase alpha-subunit (amoA) genes were comparatively analyzed to study genetic potential for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0-1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1 x 10(7) to 4.9 x 10(7) per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria.     

Niche Differentiation of Ammonia-Oxidising Archaea (AOA) and Bacteria (AOB) in Response to Paper and Pulp Mill Effluent

Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification–denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.     

Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient

The relationship between ammonia-oxidizing bacteria (AOB) and potential nitrification rates was examined along a salinity gradient in a New England estuary in spring and late summer over 3 years. Ammonia-oxidizing bacteria abundance was estimated by measuring gene copies of the ammonia monooxygenase catalytic subunit (amoA) using real-time polymerase chain reaction. Ammonia-oxidizing bacteria abundance ranged from below detection to 6.0 x 10(7)amoA copies (gdw sediment)(-1). Mean potential nitrification rates ranged from 0.5 to 186.5 nmol N (gdw sediment)(-1) day(-1). Both AOB abundance and potential rates were significantly higher in spring than late summer. Correlations between rates and abundance varied significantly among sites, but showed site-specific ammonia oxidation kinetics related to AOB community structure. The effect of salinity on potential nitrification rates was evaluated by incubating sediment from each site under four salinity conditions (0, 5, 10 and 30 psu). At all sites, rates were generally highest in the intermediate salinity treatments, but rates at the upstream site were inhibited at high salinity, while rates at the two downstream sites were inhibited at the lowest salinity. Although salinity appears to be an important factor in determining AOB distribution, it may not be the primary factor as AOB exhibited a broad range of salinity tolerance in our experiments. Our results indicate that there are significant differences in abundance and community composition of AOB along the salinity gradient, and the differences are reflected in community function.     

Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahía del Tóbari, Mexico

Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase alpha-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.     

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) across physicochemical gradients in San Francisco Bay--the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than beta-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that beta-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than beta-AOB in the low-salinity region of the estuary. Both AOA and beta-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the beta-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and beta-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive.     

Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary

Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A ( amoA ). The abundance of β-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of β-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a β-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA . Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and β-AOB by elucidating conditions that may favour the numerical dominance of β-AOB over AOA in coastal sediments.     

Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments

Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11?×?10⁴–6.47?×?10⁵?copies?g^?1 sediment) was always greater than that of AOA amoA gene (7.98?×?10³–3.51?×?10⁵?copies?g^?1 sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03–5.39 pmol?N?copy^?1?day^?1) compared with winter (0.16–0.38 pmol?N?copy^?1?day^?1), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons.     

Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes

The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ± 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.     

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.     

南美白对虾养殖底泥中氨氧化细菌与氨氧化古菌多态性分析

【目的】本研究皆在了解虾养殖底泥中氨氧化细菌与氨氧化古菌群落多态性。【方法】以功能基因为基础,构建氨氧化细菌(AOB)与氨氧化古菌(AOA)的氨单加氧酶α亚基基因(amoA)克隆文库。利用限制性片段长度多态性(Restriction Fragment Length Polymorphism,RFLP)技术将克隆文库阳性克隆子进行归类分析分成若干个可操作分类单元(Operational Taxa Units,OTUs)。【结果】通过序列多态性分析,表明AOB amoA基因克隆文库中所有序列都属于变形杆菌门β亚纲(β-Proteobacteria)中的亚硝化单细胞菌属(Nitrosomonas)及Nitrosomonas-like,未发现亚硝化螺旋菌属(Nitrosospira)。AOA amoA基因克隆文库中只有一个OTU序列属于未分类的古菌(Unclassified-Archaea),其余序列都属于泉古菌门(Crenarchaeote)。AOA群落结构单一且存在一个绝对优势类群OTU3,其克隆子数目占克隆文库的57.45%。AOB和AOA amoA基因克隆文库分别包括13个OTUs和9个OTUs,其文库覆盖率分别为73.47%和90.43%。AOB amoA基因克隆文库的Shannon-Wiener指数、Evenness指数、Simpson指数、Richness指数均高于AOA。【结论】虾养殖塘底泥中存在氨氧化古菌的amoA基因,且多态性低于氨氧化细菌,表明氨氧化古菌在虾养殖塘底泥的氮循环中可能具有重要的作用。     

Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal Arctic ocean in summer and winter

Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial amoA clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal amoA genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal amoA genes were more abundant than betaproteobacterial amoA genes in the first year, but betaproteobacterial amoA was more abundant than archaeal amoA the following year. The ratio of archaeal amoA gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in Crenarchaea at this location. Potential nitrification rates, as well as the total amoA gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing Betaproteobacteria and Crenarchaea.     

Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu

The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91?× 10(5) to 8.65?× 10(6) copies/g dry sediment for the archaeal amoA gene and from 3.74?× 10(4) to 3.86?× 10(5) copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P?< 0.05). Concentrations of ammonia (NH(4)(+)), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P?< 0.05 or P?< 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.     

Distinct responses in ammonia-oxidizing archaea and bacteria after addition of biosolids to an agricultural soil

The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare(-1) year(-1)) and double the agronomic rate (54 Mg hectare(-1) year(-1)), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare(-1) year(-1)). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial amoA genes. In addition, only archaeal amoA gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal amoA genes were significantly higher than copy numbers of bacterial amoA genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.     

High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition

Nitrification has been believed to be performed only by autotrophic ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) until the recent discovery of ammonia-oxidizing archaea (AOA). Meanwhile, it has been questioned whether AOB are significantly responsible for NH(3) oxidation in acidic forest soils. Here, we investigated nitrifying communities and their activity in highly acidified soils of three subtropical forests in southern China that had received chronic high atmospheric N deposition. Nitrifying communities were analyzed using PCR- and culture (most probable number)-based approaches. Nitrification activity was analyzed by measuring gross soil nitrification rates using a (15) N isotope dilution technique. AOB were not detected in the three forest soils: neither via PCR of 16S rRNA and ammonia monooxygenase (amoA) genes nor via culture-based approaches. In contrast, an extraordinary abundance of the putative archaeal amoA was detected (3.2?×?10(8) -1.2?×?10(9) g?soil(-1) ). Moreover, this abundance was correlated with gross soil nitrification rates. This indicates that amoA-possessing archaea rather than bacteria were predominantly responsible for nitrification of the soils. Furthermore, sequences of the genus Nitrospira, a dominant group of soil NOB, were detected. Thus, nitrification of acidified subtropical forest soils in southern China could be performed by a combination of AOA and NOB.     

Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils

Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.     

Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps

Previous results from a 16S rRNA gene library analysis showed high diversity within the prokaryotic community of a subterranean radioactive thermal spring, the "Franz-Josef-Quelle" (FJQ) in Bad Gastein, Austria, as well as evidence for ammonia oxidation by crenarchaeota. This study reports further characterization of the community by denaturing gradient gel electrophoresis (DGGE) analysis, fluorescence in situ hybridization (FISH), and semiquantitative nitrification measurements. DGGE bands from three types of samples (filtered water, biofilms on glass slides, and naturally grown biofilms), including samples collected at two distinct times (January 2005 and July 2006), were analyzed. The archaeal community consisted mainly of Crenarchaeota of the soil-subsurface-freshwater group (group 1.1b) and showed a higher diversity than in the previous 16S rRNA gene library analysis, as was also found for crenarchaeal amoA genes. No bacterial amoA genes were detected. FISH analysis of biofilms indicated the presence of archaeal cells with an abundance of 5.3% (+/-4.5%) in the total 4',6-diamidino-2-phenylindole (DAPI)-stained community. Microcosm experiments of several weeks in duration showed a decline of ammonium that correlated with an increase of nitrite, the presence of crenarchaeal amoA genes, and the absence of bacterial amoA genes. The data suggested that only ammonia-oxidizing archaea (AOA) perform the first step of nitrification in this 45 degrees C environment. The crenarchaeal amoA gene sequences grouped within a novel cluster of amoA sequences from the database, originating from geothermally influenced environments, for which we propose the designation "thermal spring" cluster and which may be older than most AOA from soils on earth.     

Effect of Different Ammonia Concentrations on Community Succession of Ammonia-oxidizing Microorganisms in a Simulated Paddy Soil Column

Ammonia oxidation is performed by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). To explore the effect of ammonia concentration on the population dynamic changes of ammonia-oxidizing microorganisms, we examined changes in the abundance and community composition of AOA and AOB in different layers. Most of the archaeal amoA sequences were Nitrosotalea-related and the proportion that Nitrosotalea cluster occupied decreased in the surface layer and increased in the deep layer during the cultivation process. Nitrosopumilus-related sequences were only detected in the deep layer in the first stage and disappeared later. Both phylogenetic and quantitative analysis showed that there were increased Nitrosomonas-related sequences appeared in the surface layer where the ammonia concentration was the highest. Both AOA and AOB OTU numbers in different layers decreased under selective pressure and then recovered. The potential nitrification rates were 25.06 μg·N·L(-1)·g(-1) dry soil·h(-1) in the mid layer which was higher than the other two layers. In general, obvious population dynamic changes were found for both AOA and AOB under the selective pressure of exogenous ammonia and the changes were different in three layers of the soil column.     

Rapid and dissimilar response of ammonia oxidizing archaea and bacteria to nitrogen and water amendment in two temperate forest soils

Biochemical processes relevant to soil nitrogen (N) cycling are performed by soil microorganisms affiliated with diverse phylogenetic groups. For example, the oxidation of ammonia, representing the first step of nitrification, can be performed by ammonia oxidizing bacteria (AOB) and, as recently reported, also by ammonia oxidizing archaea (AOA). However, the contribution to ammonia oxidation of the phylogenetically separated AOA versus AOB and their respective responsiveness to environmental factors are still poorly understood. The present study aims at comparing the capacity of AOA and AOB to momentarily respond to N input and increased soil moisture in two contrasting forest soils. Soils from the pristine Rothwald forest and the managed Schottenwald forest were amended with either NH(4)(+)-N or NO(3)(-)-N and were incubated at 40% and 70% water-filled pore space (WFPS) for four days. Nitrification rates were measured and AOA and AOB abundance and community composition were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP) analysis of bacterial and archaeal amoA genes. Our study reports rapid and distinct changes in AOA and AOB abundances in the two forest soils in response to N input and increased soil moisture but no significant effects on net nitrification rates. Functional microbial communities differed significantly in the two soils and responded specifically to the treatments during the short-term incubation. In the Rothwald soil the abundance and community composition of AOA were affected by the water content, whereas AOB communities responded to N amendment. In the Schottenwald soil, by contrast, AOA responded to N addition. These results suggest that AOA and AOB may be selectively influenced by soil and management factors.