Ammonia-oxidizing Microorganisms Research Articles

Microbial communities in rare earth mining soil after in-situ leaching mining

In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.

Distribution and Potential Nitrification Rates of Aerobic Ammonia-Oxidizing Microorganisms in Surface Sediments of Mangrove in Sanya River

The ammonia oxidation process is a rate-limiting step in nitrification. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are the major drivers of ammonia oxidation. Their distribution and relative contributions to nitrification are the research highlights in the nitrogen cycle. Real-time quantitative polymerase chain reaction (qPCR) was used to study the distribution of aerobic ammonia-oxidizing microorganisms in the surface sediments of mangrove in the Sanya River, and the relative contribution rates of AOB and AOA to nitrification were calculated through the determination of the potential nitrification rates (PNR). The results showed that, in most sampling sites, the abundance of AOA amoA genes was higher than that of AOB amoA genes. The abundance of AOB was higher during the winter, whereas that of AOA was higher during the summer, and the ratio of AOA to AOB abundance was lower during the winter. The dissolved oxygen (DO) content, pH, total organic carbon (TOC) content, and nitrate concentration greatly influenced the abundance of AOB and AOA. The potential nitrification rates of AOB and AOA were both higher during the summer than during the winter, and the relative contribution rate of AOA to nitrification was higher during the winter, whereas that of AOB was higher during the summer. There were no significant correlations between the PNR and amoA genes abundance of AOB and AOA.

Acute glyphosate exposure does not condition the response of microbial communities to a dry–rewetting disturbance in a soil with a long history of glyphosate-based herbicides

Abstract. Dry–rewetting perturbations are natural disturbances in the edaphic environment and particularly in dryland cultivation areas. The interaction of this disturbance with glyphosate-based herbicides (GBHs) deserves special attention in the soil environment due to the intensification of agricultural practices and the acceleration of climate change with an intensified water cycle. The objective of this study was to assess the response of microbial communities in a soil with a long history of GBHs to a secondary imposed perturbation (a single dry–rewetting event). A factorial microcosm study was conducted to evaluate the potential conditioning effect of an acute glyphosate exposure on the response to a following dry–rewetting event. A respiratory quotient (RQ) based on an ecologically relevant substrate (p-coumaric acid) and basal respiration was used as a physiological indicator. Similarly, DNA-based analyses were considered, including quantitative PCR (qPCR) of functional sensitive microbial groups linked to cycles of carbon (Actinobacteria) and nitrogen (ammonia-oxidizing microorganisms), qPCR of total bacteria and denaturing gradient gel electrophoresis (DGGE) of ammonia-oxidizing bacteria (AOB). Significant effects of herbicide and of dry–rewetting perturbations were observed in the RQ and in the copy number of the amoA gene of AOB, respectively. However, no significant interaction was observed between them when analyzing the physiological indicator and the copy number of the evaluated genes. PCR–DGGE results were not conclusive regarding a potential effect of dry–rewetting × herbicide interaction on AOB community structure, suggesting further analysis by deep sequencing of the amoA gene. The results of this study indicate that the perturbation of an acute glyphosate exposure in a soil with a long history of this herbicide does not have a conditioning effect on the response to a subsequent dry–rewetting disturbance according to a physiological indicator or the quantified bacterial/archaeal genes. This is particularly relevant for the sustainability of soils in rainfed agriculture, where frequent exposure to GBHs along with intensification of hydrological cycles are expected to occur. Further studies considering multiple dry–rewetting disturbances and in different soil types should be conducted to simulate those conditions and to validate our results.

Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant

Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of ‘Candidatus Methylomirabilis oxyfera’ bacteria and two strains of ‘Ca. Brocadia’-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while ‘Ca. Methylomirabilis’ contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, ‘Ca. Methylomirabilis’ and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two ‘Ca. Methylomirabilis’ species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to ‘Ca. Brocadia fulgida’ included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h−1 L−1 and ammonium oxidation rate of 0.5 mmol h−1 L−1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way.Key points• An enrichment culture containing both N-damo and anammox bacteria was obtained.• Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions.• In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.

Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China

Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China. Our results showed that comammox microorganisms in mangrove sediments were extremely diverse. Phylogenetic analysis revealed a novel comammox group within clade A that formed a distinct cluster for which no reference sequence existed, implying their potential uniqueness. Quantitative PCR demonstrated that comammox abundance was slightly higher than that of the canonical ammonia-oxidizing bacteria but significantly lower than that of ammonia-oxidizing archaea, indicating they are not the dominant ammonia oxidizers in mangrove ecosystems. Finally, variation partition analysis revealed a significant decrease in similarity of comammox communities along the geographical distance, and a pronounced effect of the geographic factors and sediment attributes on the composition of comammox microorganisms and the abundance variations of ammonia oxidizers. Temperature and salinity were the most important contributing factors that shaped the comammox community. Further, detection of diverse comammox microorganisms in extremely high-salinity sediments suggested that this community could adapt to high salinity environments, which indicates salinity may not be a critical factor resulting in the absence of comammox microorganisms in open-ocean environments. This study expanded the current understanding of the diversity and niche preference of comammox in mangrove ecosystems, and further enhanced our understanding of adaptation potential of comammox communities.

Negative effects of rare earth oxide nanoparticles of La2O3, Nd2O3, and Gd2O3 on the ammonia-oxidizing microorganisms

Nanoparticles released into soil environment potentially impact microorganisms, which furtherly disturb terrestrial biogeochemical cycles. However, how rare earth oxide nanoparticles affect the functional microorganisms inhabited in natural soil is still unknown. This study was aimed to investigate the effect of different types of rare earth oxide nanoparticles on the ammonia-oxidizing microorganisms. Soil respectively added with 0, 10, 50, and 100 mg kg−1 of La2O3, Nd2O3, or Gd2O3 nanoparticle were incubated at 25 °C in the dark for 60 days. The potential ammonia oxidation (PAO), abundance and communities of ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) were measured at the 1st, 7th, and 60th day. Our results showed that the PAO in soils with nanoparticles significantly decreased due to nanoparticle toxicity at the 1st day, but it gradually increased to the control level owing to the adaptation of AOA and AOB in soils with nano-Nd2O3 and nano-Gd2O3. Interestingly, the abundance of AOB as reflected by the qPCR analysis was upregulated for the hormesis effect of AOB responding to nano-Nd2O3 or nano-Gd2O3 with 50 mg kg−1 level. Moreover, terminal restriction fragment length polymorphism (T-RFLP) results suggested that the communities for AOA and AOB shifted with nanoparticles type and incubation time. Rare earth oxide nanoparticles could inhibit activities of ammonia-oxidizing microorganisms, and thus they might be used as potential nitrification inhibitors to improve nitrogen use efficiency in the agricultural ecosystems.

Effects of long-term fertilization on soil ammonia-oxidizing microorganisms

Long-term fertilization can change the supply of soil carbon and nitrogen (N), with consequences on the abundance and community structure of soil microorganisms. Based on the long-term fertilization positioning experiment station of brown earth, we analyzed the dynamics of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) under different fertilization treatments, including no fertilization (CK), low level of inorganic N fertilizer (N2), high level of inorganic N fertilizer (N4), and organic manure combined with inorganic N fertilizer (M2N2), aiming to provide a basis for microbiological mechanism of soil N transformation and improvement of soil fertility. The results showed that the ratio of AOA to AOB abundance was 2.28-61.95 under different fertilization treatments. Compared with that in CK, the AOA abundance was reduced by 1.6%-13.6% after long-term fertilization. The abundance of AOB in N4 treatment decreased first and then increased with soil depths, but with contrary results in other treatments. The Shannon diversity index (H), evenness index (J), and Simpson index (S) of AOB were higher than those of AOA. The AOB diversity was increased at 0-20 cm soil layer in M2N2 treatment, while that of AOA was decreased. Soil AOB clustered with soil depths, and neither AOA nor AOB community clustered with fertilization treatments. In summary, long-term fertilization altered the composition of AOA and AOB. AOA was sensitive to environment, whereas AOB was more abundant and stable.

Diversity and abundance of comammox bacteria in the sediments of an urban lake.

Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia-oxidizing microbe exists in urban lakes and to determine the factors influencing its existence. This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia-oxidizing micro-organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co-existed with ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43×108 , 1·07×108 , 3·24×107 and 3·21×1011 copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria. Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments. Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils

Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC1:5) and NH4-N compared to irrigation with freshwater, while NO3-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO3−N, and pH, while AOB communities were only significantly associated with NO3−N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.

Conversion of ammonium to nitrate and abundance of ammonium-oxidizing-microorganism in Tropical soils with nitrification inhibitor

The use of nitrification inhibitors (NIs; dicyandiamide - DCD) is an alternative to reduce oxidation of ammonium (NH4 +-N) to nitrate (NO3 – -N) in the soil, reducing NO3 – -N losses from fertilization practices. Based on the hypothesis that DCD reduces conversion of NH4 +-N to NO3 – -N in tropical soils and inhibits ammonia oxidizing microorganisms (AOM) abundance, soils from the Piracicaba region, Sao Paulo, with different textures (sand, loam and clay) were incubated with ammonium sulphate (AS) and DCD. Contents of NH4 +-N, NO3 – -N, soil pH, and AOM abundance were quantified periodically. Ammonium sulphate increased AOM abundance in all soils, but AS+DCD presented AOM abundances similar to the control. During 90 days of incubation, the effectiveness of DCD in reducing NO3 – -N production was 1.8, 86.4, and 145.6 mg kg–1, while the effectiveness of DCD in reducing AOM abundance was 1.2, 3.0 and 2.3 × 10–3 g soil–1 for sandy, loamy, and clayey soils, respectively. DCD effectiveness was greater in loamy and clayey soils due to the naturally low nitrification in sandy soils. Application of AS treated with DCD showed potential not only to reduce NO3 – -N production in loamy and clayey soils, but also to decrease the soil nitrification rate. Overall, DCD was effective in reducing AOM abundance and conversion of NH4 +-N to NO3 – -N in loamy and clay soils evaluated here. The increase in clay content directly influences DCD effectiveness in reducing conversion of NH4 +-N to NO3 – -N.

Nitrogen oxidation consortia dynamics influence the performance of full-scale rotating biological contactors

Ammonia oxidising microorganisms (AOM) play an important role in ammonia removal in wastewater treatment works (WWTW) including rotating biological contactors (RBCs). Environmental factors within RBCs are known to impact the performance of key AOM, such that only some operational RBCs have shown ability for elevated ammonia removal. In this work, long-term treatment performance of seven full-scale RBC systems along with the structure and abundance of the ammonia oxidising bacteria (AOB) and archaea (AOA) communities within microbial biofilms were examined. Long term data showed the dominance of AOB in most RBCs, although two RBCs had demonstrable shift toward an AOA dominated AOM community. Next Generation Sequencing of the 16S rRNA gene revealed diverse evolutionary ancestry of AOB from RBC biofilms while nitrite-oxidising bacteria (NOBs) were similar to reference databases. AOA were more abundant in the biofilms subject to lower organic loading and higher oxygen concentration found at the distal end of RBC systems. Modelling revealed a distinct nitrogen cycling community present within high performing RBCs, linked to efficient control of RBC process variables (retention time, organic loading and oxygen concentration). We present a novel template for enhancing the resilience of RBC systems through microbial community analysis which can guide future strategies for more effective ammonia removal. To best of the author’s knowledge, this is the first comparative study reporting the use of next generation sequencing data on microbial biofilms from RBCs to inform effluent quality of small WWTW.

Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia.

Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.

Three kinds of ammonia oxidizing microorganisms play an important role in ammonia nitrogen self-purification in the Yellow River.

To develop the microbial resources of the Yellow River, seven water samples were collected along the Lanzhou region of the river from upstream to downstream for testing. Analysis of various physico-chemical indexes was conducted, and key parameters influencing the water quality were selected through principal component analysis, after which the decisive factors impacting water quality were determined by correlation and regression analysis. The results indicated that (1) DO, NH3-N, NO2--N, TN, TC, As, Cr6+ and Pb were the main physico-chemical factors influencing water quality in the Lanzhou region, with NH3-N having the greatest effect. (2) Ammonia-oxidizing microorganisms [ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonia-oxidizing bacteria (AMX)] were found to mediate the transformation of NH3-N in the studied section. AOA was the primary microbe community among the two aerobic ammonia-oxidizing microorganisms (AOA and AOB) in the Yellow River. (3) Phylogenetic analysis showed that there were some known groups, and there were still many unknown species in the water of the studied section, especially within the AMX population. (4) Correlation analysis revealed that AOA has strong adaptability to unhealthy environments, and that some environmental factors (higher concentrations of carbon, nitrogen and some heavy metals) could increase the AOA gene abundance. Overall, these results suggested there are rich ammonia-oxidizing microbial resources, especially AOA, in the Lanzhou section of the Yellow River, which have the potential for application in nitrogen sewage treatment.

Emerging perfluoroalkyl substance impacts soil microbial community and ammonia oxidation

Legacy perfluoroalkyl and poly-fluoroalkyl substances (PFASs) are gradually phased out because of their persistence, bioaccumulation, toxicity, long-distance transport and ubiquity in the environment. Alternatively, emerging PFASs are manufactured and released into the environment. It is accepted that PFASs can impact microbiota, although it is still unclear whether emerging PFASs are toxic towards soil microbiota. However, it could be assumed that OBS could impact soil microorganisms because it had similar chemical properties (toxicity and persistence) as legacy PFASs. The present study aimed to explore the influences of an emerging PFAS, namely sodium p-perfluorous nonenoxybenzene sulfonate (OBS), on archaeal, bacterial, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and ammonia oxidation. Grassland soil was amended with OBS at different dosages (0, 1, 10 and 100 mg/kg). After OBS amendment, tolerant microorganisms (e.g., archaea and AOA) were promoted, while susceptive microorganisms (e.g., bacteria and AOB) were inhibited. OBS amendment greatly changed microbial structure. Potential nitrifying activity was inhibited by OBS in a dose-dependent manner during the whole incubation. Furthermore, AOB might play a more important role in ammonia oxidation than AOA. Overall, OBS influenced ammonia oxidation by regulating the activity, abundance and structure of ammonia-oxidizing microorganisms, and could also exert influences on total bacterial and archaeal populations.

Differential responses of encoding-amoA nitrifiers and nir denitrifiers in activated sludge to anatase and rutile TiO2 nanoparticles: What is active functional guild in rate limiting step of nitrogen cycle?

The long-terms effects of different crystal-composition TiO2 nanoparticles (NPs) on nitrogen-cycle-related functional guilds in activated sludge remain unclear, especially under natural light irradiation. Accordingly, activated sludge was exposed to anatase TiO2-NPs (TiO2-A) and rutile TiO2-NPs (TiO2-R) for up to 45 days. With markedly (p < 0.05) reducing nitrification-/denitrification-enzymatic-activities and abundances of ammonia-oxidizing-microorganisms (AOMs) and nitrite-reducing-bacteria (NRB), TiO2-NPs triggered bacteria and archaea UPGMA clustering and a deep modification of N-cycling functional diversity guided by crystal structure. in situ13C-DNA-SIP confirmed ammonia-oxidizing-bacteria (AOB) (Nitrosomonas and Nitrosospira) in original sludge as main active AOMs with 75.4 times more abundance than ammonia-oxidizing-archaea (AOA), while AOA within Nitrosopumilus and Nitrososphaera genera were the main active AOMs and tended to aggregate inside sludge after 10-mg/L TiO2-NPs exposure. Encoding-nirK NRB were more sensitive, while encoding-nirS Zoogloea with a total share of 4.97% to 14.93%, etc. were the main active NRB. AOB was more sensitive to TiO2-A, while TiO2-R showed the stronger toxicity to AOA and NRB resulting from differences in water environmental behaviors and crystal characteristics of two TiO2-NPs. This work expands understanding of the ecological risks of titanium-dioxide-crystal-NPs in aquatic environment and may help devise better methods to alleviate environmental stress caused by NPs at wastewater treatment plants.

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Complete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting both clades of CAOB amoA gene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in which N. nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

Seasonal and vertical variations in the characteristics of the nitrogen-related functional genes in sediments from urban eutrophic lakes

Urban lakes play an important role in urban residents' lives, but they are more vulnerable to nitrogen pollution due to the large number of pollution sources in urban areas. Analyzing the characteristic variation of nitrogen-related functional genes in sediments could improve our understanding of nitrogen removal from urban lakes. Based on field samples of lake sediments in Wuhan, China, the seasonal and vertical variations in the characteristics of seven genes were detected using metagenome sequencing and qPCR. The genes examined were the ammonia-oxidizing bacteria gene (AOB amoA), ammonia-oxidizing archaea gene (AOA amoA), anammox gene (anammox 16S rRNA), denitrification genes (narG, nirS, nosZ), and dissimilatory nitrate reduction to ammonium gene (nrfA). The sequencing results revealed that the strain types of nosZ and nrfA were more abundant than amoA, anammox 16S rRNA, narG, and nirS. The nitrogen-related genes' abundances were much lower in summer than in winter. In the vertical zones of the sediments, the abundances of the seven genes mainly decreased as the sediment depth increased. The abundances of ammonium-oxidizing microorganisms had no significant difference in the vertical direction (P > 0.05), but there were significant differences in the vertical direction for the abundances of narG, nirS, nosZ, and nrfA (P < 0.05). Canonical correspondence analysis (CCA) illustrated that the main environmental factors affecting the gene abundances were NH4+-N in the interstitial water, dissolved oxygen (DO) and electrical conductivity (EC) in the overlying water, and total nitrogen (TN) in the sediment. The anammox 16S rRNA abundances were significantly correlated with the nrfA abundances, while the narG abundances were also significantly correlated with nirS abundances. The results extend the knowledge of spatiotemporal variations of nitrogen-cycle microorganisms' characteristics in urban eutrophic lakes.

More obvious air pollution impacts on variations in bacteria than fungi and their co-occurrences with ammonia-oxidizing microorganisms in PM2.5

Based on long-term systematic sampling, information is currently limited regarding the impacts of different air pollution levels on variations of bacteria, fungi and ammonia-oxidizing microorganisms (AOMs) in fine particulate matter (PM2.5), especially their interactions. Here, PM2.5 samples were weekly collected at different air pollution levels in Beijing, China during one-year period. Microbial composition was profiled using Illumina sequencing, and their interactions were further investigated to reveal the hub genera with network analysis. Diversity of bacteria and fungi showed obvious seasonal variations, and the heavy- or severe-pollution levels mainly affected the diversity and composition of bacteria, but not fungi. While, the community structure of both bacteria and fungi was influenced by the combination of air pollution levels and seasons. The most abundant bacterial genera and some genera with highest abundance in heavy- or severe-pollution days were the hub bacteria in PM2.5. Whereas, only the dominant fungi in light-pollution days in winter were the hub fungi in PM2.5. The complex positive correlations of bacterial or fungal pathogens would aggravate the air pollution effects on human health, despite of their low relative abundances. Moreover, the strong co-occurrence and co-exclusion patterns of bacteria and fungi in PM2.5 were identified. Furthermore, the hub environmental factors (e.g., relative humidity and atmospheric pressure) may play central roles in the distributions of bacteria and fungi, including pathogens. Importantly, AOMs showed significant co-occurrence patterns with the main bacterial and fungal genera and potential pathogens, providing possible microbiological evidences for controlling ammonia emissions to effectively reduce PM2.5 pollution. These results highlighted the more obvious air pollution impacts on bacteria than fungi, and the complex bacterial-fungal interactions, as well as the important roles of AOMs in airborne microbial interactions webs, improving our understanding of bioaerosols in PM2.5.

Correlation between ammonia-oxidizing microorganisms and environmental factors during cattle manure composting

Cattle manure composting was performed in an aerated vessel. Community structure and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) techniques targeting the ammonia monooxygenase alpha subunit (amoA) gene and the correlation between AOB and AOA communities and environmental factors was explored. Thirteen (13) AOB sequences were obtained, which were closely related to Nitrosomonas spp., Nitrosomonas eutropha, and Nitrosospira spp. and uncultured bacteria, among which Nitrosomonas spp. were predominant. Excessively high temperature and high ammonium concentration were not favorable for AOB growth. Five AOA sequences, belonging to CandidatusNitrososphaera gargensis and to an uncultured archaeon, were obtained. During composting, community diversity of AOB and AOA fluctuated, with AOA showing a higher Shannon–Wiener index. The AOB community changed more dramatically in the mesophilic stage and the early thermophilic stage, whereas the most obvious AOA community succession occurred in the late thermophilic stage, the cooling stage and the maturity stage. Water content, total nitrogen (TN) and ammonium concentration were more relevant to the AOB community structure, while higher correlations were observed between ammonia, nitrate and TN and the AOA community. AOB community diversity was negatively correlated with pH (r = −0.938, p < 0.01) and water content (r = −0.765, p < 0.05), while positively correlated with TN (r = 0.894, p < 0.01). AOA community diversity was negatively correlated with ammonium concentration (r = −0.901, p < 0.01). Ammonium concentration played an important role in the succession of AOB and AOA communities during composting.

Response of the Soil N2O Emission and Ammonia-oxidizing Microorganism Community to the Maize Straw Return with Reducing Fertilizer in Purple Soil

Crop straw is an important agricultural source, which can replace chemical fertilizers. A field experiment with six different amounts of fertilization combined with maize straw residues was carried out in purple soil, including the control (CK), conventional fertilizing (F), straw return with conventional fertilizing (100FS), straw return with 70% conventional fertilizing (70FS), straw return with 60% conventional fertilizing (60FS), and straw return with 50% regular fertilizing (50FS), to determine the response of the soil N2O emission and ammonia-oxidizing microorganism community distribution to straw return with reducing fertilizer. The dynamic characteristics of the N2O emission in purple soil were observed using an in situ closed chamber and gas chromatography-based system. The ammonia-oxidizing microorganism community distribution was analyzed with multiple molecular techniques (DNA-based clone library and qPCR) linked to physical-chemical soil properties. The results show that the combination of straw with fertilizer increases the N2O emission and cumulative N2O emission. The highest N2O emission[57.59-6238.02 μg·(m2·h)-1]and cumulative N2O emission (60.76 kg·hm-2) were observed for the 100FS treatment. Compared with the F treatment, the soil ammonium nitrogen and nitrate nitrogen contents are reduced and the soil organic matter increases after crop straw return with chemical fertilizer. However, significant changes of the soil total nitrogen and pH were not observed. The bacterial ammonia oxidizer (AOB) amoA gene abundance is higher than that of the archaeal ammonia oxidizer (AOA). The AOA amoA gene abundance during F treatment (50.9×103 copies·g-1) is significantly higher than that of others, while the AOB amoA abundance gene of the F treatment is the lowest (1.36×105 copies·g-1). The 100FS reduces the community diversity and Pielou index of AOA and AOB amoA gene. Their amoA gene abundance significantly declines during 100FS treatment. However, the increment of the AOA and AOB amoA gene diversity and dominant increment of AOB amoA gene abundance are significant when applying straw with reducing fertilizer. The specific AOA indicator OTU1 may be most important with respect to the direct and indirect production of N2O in purple soil. The redundancy analysis (RDA) shows that the community structure of AOA is remarkably relevant to the soil ammonium nitrogen, organic matter, and available phosphorus (P<0.05) and that the community structure of AOB is remarkably relevant to the soil dissolved organic nitrogen, total nitrogen, available potassium, and available phosphorus (P<0.05). The tolerance to different environments and ecological niches of AOB is weaker than that of AOA. Our results illustrate that the maize straw return with 60%-70% regular fertilizing dramatically increases the community diversity and abundance of the AOA and AOB amoA genes and partly mitigates the soil N2O emission without significantly decreasing the vegetable yields.