Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria

Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone

The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.

Interaction mechanism between nitrogen conversion and the microbial community in the hydrodynamic heterogeneous interaction zone

To study the inorganic nitrogen in the process of interaction of river and groundwater and the changes in the microbial community, a vertical simulation device was used to simulate groundwater recharge to river water (upwelling) and river water recharge to groundwater (downwelling). The inorganic nitrogen concentrations in the soil and water solution as well as the characteristics of the microbial community were assessed to determine the inorganic nitrogen transformation and microbial community response in the heterogeneous interaction zone under hydrodynamic action, and the interaction mechanism between nitrogen transformation and the microbial community in the interaction zone was revealed. The removal rates of NO₃^--N in the simulated solution reached 99.1% and 99.3% under the two fluid-groundwater conversion modes, and the prolonged hydraulic retention time (HRT) of the oxidization-reduction layer in the fine clay area and the high organic matter content made the inorganic nitrogen transformation process dominated by microorganisms more complete. The denitrification during upwelling, dominated by denitrifying bacteria in Sphingomonas, Pseudomonas, Bacillus, and Arthrobacter, was stronger than that during downwelling. Dissimilatory nitrate reduction to ammonium (DNRA), controlled by some aerobic bacteria in Pseudomonas, Bacillus, and Desulfovibrio, was more intense in downflow mode than upflow mode.

Rapid soil rewetting promotes limited N2O emissions and suppresses NH3 volatilization under urea addition

The alternation of dry and wet is an important environmental factor affecting the emission of nitrous oxide from soil. However, the consistent or opposite effects on NH₃ and N₂O emissions caused by adding exogenous urea in this process have not been fully considered. Here, we controlled the initial (slow drying) and final (adding water) water-filled pore space (WFPS) at 70%, 60%, or 50% through microculture experiment to simulate a process of slow drying-fertilization and rapid wetting of the soil from rice harvest to dryland crop fertilization. Through measuring soil chemical properties and the abundance and composition of related microbial communities during drying process, we studied the pathways of influence of drying and rewetting on the emission of N₂O and NH₃ after urea application. During the progressive drying process (WFPS decreasing from 70% to 60% and 50%), soil N₂O and NH₃ emissions decreased by 49.77%-72.13% and 17.89%-42.19%, respectively. After rapid rewetting (WFPS increasing from 60% to 70%, 50%-60% and 70%), N₂O emissions showed a slight increase, while NH₃ volatilization continued to decrease. Soil NH₄⁺-N and DOC contents both decreased during progressive drying, while the soil NO₃^--N content was enhanced. The drying process changed the community structure of ureC and amoA-b and reduced their abundance but had no effect on amoA-a, nirK or nirS. Correlation analysis indicated that the reductions in NH₄⁺-N content and the abundances of ureC and amoA-b were the main factors suppressing N₂O and NH₃ emissions. We believe that drying process limits the related microbial activity and substrate supply during ammonia oxidation process in terms of N₂O emissions, while in terms of NH₃ volatilization, it reduces the related microbial activity of urea hydrolysis process and increases the ammonium adsorption to the soil.

A review on effective soil health bio-indicators for ecosystem restoration and sustainability

Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.

Distribution of ammonia oxidizers and their role in N2 O emissions in the reservoir riparian zone

As a transitional boundary between terrestrial and aquatic ecosystems, the riparian zone is considered a hotspot for N₂ O production because of the active nitrogen processes. Ammoxidation is an important microbial pathway for N₂ O production, but the distribution of ammonia oxidizers under different land-use types in the reservoir riparian zone and what role they played in N₂ O emissions are still not clear. We investigated spatiotemporal distributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their role in N₂ O emissions in different land-use types along the riparian zone of Miyun Reservoir: grassland, sparse woods, and woodland. We found significant differences in both AOA abundance and AOB diversity indices among land-use types. AOA and AOB communities were significantly separated by different land-use types. The main drivers to determine the distribution of ammonia-oxidizing microbial community were soil water content, NH₄ ⁺ , NO₃ ^- , and total organic carbon (TOC). In situ N₂ O flux was highest in woodland with a mean value of 12.28 μg/m² ·h, and it was substantially decreased by 121% and 123% in sparse woods and grassland. TOC content was decreased by 20% and 40% in sparse woods and grassland compared with woodland, and it was significantly positively correlated with in situ N₂ O flux. Meanwhile, AOB diversity indices were significantly correlated with in situ N₂ O flux. These results showed that the heterogeneity of physicochemical properties among different land-use types affected the community of AOA and AOB in riparian zones. AOB not AOA, and community diversity rather than abundance, played a role in N₂ O emissions.

Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.

Straw mulching and nitrogen application altered ammonia oxidizers communities and improved soil quality in the alkaline purple soil of southwest China

Microbe-mediated ammonia oxidation is a key process in soil nitrogen cycle. However, the effect of maize straw mulching on the ammonia oxidizers in the alkaline purple soil remains largely unknown. A three-year positioning experiment was designed as follows: straw mulching measures as the main-plot treatment and three kinds of nitrogen application as the sub-plot treatment. We found the contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK), available nitrogen (AN), available phosphorus (AP), and NH₄⁺-N were increased after straw mulching and nitrogen application in alkaline purple soil, so did the amoA genes abundance of ammonia-oxidizing archaeal (AOA) and bacterial (AOB). Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that Thaumarchaeote (448-bp T-RF) was dominated the AOA communities, whereas Nitrosospira sp (111-bp T-RF) dominated the AOB communities. The community compositions of both AOA and AOB were altered by straw mulching and nitrogen application in alkaline purple soil, however, the AOB communities was more responsive than AOA communities to the straw mulching and nitrogen application. Further analysis indicated that SOC and AP were the main factors affecting the abundance and community compositions of AOA and AOB in alkaline purple soil. The present study reported that straw mulching and nitrogen strategies differently shape the soil ammonia oxidizers community structure and abundance, which should be considered when evaluating agricultural management strategies regarding their sustainability and soil quality.

Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment

Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.

Effect of Long-Term Fertilization on Ammonia-Oxidizing Microorganisms and Nitrification in Brown Soil of Northeast China

The objective of this study was to find out changes in ammonia oxidation microorganisms with respect to fertilizer as investigated by real-time polymerase chain reaction and high-throughput sequencing. The treatments included control (CK); chemical fertilizer nitrogen low (N) and high (N₂); nitrogen and phosphorus (NP); nitrogen phosphorus and potassium (NPK) and organic manure fertilizer (M); MN; MN₂; MNPK. The results showed that long-term fertilization influenced soil fertility and affected the abundance and community of ammonia-oxidizing microorganisms by changing the physical and chemical properties of the soil. The abundance and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was influenced by soil organic carbon, total nitrogen, total soil phosphorus, available phosphorus, available potassium, and soil nitrate. Soil environmental factors affected the nitrification potential by affecting the structure of ammonia-oxidizing microorganisms; specific and rare AOA and AOB rather than the whole AOA or AOB community played dominant role in nitrification.

Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques

In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO₃)₂ injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO₃)₂ injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO₃)₂ injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO₃)₂ runs. Taken together, Ca(NO₃)₂ was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.

Surface ammonium loading rate shifts ammonia-oxidizing communities in surface water-fed rapid sand filters

Nitrification is important in drinking water treatment plants (DWTPs) for ammonia removal and is widely considered as a stepwise process mediated by ammonia- and nitrite-oxidizing microorganisms. The recent discovery of complete ammonia oxidizers (comammox) has challenged the long-held assumption that the division of metabolic labor in nitrification is obligate. However, little is known about the role of comammox Nitrospira in DWTPs. Here, we explored the relative importance of comammox Nitrospira, canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 12 surface water-fed rapid sand filters (RSFs). Quantitative PCR results showed that all the three ammonia-oxidizing guilds had the potential to dominate nitrification in DWTPs. Spearman's correlation and redundancy analysis revealed that the surface ammonium loading rate (SLR) was the key environmental factor influencing ammonia-oxidizing communities. Comammox Nitrospira were likely to dominate the nitrification under a higher SLR. PCR and phylogenetic analysis indicated that most comammox Nitrospira belonged to clade A, with clade B comammox Nitrospira almost absent. This work reveals obvious differences in ammonia-oxidizing communities between surface water-fed and groundwater-fed RSFs. The presence of comammox Nitrospira can support the stability of drinking water production systems under high SLR and warrants further investigation of their impact on drinking water quality.

Airborne microorganisms exacerbate the formation of atmospheric ammonium and sulfate

Haze pollution is inseparable from the transformation of air pollutants especially the ammonium and sulfate. Chemical and physical processes play important roles in this transformation. However, the role of microbial processes has rarely been studied. In this report, we applied the cultivation-independent metagenomic approach to study airborne microorganisms, investigating the potential microbial-catalyzed transformation of ammonium and sulfate in PM_2.5 samples. Functional genes predict that airborne microorganisms have the potential to catalyze ammonium formation but not ammonium oxidation since no ammoxidation genes were identified. We also found that the frequency of sulfate-forming genes was 1.56 times of those for sulfate-reducing genes. It was speculated that microbial metabolisms in the atmosphere could contribute to the accumulation of ammonium and sulfate. With the increase of PM_2.5 concentration, the frequency of functional genes and the relative abundance of genera which involved in nitrogen and sulfur metabolisms increased. That suggested air pollution was conducive to the microbial-mediated formation of ammonium and sulfate. Overall, our results provided evidence for the possible role of microbial processes in the air pollutant transformation and brought a new perspective for studying the formation of secondary air pollutants.

Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil

Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.

Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China

Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 10⁸ gene copies (g-soil⁻¹) to 2.23 × 10⁸ gene copies (g-soil⁻¹) and 5.45 × 10⁸ gene copies (g-soil⁻¹) to 3.30 × 10⁷ gene copies (g-soil⁻¹), respectively. Five environmental variables, namely, ORP, DO, NO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{3}^{-}$\end{document}3−, Temp, and NH\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{4}^{+}$\end{document}4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment.

Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone

The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (10⁷-10⁸amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.

Prokaryotic footprints in urban water ecosystems: A case study of urban landscape ponds in a coastal city, China

The urban water ecosystems, such as the landscape ponds are commonly considered under the influence of anthropogenic disturbances, which can lead to the deterioration of the water quality. The prokaryotic communities are considered as one of the best indicators of the water quality. However, there are significant gaps in understanding the ecological processes that shape the composition and function of prokaryotic communities in the urban water ecosystems. Here, we investigated the biogeographic distribution of prokaryotic assemblages in water environments including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city (Xiamen), China, by using 16S rDNA amplicon sequencing. Our results indicated that the ponds had higher α-diversity of prokaryotic communities than those in the reservoirs, while there were significant variations in the community compositions among ponds, reservoirs, IFs and EFs. Moreover, ponds harbored a significantly higher proportion of sewage- and fecal-indicator taxa than those in the reservoirs, suggesting the occurrence of exogenous pollution in the urban ponds. Null model analysis revealed that dispersal limitation was the main ecological processes resulting in the divergence of prokaryotic community compositions between ponds and other environments, while dispersal limitation and variable selection played an essential role in the formation of unique prokaryotic assemblages in the reservoirs. Function predication analysis demonstrated that the ponds shared more similar functional profiles with IFs or EFs (e.g., chemoheterotrophy, fermentation, chlorate reducers, nitrate reduction and respiration) than the reservoirs, whereas dominance of photoautotrophy was observed in the reservoirs. Overall, this study provides a profound insight of the ecological mechanisms underlying the responses of prokaryotic communities in the urban landscape ponds to the anthropogenic disturbances.

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance

Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding. The samples were classified into three groups (flooding, recovery, and control) for a high-throughput sequencing and quantitative PCR analysis. We used a relative quantitative index of both the resistance (RS) and resilience (RL) to assess the variation of gene abundance, alpha-diversity, and community composition. The AOA generally demonstrated a better recovery capability after the flooding disturbance compared to AOB. In particular, AOA were more resilient after the flooding disturbance. Taxa within the AOA and AOB showed different RS and RL values, with the most abundant taxa showing in general the highest RS indices. Soil NH₄⁺ and Fe²⁺/Fe³⁺ were the main variables controlling the key taxa of AOA and AOB and probably influenced the resistance and resilience properties of AOA and AOB communities. The distinct mechanisms of AOA and AOB in maintaining community stability against the flooding disturbance might be linked to the different life-history strategies: the AOA community was more likely to represent r-strategists in contrast to the AOB community following a K-life strategy. Our results indicated that the AOA may play a vital role in ammonia oxidation in a fluctuating habitat and contribute to the stability of riparian ecosystem.

Biostimulation of nutrient additions on indigenous microbial community at the stage of nitrogen limitations during composting

Microorganisms can play a crucial role in the efficiency for composting, which are essential for converting the organic wastes into a well-stabilized, value added product. However, the activity of most of the key functional microorganisms were inhibited due to the limited special nutrient substances or other physiochemical factors during composting, which further affected the quality of compost. The study was conducted to investigate the effects of enriched ammonium (NH₄⁺-N) and organic nitrogen (Org-N) on indigenous microbial community and whether nitrogen (N) nutrient additions could modify the special species during composting. The results showed that the abundance and structure of bacterial community had distinctly diverse responses to different N nutritional treatments (no nutrient addition, NH₄⁺-N addition, and Org-N addition). The addition of N sources enhanced the abundance of corresponding uncultured indigenous species negatively related to the factor of NH₄⁺ and Org-N in redundancy analysis (RDA) during composting but the effect of NH₄⁺ was more significant than Org-N. Nonmetric multidimensional scaling ordination (NMDS) demonstrated that both the two N additions changed bacterial community but had different duration for affecting bacterial composition. Conclusively, an optimized method for regulating the key stains with special biological capacity is proposed by controlling the single limiting-nutrient factor sharply decreasing at one of composting stages and negatively related to the key species in RDA.

Dominant role of ammonia-oxidizing bacteria in nitrification due to ammonia accumulation in sediments of Danjiangkou reservoir, China

Surface sediments are the inner source of contaminations in aquatic systems and usually maintain aerobic conditions. As the key participators of nitrification process, little is known about the activities and contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. In this study, we determined the net and potential nitrification rates and used 1-octyne as an AOB specific inhibitor to detect the contributions of AOA and AOB to nitrification in surface sediments of Danjiangkou reservoir, which is the water source area of the middle route of South-to-North Water Diversion Project in China. Quantitative PCR and Illumina high-throughput sequencing were used to evaluate the abundance and diversity of the amoA gene. The net and potential nitrification rates ranged from 0.42 to 1.93 and 2.06 to 8.79 mg N kg^-1 dry sediments d^-1, respectively. AOB dominated in both net and potential nitrification, whose contribution accounted for 52.7-78.6% and 59.9-88.1%, respectively. The cell-specific ammonia oxidation rate calculation also revealed the cell-specific rates of AOB were higher than that of AOA. The Spearman's rank correlation analysis suggested that ammonia accumulation led to the AOB predominant role in net nitrification activity, and AOB abundance played the key role in potential nitrification activity. Furthermore, phylogenetic analysis suggested AOB were predominantly characterized by the Nitrosospira cluster, while AOA by the Nitrososphaera and Nitrososphaera sister clusters. This study will help us to better understand the contributions and characteristics of AOA and AOB in aquatic sediments and provide improved strategies for nitrogen control in large reservoirs.

Effects of decabromodiphenyl ether and planting on the abundance and community composition of nitrogen-fixing bacteria and ammonia oxidizers in mangrove sediments: A laboratory microcosm study

While nitrogen (N) fixation and ammonia oxidation by microorganisms are two important N cycling processes, little is known about how the microbes that drive these two processes respond when sediments are contaminated with persistent organic pollutants. In this study, we carried out a laboratory microcosm experiment to examine the effects of decabromodiphenyl ether (BDE-209), either on its own or combined with a common mangrove species, Avicennia marina, on the abundance, diversity, and community composition of N-fixing bacteria (NFB) and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in mangrove sediments. The sediments were very N-limited after one year. The rates of N fixation and NFB abundance were significantly higher in the sediments that contaminated by BDE-209, especially in the planted sediment, indicating that both BDE-209 and planting stimulated N fixation in N-limited mangrove sediments. In contrast, the potential nitrification rate and abundance of AOA and AOB decreased significantly under BDE-209 and planting, and the inhibitory effects were stronger in the sediment with both planting and BDE-209 than in the sediments with either BDE-209 or planting. The results from pyrosequencing showed that the richness and diversity of NFB increased, while those of AOA and AOB decreased, in the sediments treated with BDE-209 only and with BDE-209 combined with planting. The community compositions of NFB, AOA, and AOB in the sediments shifted significantly because of BDE-209, either alone or particularly when combined with planting, as shown by the increases in some NFB from the Proteobacteria phylum and decreases in AOA in the Nitrosopumilus genus and AOB in the Nitrosospira genus, respectively.

A regulating method for the distribution of phosphorus fractions based on environmental parameters related to the key phosphate-solubilizing bacteria during composting

This study was conducted to assess the abundance, incidence and diversity of the culturable phosphate-solubilizing bacteria (PSB) community during different organic wastes composting. The key PSB affecting different phosphorus (P) fractions and their relationship with environmental variables were analyzed by redundancy analysis (RDA). The results showed that there were distinct differences in amounts, incidence and community composition of PSB for the composts from different sources. Regression analysis demonstrated significant corrections between the density and incidence of PSB and pH, temperature, OM and DOC/DON. Most of culturable PSB showed high percentages of identity with the phyla of Firmicutes and Proteobacteria. There were thirteen key PSB correlated closely (p<0.05) with different P fractions variation. Conclusively, we suggested a process control method to regulate the distribution of P fractions during composting based on the relationship between the key PSB and P fractions as well as environmental parameters.