Community Structure Of Ammonia-oxidizing Bacteria Research Articles

Biochar Combined with Garbage Enzyme Enhances Nitrogen Conservation during Sewage Sludge Composting: Evidence from Microbial Community and Enzyme Activities Related to Ammoniation

Nitrogen loss is an unavoidable problem during composting processes, and the ammonia oxidation process significantly affects nitrogen transformation. The objective of this study was to evaluate nitrogen transformation when garbage enzyme (GE), biochar (BC), pelelith (PL) and combinations thereof were added during sewage sludge composting. Meanwhile, the succession of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were also explored via quantitative polymerase chain reaction and high-throughput sequencing. The results showed that GE + BC and GE + PL treatments decreased ammonia (NH3) formation by 23.8% and 8.3%, and that of nitrous oxide (N2O) by 25.7% and 26.3% relative to the control, respectively. Simultaneously, the GE, GE + BC, and GE + PL treatments boosted the succession of AOA and AOB, and increased the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO) activities and the gene copies of AOA and AOB. The AMO activities, NH4-N, NO3-N, and C/N, significantly affect AOA and AOB community structures. The network analysis predicted that the AMO and HAO were secreted mainly by the unclassified_Archaea and norank_Crenarchaeota, whereas it also showed that the GE + BC improved microbial associations with AOA, enzymatic activity, and environmental factors. Thus, the addition of garbage enzyme and biochar appears to be a promising mitigation strategy to reduce nitrogen losses during the composting process.

Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater.

Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.

Temperate grassland soil nitrifiers are more sensitive to nitrogen addition than simulated warming

Soil nitrogen transformations are influenced by both global climate change and human activities. Nitrification, affected by ammonia-oxidizing and nitrite-oxidizing microorganisms, is one of the crucial N transformation processes. However, the impact of environmental change on the diversity and community structure of these microorganisms in grassland ecosystems remains poorly understood. This study explored the alpha diversity and community structures of N-cycling microorganisms in response to simulated warming and N addition in a temperate steppe. The results showed that N addition significantly increased the taxon richness of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria but significantly decreased the diversity of total archaea. Also, N addition significantly changed the community structures of ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and total archaea and bacteria. However, warming had no effect on the whole microbiome alpha and beta diversity. The alternations of microbial communities were mainly induced by changes in soil pH and inorganic N concentrations. This study illustrates that the temperate grassland microbial communities are more sensitive to N addition than simulated warming under future climate change scenes.

The elevation of salinity above 1% deteriorated nitrification performance and reshaped nitrifier community of an MBR: An often overlooked factor in the treatment of high-strength ammonium wastewater

The effects of synchronous variations of influent salinity with the elevation of NH4+-N concentration on nitrification performance and microbial community structure of bioreactor are often ignored. In this study, we investigated the dynamic response of nitrifying activated sludge to synchronously increased salinity and ammonia loading rate (ALR) in a nitrification membrane bioreactor (MBR). We found that the increase in influent salinity above 1% (from 0.91 to 1.32%) led to the deterioration of the nitrification performance of the MBR. The combined inhibition effect of salinity (1.32%), free ammonia (FA, an average of 1.37 mg/L), and free nitrous acid (FNA, an average of 0.155 mg/L) on nitrite-oxidizing bacteria (NOB) resulted in long-term (35 days) nitrite accumulation. The further increase of salinity and ALR exhibited little influence on the nitrification performance of MBR after the activated sludge had adapted to high salinity (>1%), effective nitrification performance was achieved at high ALR up to 1.71 kg NH4+-N/m3·d and high salinity (2.13%). The microbial analysis showed that the elevated salinity and accumulation of FNA reshaped the microbial community structure of ammonia-oxidizing bacteria (AOB) and NOB. The dominant species of AOB and NOB shifted from the salinity-resistant species Nitrosomonas aestuarii to the species Nitrosomonas mobilis with dual resistant to salinity and FNA, and from non-salinity-resistant species Candidatus Nitrospira defluvii to salinity-resistant species Nitrobacter winogradskyi and Nitrospira marina, respectively. Therefore, the salinity of 1% may be a critical level for the nitrification performance and the shift in the nitrifier community of activated sludge without salinity acclimation.

Does subjecting plants to water stress enhance biological nitrification inhibition potential of rice?

Biological nitrification inhibition (BNI) is a trait that could improve nitrogen-use efficiency of a crop. We studied varietal differences in BNI potential of rice at the vegetative phase when plants were subjected to water stress. We obtained water-soluble root exudates (RE) and water-extracts of crushed root tissues (RT) from two-week-old seedlings of five rice cultivars grown continuously under adequate water or under water stress and assessed their ability to suppress the activity of Nitrosomonas europaea and the growth of lettuce seedlings. We also investigated how growing rice under continuously saturated (TC) and unsaturated (TU) soil moisture conditions affected potential nitrification rate (PNR) and community structure of ammonia-oxidizing bacteria (AOB) in the rhizosphere compared with bulk soil. We observed that only RT at ≥ 0.50 mg ml−1 suppressed the activity of N. europaea with significant (p < 0.05) differences among rice cultivars. Subjecting rice cultivars PI312777 and PI338046 to water stress significantly (p < 0.05) increased BNI of RT. Inhibition of lettuce root growth by RT was strongly correlated with its BNI (r = 0.83, p < 0.05). In T-RFLP profiles of AOB, the relative abundance of T-RF R205 was lower in TU than in TC in all cultivars except Rexmont. The rice cultivars studied produced compounds that could inhibit ammonia oxidizers, but the degree of BNI differed based on the moisture stress experienced by the crop. Lineages of rice cultivars with known allelopathic potential would be promising candidates to consider for BNI potential.

Proper organic substitution attenuated both N2O and NO emissions derived from AOB in vegetable soils by enhancing the proportion of Nitrosomonas

The ammonia oxidation process driven by microorganisms is an essential source of nitrous oxide (N2O) and nitric oxide (NO) emissions. However, few evaluations have been performed on the changes in the community structure and abundance of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under substituting portion of chemical fertilizers with organic manure (organic substitution) and their relative contribution to the ammonia oxidation process. Here, five long-term fertilization strategies were applied in field (SN: synthetic fertilizer application; OM: organic manure; M1N1: substituting 50 % of chemical N fertilizer with organic manure; M1N4: substituting 20 % of chemical N fertilizer with organic manure; and CK: no fertilizer). We investigated the response characteristics of AOB and AOA community structures by selective inhibitor shaking assays and high-throughput sequencing and further explained their relative contribution to the ammonia oxidation process during three consecutive years of vegetable production. Compared to SN and M1N4, the potential of ammonia oxidation (PAO) was significantly reduced by 26.4 % and 22.3 % in OM and 9.5 % and 4.4 % in M1N1, resulting in N2O reductions of 38.9 % and 30.8 % (OM) and 31.2 % and 21.1 % (M1N1), respectively, and NO reductions of 45.0 % and 34.1 % (OM) and 40.1 % and 28.3 % (M1N1). RDA and correlation analyses showed that the soil organic carbon and ammonium nitrogen content increased while AOB gene abundance and diversity significantly decreased with increasing organic replacement ratio; however, the relative abundance of Nitrosomonas in AOB increased in OM and M1N1, which further demonstrates that AOB are the main driver in vegetable soils. Therefore, the appropriate proportion of organic substitution (OM and M1N1) could decrease the N2O and NO emissions contributed by AOB by affecting the soil physicochemical properties and AOB community structure.

The activity of ammonia-oxidizing bacteria on the residual effect of biochar-compost amended soils in two cropping seasons

Ammonia-oxidizing bacteria (AOB) are vital in regulating nitrification in agricultural soils. Nevertheless, the knowledge of the AOB community's response to fortified and composted biochar application in the maize/soybean agroecosystem is scarce. This study examined the residual effects of a control soil (CNZ), biochar (BIZ), compost (CPZ), composted biochar (CBZ), and fortified biochar (FBZ) on the AOB community composition, soil chemical properties, and enzyme activities in 2018 and 2019 of a maize/soybean agroecosystem. The AOB community was unravelled using Illumina Miseq sequencing, and multivariate approaches were used to explain the data collected. In 2018, FBZ increased the content of NO3--N, while CPZ, CBZ, and FBZ improved total nitrogen (TN) in the soil. In 2019, CBZ and FBZ increased NO3--N content, while CPZ improved TN and NO2--N in the soil. Likewise, CPZ significantly differed from FBZ, CBZ, and BIZ in AOB richness, while CBZ significantly differed from BIZ in AOB diversity in 2019. Furthermore, distance-based redundancy analysis (db-RDA) and Spearman correlation showed a significant correlation with NH4+-N and NO2--N in 2018 and TN and NO3--N in 2019, while Nitrosomonas eutropha and Nitrosomonas nitrosa had the highest weighted degree in the co-occurrence network in both years. This research demonstrates that co-application of biochar with compost in the maize/soybean agroecosystem could result in changes in the AOB community structure.

Long-term enclosure at heavy grazing grassland affects soil nitrification via ammonia-oxidizing bacteria in Inner Mongolia

Enclosure and grazing can significantly change the turnover of nitrogen in grassland soil. Changes of soil nitrogen mineralization and ammonium-oxidizing microorganisms caused by enclosure in different grazing intensities (about 30 years of grazing history) grassland, however, has rarely been reported. We selected the grassland sites with high and medium grazing intensity (HG and MG, 4 and 2 sheep ha−1, respectively) and had them enclosed (45 × 55 m) in 2005 while outside the enclosure was continuously grazed year-round. A two factorial study was designed: grazing intensity (MG and HG sites) and enclosure (fence and non-fence). Nitrogen mineralization was detected through a laboratory incubation experiment. The abundance and community structure of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed using quantitative PCR (q-PCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning, and sequencing. Results showed that compared with MG site, at HG site the AOB abundance and community structure of AOB changed significantly while the AOA abundance and community structure did not change obviously. Enclosure significantly decreased the cumulative mineralized N, N mineralization rate, the abundance of AOB and the AOB community structure at the HG site, while at MG site, enclosure did not change these parameters. Potential nitrification rate (PNR) was positively correlated with the abundance of AOA and AOB at the MG and HG sites, respectively. The abundance of AOA was significantly correlated with soil pH; however, AOB abundance was significantly correlated with soil available N, total N, C/N ratio, pH, etc. The phylogenetic analysis showed that Nitrososphaeraceae and Nitrosomonadaceae were the dominant AOA and AOB, respectively. Totally, the responses of AOB and AOA mainly were associated to changes in soil physicochemical properties caused by different intensity grazing; AOB and AOA may be the dominant functional players in ammonia oxidation processes at HG and MG site, respectively.

Effect of gradual increase of atmospheric CO2 concentration on nitrification potential and communities of ammonia oxidizers in paddy fields

Currently, the influence of elevated atmospheric CO2 concentration (eCO2) on ammonia oxidation to nitrite, the rate-limiting step of nitrification in paddy soil, is poorly known. Previous studies that simulate the effect of eCO2 on nitrification are primarily based on an abrupt increase of atmospheric CO2 concentration. However, paddy ecosystems are experiencing a gradual increase of CO2 concentration. To better understand how the nitrification potential, abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) respond to eCO2 in paddy ecosystems, a field experiment was conducted using the following two treatments: a gradual increase of CO2 (EC, increase of 40 ppm per year until 200 ppm above ambient) and ambient CO2 (CK). The results demonstrated that the EC treatment significantly (P < 0.05) stimulated the soil potential nitrification rate (PNR) at the jointing and milky stages, which increased by 127.83% and 27.35%, respectively, compared with CK. Furthermore, the EC treatment significantly (P < 0.05) stimulated the AOA and AOB abundance by 56.60% and 133.84%, respectively, at the jointing stage. Correlation analysis showed that the PNR correlated well with the abundance of AOB (R2 = 0.7389, P < 0.001). In addition, the EC treatment significantly (P < 0.05) altered the community structure of AOB, while it had little effect on that of AOA. A significant difference in the proportion of Nitrosospira was observed between CO2 treatments. In conclusion, the gradual increase of CO2 positively influenced the PNR and abundance of ammonia oxidizers, and AOB could be more important than AOA in nitrification under eCO2.

Nitrogen and Phosphorus Fertilization Reshapes the Abundance and Structure of Ammonia Oxidizers on a Leymus chinensis Steppe in Northern China

Although nitrogen (N) and phosphorus (P) fertilization are important for maintaining the health and productivity of Leymus chinensis steppe, their impact on the abundance and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in this ecosystem is still unclear. We used the amoA gene as a molecular marker to monitor changes in AOA and AOB under low and high N and P fertilization and applied the resin-core technique to measure soil N mineralization. We found that the abundance of AOA based on amoA gene copies, ranging from 7.51 × 107 to 1.23 × 108 copies g−1 soil, was higher than that of AOB. Fertilization, especially high N and P, increased the number of amoA copies associated with AOB. AOA and AOB communities were dominated by Crenarchaeota and Proteobacteria, respectively. Fertilization decreased the relative abundances of Thaumarchaeota in the AOA community and Proteobacteria in the AOB community and increased the relative abundance of Ammonia_oxidizing_bacteria_ensemble. In N and P fertilization treatments, soil N transformation was closely related to AOB but not AOA. Soil ammonium N and nitrate N reshape the structure of ammonia oxidizers of AOB but not those of AOA on L. chinensis steppes.

Effects of aquatic nitrogen pollution on particle-attached ammonia-oxidizing bacteria in urban freshwater mesocosms.

Ammonia-oxidizing bacteria (AOB) attached to aquatic particles are important participants in ammonia oxidation within hypereutrophic urban river systems. To explore the effects of aquatic nitrogen pollution on particle-attached AOB in urban river, we utilized laboratory mesocosms to investigate the responses of abundances and community structure of particle-attached AOB to ammonium (NH4+) and glycine (C2H5NO2) amendments. The abundance and community structure of particle-attached AOB were determined with quantitative real-time polymerase chain reaction (qRT-PCR) analysis and high-throughput sequencing based on the AOB amoA gene, respectively. Most of the bacterial amoA sequences from different treatments were affiliated with uncultured Nitrosomonadaceae bacterium, uncultured Nitrosomonadales bacterium, and uncultured Nitrosomonas sp., which are closely associated with organic pollution. The species richness and diversity of particle-attached AOB communities increased with increasing NH4+ and glycine concentrations. Treatment effects contributed significantly to the variance in particle-attached AOB communities. Although, glycine was completely transformed to ammonium within a few days and ammonium amendments would change the community structure of particle-attached AOB, the effect of glycine on the particle-attached AOB community was regulated by both the resulting ammonium concentration, as well as organic matter availability to the heterotrophic bacteria. Results suggested that high anthropogenic nitrogen loadings appeared to promote higher particle-attached AOB richness and diversity in the hypereutrophic urban river, but the effect of organic nitrogen on the particle-attached AOB community was different from the effect of inorganic nitrogen. This study informs ammonia oxidization mechanisms in the hypereutrophic urban rivers, which contributes to remediation/restoration strategies.

Biochar Addition Inhibits Nitrification by Shifting Community Structure of Ammonia-Oxidizing Microorganisms in Salt-Affected Irrigation-Silting Soil.

Biochar has been widely recognized as an effective and eco-friendly ameliorant for saline soils, but information about the mechanism of how biochar influences nitrification in salt-affected agroecosystem remains fragmented. An incubation experiment was performed on the salt-affected soil collected from a three-consecutive-year experiment at biochar application gradients of 7.5 t⋅ha−1, 15 t⋅ha−1 and 30⋅t ha−1 and under nitrogen (N) fertilization. Responses of the nitrification rate (NR), numbers of ammonia monooxygenase (amoA) gene copies, and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to biochar application were investigated. The results indicated that, under N fertilization, the NR and numbers of amoA-AOB and amoA-AOA gene copies negatively responded to biochar addition. Biochar application increased the community diversity of AOB but decreased that of AOA. Biochar addition and N fertilization shifted the AOB community from Nitrosospira-dominated to Nitrosospira and Nitrosomonas-dominated, and altered the AOA community from Nitrososphaera-dominated to Nitrososphaera and Nitrosopumilus-dominated. The relative abundance of Nitrosospira, Nitrosomonas and Nitrosopumilus decreased, and that of Nitrosovibrio and Nitrososphaera increased with biochar application rate. Soil SOC, pH and NO3−-N explained 87.1% of the variation in the AOB community, and 78.1% of the variation in the AOA community was explanatory by soil pH and SOC. The SOC and NO3−-N influenced NR through Nitrosovibrio, Nitrosomonas, Norank_c_environmental_samples_p_Crenarchaeota and amoA-AOB and amoA-AOA gene abundance. Therefore, biochar addition inhibited nitrification in salt-affected irrigation-silting soil by shifting the community structures of AOB and AOA and reducing the relative abundance of dominant functional ammonia-oxidizers, such as Nitrosospira, Nitrosomonas and Nitrosopumilus.

Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils

Nitrous oxide (N2O) production in tropical soils cultivated with sugarcane is associated with ammonia-oxidizing bacteria (AOB) and fungal denitrifiers. However, the taxonomic identities and the community diversities, compositions, and structures of AOB and fungal denitrifiers in these soils are not known. Here, we examined the effects of applying different concentrations of an organic recycled residue (vinasse: regular non-concentrated or 5.8-fold concentrated) on the dynamics of AOB and fungal denitrifier community diversity and composition and greenhouse gas emissions during the sugarcane cycle in two different seasons, rainy and dry. DNA was extracted from soil samples collected at six timepoints to determine the dynamics of amoA-AOB and nirK-fungal community diversity and composition by amplicon sequencing with gene-specific primers. Bacterial and archaeal amoA, fungal and bacterial nirK, bacterial nirS and nosZ, total bacteria (16S rRNA) and total fungi (18S rRNA) were quantified by real-time PCR, and N2O and CO2 emissions were measured. The genes amoA-AOB and bacterial nirK clade II correlated with N2O emissions, followed by fungal nirK. The application of inorganic nitrogen fertilizer combined with organic residue, regardless of concentration, did not affect the diversity and structure of the AOB and fungal denitrifier communities but increased their abundances and N2O emissions. Nitrosospira sp. was the dominant AOB, while unclassified fungi were the dominant fungal denitrifiers. Furthermore, the community structures of AOB and fungal denitrifiers were affected by season, with dominance of uncultured Nitrosospira and unclassified fungi in the rainy season and the genera Nitrosospira and Chaetomium in the dry season. Nitrosospira, Chaetomium, Talaromyces purpureogenus, and Fusarium seemed to be the main genera governing N2O production in the studied tropical soils. These results highlight the importance of deciphering the main players in N2O production and demonstrate the impact of fertilization on soil microbial N functions.

Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.

The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.

Effects of biochar and biochar compound fertilizer on the communities of nitrifier and denitrifier in a reclaimed soil from coal-mining area

As a new soil amendment strategy, the effects of biochar application on soil microbial community have been reported in literature, but little information is available on the response of nitrogen-related microbial communities to biochar application in the reclaimed soil from coal-mining area. Through an outdoor pot experiment with reclaimed soil from coal-mining area of Huaibei, the effects of biochar and biochar compound fertilizer on nitrifier and denitrifier communities were investigated by real time PCR (qPCR) and terminal-restricted fragment length polymorphism (T-RFLP). There were five treatments: control (CK), NPK fertilizer (CF), biochar compound fertili-zer (BF), 2% biochar and NPK fertilizer (LB), 4% biochar and NPK fertilizer (HB). Results showed that compared with the CK, the treatments CF, BF, LB and HB significantly increased the abundance of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB), nirK and nirS genes of denitrifier. Compared with the CF treatment, BF, LB and HB significantly increased the abundance of AOB and nirK genes by 42.9%-82.1% and 33.5%-62.7%, respectively. Results of redundancy analysis showed that soil organic carbon, pH, NH4+-N and available potassium significantly affected AOB community structure, while soil organic carbon concentration, pH and NO3--N concentration significantly altered nirK-denitrifier community structure. Therefore, the application of biochar and biochar compound fertilizer could improve soil quality of the reclaimed soil from coal-mining area, and increase the abundances of nitrifier and denitrifier and alter community structure of AOB and nirK-denitrifier.

Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO2 concentration

The elevated atmospheric CO2 concentration is well known to have an important effect on soil nutrient cycling. Ammonia oxidation, mediated by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is the rate-limiting step in soil nitrification, which controls the availability of two key soil nutrients (ammonium and nitrate) for crops. Until now, how the AOA and AOB communities in paddy soils respond to elevated CO2 remains largely unknown. Here, we examined the communities of AOA and AOB and nitrification potential at both surface (0–5 cm) and subsurface (5–10 cm) soil layers of paddy fields under three different CO2 treatments, including CK (ambient CO2 concentration), LT (CK + 160 ppm of CO2) and HT (CK + 200 ppm of CO2). The elevated CO2 was found to have a greater impact on the community structure of AOB than that of AOA in surface soils as revealed by high-throughput sequencing of their amoA genes. However, no obvious variation of AOA or AOB communities was observed in subsurface soils among different CO2 treatments. The abundance of AOA and AOB, and nitrification potential were significantly increased in surface soils under elevated CO2. The variation of AOB abundance correlated well with the variation of nitrification potential. The soil water content and dissolved organic carbon content had important impacts on the dynamic of AOB communities and nitrification potential. Overall, our results showed different responses of AOA and AOB communities to elevated CO2 in paddy ecosystems, and AOB were more sensitive to the rising CO2 concentration.

Responses of Ammonia-Oxidizing Microorganisms to Intercropping Systems in Different Seasons

Intercropping plays an essential role in agricultural production, impacting the soil’s physical and chemical properties and microbial communities. However, the responses of ammonia-oxidizing microorganisms in the continuous-cropping soil to different intercropping systems in different growing seasons are still insufficiently studied. Here, we investigated the effects of seven intercropping systems (alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber) on soil physical and chemical properties, potential nitrification rate (PNR), soil ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) communities in the greenhouse in spring and autumn. The results showed that, compared with cucumber monoculture, intercropping increased the soil NH4+-N and NO3−-N. The chrysanthemum–cucumber, rape–cucumber, and mustard–cucumber treatments increased soil PNR. Intercropping increased the AOA and AOB abundances in two seasons, especially in rape–cucumber, wheat–cucumber, chrysanthemum–cucumber, and trifolium–cucumber treatments. The ratio of AOA and AOB decreased with seasonal variation. The wheat–cucumber and rape–cucumber treatments increased soil AOA community diversity. Seasonal variation had a significant effect on the relative abundance of the AOB community. Nonmetric multidimensional scaling analysis showed that the AOA and AOB community structures were obviously different from spring to autumn. Redundancy analysis showed that the AOA community was significantly regulated by moisture, NO3−–N, and available potassium (AK), while the AOB community was significantly regulated by moisture, available phosphorus (AP), AK, NO3−-N, and pH. Network analysis showed that the co-occurrence relationship and complexity of AOA and AOB communities were different in two growing seasons. The AOB community may play a critical role in ammonia oxidation in autumn. Taken together, intercropping improved soil physicochemical state, increased soil PNR and significantly altered soil AOA and AOB communities. Seasonal variation significantly altered the AOA and AOB communities’ structure and interaction between them. The effect of seasonal variation on AOA and AOB communities was greater than intercropping.

Long-term mineral fertilizer substitution by organic fertilizer and the effect on the abundance and community structure of ammonia-oxidizing archaea and bacteria in paddy soil of south China

Ammonia oxidation in the soil is related to nitrogen (N) availability for plants, nitrate loss, and N fertilizer use efficiency, which is important for studies on the N cycle of paddy field ecosystems. Substitution of partial mineral N fertilizer with organic amendments is commonly considered to optimize fertilization practices and reduce the application of mineral N fertilizer in the paddy fields. However, little is known about the effects of this type of fertilization on the relative contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to soil nitrification. Therefore, a 34-year field trial including five fertilization regimes (CK, without fertilizer; NPK, mineral NPK fertilizer; NPKM1, 70% inorganic N + 30% organic N + PK; NPKM2, 50% inorganic N + 50% organic N + PK; NPKM3, 30% inorganic N + 70% organic N + PK; P: phosphorus, K: potassium) was conducted. AOA and AOB abundance and community structures were determined by quantitative PCR and high-throughput sequencing analyses. Although the abundance of AOA and AOB increased with the increase in the percentage (30%–70%) of organic N substitution, the abundance ratio of AOA to AOB (133.9–84.7) decreased. Soil potential nitrification rate (PNR) increased dramatically (p < 0.05) after replacing chemical N with organic N, and with the increase in the substitution ratio of organic N in paddy soils. AOA and AOB both correlated significantly (p < 0.05) with PNR, but the contribution of AOB to PNR exceeded that of AOA. Soil carbon (C) to N ratio was the best predictor (43.0%) for AOA abundance, while total N and NH4+-N incorporating models were the best predictors (90.3%) for AOB abundance. Variations in AOA composition correlated strongly with fertilizer-induced changes in soil pH and ammonia concentration, whereas the AOB community was only markedly correlated with pH (p = 0.004). The substitution of 30%–70% of mineral N with organic N could increase the soil pH to 5.54–5.87, and that of ammonia concentration to 8.37–24.1 μM, which was the main reason that AOB contributed more to PNR than AOA. These results indicate that the organic substitution fertilizer regime had much stronger effects on the abundance and composition of AOB than AOA, and the potential contribution of AOB to ammonia oxidation in paddy soils should not be ignored after mineral N partial substitution by organic N.

Higher Sensitivity of Soil Microbial Network Than Community Structure under Acid Rain

Acid rain (AR), as a global environmental threat, has profoundly adverse effects on natural soil ecosystems. Microorganisms involved in the nitrogen (N) cycle regulate the global N balance and climate stabilization, but little is known whether and how AR influences the structure and complexity of these microbial communities. Herein, we conducted an intact soil core experiment by manipulating the acidity of simulated rain (pH 7.5 (control, CK) vs. pH 4.0 (AR)) in subtropical agricultural soil, to reveal the differences in the structure and complexity of soil nitrifying and denitrifying microbiota using Illumina amplicon sequencing of functional genes (amoA, nirS, and nosZ). Networks of ammonia-oxidizing archaea (AOA) and nirS-carrying denitrifiers in AR treatment were less complex with fewer nodes and lower connectivity, while network of nosZ-carrying denitrifiers in AR treatment had higher complexity and connectivity relative to CK. Supporting this, AR reduced the abundance of keystone taxa in networks of AOA and nirS-carrying denitrifiers, but increased the abundance of keystone taxa in nosZ-carrying denitrifiers network. However, AR did not alter the community structure of AOA, ammonia-oxidizing bacteria (AOB), nirS-, and nosZ-carrying denitrifiers. Moreover, AR did not change soil N2O emissions during the experimental period. AOB community structure significantly correlated with content of soil available phosphorus (P), while the community structures of nirS- and nosZ-carrying denitrifiers both correlated with soil pH and available P content. Soil N2O emission was mainly driven by the nirS-carrying denitrifiers. Our results present new perspective on the impacts of AR on soil N-cycle microbial network complexity and keystone taxa in the context of global changes.

An RNA-based study of the distribution of ammonia-oxidizing microorganisms in vertical sediment

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play crucial roles in ammonia nitrogen degradation in freshwater lake sediment. However, studies on ammonia-oxidizing microorganisms (AOM) in vertical sediment are still limited, especially with respect to the quantitative analysis of the vertical distribution of active AOM at the RNA level. Herein, by researching the AOM in a 75 cm vertical sediment from Lake Taihu, we found that although the total abundance of AOB throughout the whole vertical sediment surpassed that of AOA, active AOA had a closer correlation with the potential nitrification rate than active AOB. The active transcription abundance of AOM generally decreased with increasing depth, especially for AOA, while that of AOB decreased slightly. Compared to active transcription, the total abundance of AOM varied little. The community structures of AOA and AOB changed significantly with increasing depth, and Group I.1a and Nitrosomonas were the predominant clusters, respectively. Ultimately, our study demonstrated that research methods based on the RNA level can accurately reflect the vertical variation in AOM.