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Purpose Summer catch crop (CC) has been introduced into the vegetable rotating system in greenhouse fields to reduce nitrogen (N) losses through crop uptake and residual N immobilization. However, the effects of planting sorghum with high N uptake and biomass, and biological nitrification inhibition (BNI) potential as a CC on soil N dynamics and subsequent crop yield remain unclear. Methods In the two-year field experiment, the comprehensive effects of planting sorghum as CC on subsequent eggplant yield, soil mineral N dynamics, ammonia-oxidizing archaea (AOA) and bacteria (AOB) amoA gene abundances were determined, in comparison to the sweet corn and fallow treatments. Results Compared to the fallow and sweet corn, planting sorghum as CC increased subsequent eggplant yield by 24.88% and 18.94% in the 2014–2015 and 2015–2016 over-winter growing season, respectively. CC planting reduced soil nitrate (NO3−-N) accumulation during the summer fallow season. Sorghum planting could significantly maintain higher level of ammonium (NH4+-N) concentration during the summer fallow season and the first month of succeeding over-winter season. In addition, sorghum planting reduced soil net nitrifying potential, which could be partially attributed to the decreased amoA gene abundance of AOA at the 0–30 and 30–60 cm soil layers and AOB at 0–30 cm soil layer. Conclusion We conclude that planting sorghum in the summer fallow season is a promising strategy to retain soil NH4+-N, reduce soil NO3−-N accumulation, and enhance subsequent eggplant yield.

Synthetic nitrification inhibitors (SNI) and biological nitrification inhibitors (BNI) are promising tools to limit nitrogen (N) pollution derived from agriculture. Modern wheat cultivars lack sufficient capacity to exude BNIs, but, fortunately, the chromosome region (Lr#n-SA) controlling BNI production in Leymus racemosus, a wild relative of wheat, was introduced into two elite wheat cultivars, ROELFS and MUNAL. Using BNI-isogenic-lines could become a cost-effective, farmer-friendly, and globally scalable technology that incentivizes more sustainable and environmentally friendly agronomic practices. We studied how BNI-trait improves N-uptake, and N-use, both with ammonium and nitrate fertilization, analysing representative indicators of soil nitrification inhibition, and plant metabolism. Synthesizing BNI molecules did not mean a metabolic cost since Control and BNI-isogenic-lines from ROELFS and MUNAL presented similar agronomic performance and plant development. In the soil, ROELFS-BNI and MUNAL-BNI plants decreased ammonia-oxidizing bacteria (AOB) abundance by 60% and 45% respectively, delaying ammonium oxidation without reducing the total abundance of bacteria or archaea. Interestingly, BNI-trait presented a synergistic effect with SNIs since made it also possible to decrease the AOA abundance. ROELFS-BNI and MUNAL-BNI plants showed a reduced leaf nitrate reductase (NR) activity as a consequence of lower soil NO3− formation and a higher amino acid content compared to BNI-trait lacking lines, indicating that the transfer of Lr#-SA was able to induce a higher capacity to assimilate ammonium. Moreover, the impact of the BNI-trait in wheat cultivars was also noticeable for nitrate fertilization, with improved N absorption, and therefore, reducing soil nitrate content.

Potted Italian ryegrasses (Lolium multiflorum L.) were used to investigate the effect of ammonia-oxidizing bacterial (AOB) strain that coexisted in rhizosphere soil on Italian ryegrass regrowth. The results showed that the isolated and screened AOB strain (S2_8_1) had 100% similarity to Ensifer sesbaniae. The inoculation of S2_8_1 on day 44 before defoliation caused its copy number in rhizosphere soils to increase by 83–157% from day 34 before defoliation to day 14 after defoliation compared with that in Italian ryegrass without S2_8_1 inoculation, indicating that S2_8_1 coexisted permanently with Italian ryegrass. The coexistence promoted the delivery of root-derived cytokinin to leaves and to increase its cytokinin concentrations; thus, the Italian ryegrass regrowth accelerated. During the 14-day regrowth period, the S2_8_1 coexistence with Italian ryegrass caused its leaf and xylem sap cytokinin concentrations, rhizosphere soil nitrification rates, net photosynthetic rates, and total biomass to increase by 38%, 58%, 105%, 18%, and 39% on day 14 after defoliation, respectively. The inoculation of S2_8_1 on day 2 before defoliation also increased the regrowth of Italian ryegrass. Thus, the coexistence of AOB with Italian ryegrass increased its regrowth by regulating the delivery of cytokinins from roots to leaves.

Plantain has been suggested as a nitrous oxide (N2O) and nitrate (NO3-) leaching mitigation option as it may induce biological nitrification inhibition (BNI) via plantain root exudation, which affects the activity of ammonia-oxidizing bacteria. This preliminary study compared the abundance of the ammonia monooxygenase gene (amoA) in soils containing either plantain and white clover, or ryegrass and white clover. Plants were sown in pots and grown in a greenhouse. Two months after sowing, synthetic cattle urine was applied to half the pots, and rhizosphere and bulk soil samples were collected 30 and 90 days after urine application. The abundance of the amoA gene was measured using real time quantitative PCR. The abundance of amoA genes in rhizosphere soil around ryegrass plants and in bulk soil under ryegrass/white clover were higher in pots treated with urine than the no-urine controls. AmoA gene abundance in bulk soil under plantain/white clover was higher in pots treated with urine (P0.05) compared with the control. Furthermore, amoA gene copy numbers in the rhizosphere soil around plantain plants were lower than for ryegrass plants (P0.05). The results suggest that, in the time frame of our experiment, plantain could induce a BNI effect in the rhizosphere soil but not in the bulk soil.

Understanding the spatial and seasonal dynamics of nitrogen (N)-cycle microbial communities is pivotal for the knowledge of N biogeochemistry. The present study addressed the spatial-temporal variability of nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, and nosZI) key genes, as well as of non-denitrifying nitrous oxide (N2O) reducers (nosZII), coupled with key environmental variables, in an estuarine ecosystem (Douro, NW Portugal). Samples were collected on a monthly basis over 1 yr, key physical-chemical parameters were measured, and specific functional gene abundances were assayed. The results revealed a clear seasonality for nirS, nosZII, and bacterial and archaeal amoA abundance, with an increase during the winter/spring seasons. This period was especially characterized by high levels of dissolved oxygen, low temperature, low salinity, and increased turbidity. Indeed, turbidity emerged as the key factor controlling the distribution of nirS, nosZII bacterial, and archaeal amoA abundance. In contrast, the abundance of nosZI increased during the summer, while nirK abundance was enhanced from the fall to late spring. Additionally, the availability of dissolved inorganic nitrogen nutrients had no commensurable effect on N-cycle functional genes. This study of the annual variation of N-cycle functional genes in a temperate Atlantic estuary provides a major contribution to the understanding of how environmental factors potentially influence the distribution and abundance of N-cycle microbial communities.

Made available in DSpace on 2020-12-10T19:59:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-05-20 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) UK by the BBRSC/Newton Fund Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. In this study, the soil nitrification potential and the abundance of ammonifying microorganisms, total bacteria and total archaea (16S rRNA gene), nitrogen-fixing bacteria (NFB, nifH), ammonia-oxidizing bacteria (AOB, amoA) and archaea (AOA, amoA) were assessed in soil cultivated with ruzigrass (Urochloa ruziziensis), palisade grass (Urochloa brizantha) and Guinea grass (Panicum maximum). The abundance of ammonifying microorganisms was not affected by ruzigrass. Ruzigrass increased the soil nitrification potential compared with palisade and Guinea grass. Ruzigrass increased the abundance of N-fixing microorganisms at the middle and late growth stages. The abundances of nitrifying microorganisms and N-fixers in soil were positively correlated with the soil N-NH4+ content. Thus, biological nitrogen fixation might be an important input of N in systems of rotational production of maize with forage grasses. The abundance of microorganisms related to ammonification, nitrification and nitrogen fixing and ammonia-oxidizing archea was related to the development stage of the forage grass. Sao Paulo State Univ, Sch Agr Sci, Dept Crop Sci, Av Univ 3780, BR-18610034 Botucatu, SP, Brazil Netherlands Inst Ecol NIOO KNAW, Dept Microbial Ecol, Wageningen, Netherlands Univ Sao Paulo, Ctr Nucl Energy Agr, Piracicaba, Brazil Sao Paulo State Univ, Sch Agr Sci, Dept Crop Sci, Av Univ 3780, BR-18610034 Botucatu, SP, Brazil FAPESP: 2015/50305-8 UK by the BBRSC/Newton Fund: BB/N013201/1

To distinguish between the distribution and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in the Pearl River estuary (PRE), we investigated the DNA- and cDNA-based β-proteobacterial and archaeal amoA genes on three size-fractionated particles of >3.0 μm, 0.45–3.0 μm, and 0.22–0.45 μm. Results showed that AOB were more abundant in the freshwater with high concentrations of ammonium (NH4+) and low dissolved oxygen, whereas AOA were dominant in the NH4+-depleted seawater and sensitive to temperature. Obvious shifts in ammonia-oxidizing communities were found along the salinity gradient in the PRE. AOB clearly presented a particle-associated nature, as evidenced by higher relative abundance of amoA genes attached to the large particles (>3.0 μm) and their transcripts exclusively detected on this fraction. Moreover, higher transcriptional activity (indicated by the cDNA/DNA ratio) of AOB on the large particles, suggesting AOB were actively involved in ammonia oxidation despite their lower abundance in the mid- and lower estuarine regions. In contrast, AOA exhibited higher transcriptional activity on the 0.45–3.0 μm and 0.22–0.45 μm particles, implying the free-living strategy of these microbes. Together, these findings from field observations provide useful information on the ecological strategies of ammonia-oxidizing communities in response to different environmental conditions.

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.

Less attention has been devoted to the understanding of the sequential effect of biological nitrogen fixation (BNF) on microbial ammonia (NH3) oxidation in terrestrial soils. To shed light into this ecologically important relationship, a 15N2-DNA-stable isotope probing (SIP) technique was applied to explore the incorporation of 15N fixed by BNF into the genome of NH3 oxidizers in planted and non-planted flooded rice soils, using the α-subunit of NH3 monooxygenase (amoA gene) as a functional marker. The abundance and structural composition of archaeal and bacterial amoA genes in density-resolved fractions obtained from SIP were investigated by quantitative PCR, as well as terminal-restriction fragment length polymorphism and sequence analyses. Results revealed that bacterial rather than archaeal NH3 oxidizers assimilated 15N derived from BNF in both planted and non-planted flooded rice soils. The amoA genes in 15N-enriched “heavy” SIP gradient fractions were closely related to K-strategic Nitrosospira cluster 10, including Nitrosospira sp. AF-like bacteria, suggesting an ecological linkage of these two metabolically distinct processes. It remains unsolved from our study why exactly Nitrosospira cluster 10 was capitalizing on BNF. It could be suggested that K-strategy is the underlying ecological mechanism of sustainable, self-regulating terrestrial ecosystems such as traditional, unfertilized flooded rice soils. In this regard, it needs to be assayed if some rice-associated diazotrophs might also be classified as K-strategists, since BNF is an energy demanding metabolic process.

Aims To investigate the distribution of complete ammonia oxidizers (comammox) and canonical ammonia-oxidizing bacteria (AOB) in tidal flat sediments of the Yangtze River estuary at different depths over four seasons. Methods and results A two-step PCR with highly degenerate primers (THDP-PCR), coupled with Illumina Miseq-based sequencing, was used to analyse the distribution of comammox and AOB in tidal flat sediments. The proportion of comammox compared with that of AOB was relatively high in spring. The intermediate sediments (1-5 cm) had higher proportions of comammox than those on the surface (0-1 cm) and lower sediments (5-10 cm). Diversity indices confirmed a higher diversity of comammox in the lower sediments (5-10 cm). The proportion of comammox clade A.1 was much higher than that of comammox clade A.2 in all seasons. Redundancy analysis demonstrated that comammox clade A.1 was negatively correlated with total carbon and ammonium concentrations, whereas the opposite was observed in AOB. Conclusions Results revealed the specific distribution of comammox and AOB in tidal flat sediments of the Yangtze River estuary. Significance and impact of the study This study will contribute to the understanding of nitrification by comammox and AOB in tidal flat sediments.

Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.

Purpose Nitrogen (N) fertilizer application in agricultural soil is a primary anthropogenic nitrous oxide (N2O) source. Currently, the effect of the N fertilizer type on N2O emissions from upland soil has been rarely reported. To this end, impacts of various types of N fertilizer on N2O emissions in purple caitai (Brassica campestris L. ssp. chinensis var. purpurea) fields are investigated in this work. The field experiment was carried out with four treatments, including inorganic N fertilization (I), organic N fertilization (O), integrated organic-inorganic N fertilization (I+O) and no fertilization (CK). The nitrifier/denitrifier abundance was determined using absolute real-time quantitative PCR. Compared with I and O, I+O significantly increased dissolved organic C content, microbial biomass C and microbial biomass N by 24–63%, 12–38% and 13–36% on average, respectively. Moreover, the seasonal cumulative N2O-N emissions and fertilizer-induced N2O emission factor under I+O were significantly lower than those under I and O by 17–29% and 23–39%, respectively. The results indicate that N fertilizer type significantly affects the N2O emissions, and the integrated organic-inorganic N fertilization can mitigate the N2O emissions primarily by inhibiting the nitrification mediated by ammonia-oxidizing bacteria in purple caitai fields. Integrated organic-inorganic N fertilization is an ideal N fertilization regime to enhance soil fertility and yield and reduce N2O emissions in the upland fields.

Purpose: Both ammonia oxidizing archaea (AOA) and bacteria (AOB) perform the ammonia oxidation together. These two kinds of microbes present a convenient model for studying niche specialization. To date, few surveys concentrated on the influence of oxygen concentration on niche specialization of AOA and AOB in intertidal zones. Methods: Here, high-throughput sequencing by Illumina MiSeq and qPCR were applied to detect the change of abundance, diversity as well as community structure of both AOA and AOB with 0-60 cm sediments depth in the intertidal zone in Qingdao.Results and Conclusion: The AOA/AOB amoA gene copy numbers and AOA/AOB OTU numbers were all increased as sediment depth went deeper, which indicated that AOA were more adaptive to oxygen-limited niches compared to AOB and oxygen indeed led to the niche specialization of AOA and AOB in intertidal sediments. The dominant AOA and AOB were the Nitrosopumilus and Nitrosospira clusters, respectively, which indicated an ecological success in intertidal zone. Oxidation-reduction potential (ORP) was significantly positively correlated with AOB abundance and AOB OTU numbers (P < 0.01). In addition, both TN (P < 0.01) and pH (P < 0.05) were significantly and negatively correlated with AOB abundance. TN was also significantly and negatively correlated with AOB OTU numbers (P < 0.05).

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.

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 theamoAgenes abundance of ammonia-oxidizing archaeal (AOA) and bacterial (AOB). Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed thatThaumarchaeote(448-bp T-RF) was dominated the AOA communities, whereasNitrosospirasp (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.

Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to 2,6-dihydro-2,2,4-trimethyl-6-quinone imine (QI), and 2,4-dimethyl-6-ethoxy-quinoline (EQNL). We compared the inhibitory potential of EQ and its derivatives with that of dicyandiamide (DCD), nitrapyrin (NP), and 3,4-dimethylpyrazole-phosphate (DMPP), NIs that have been used in agricultural settings. The effect of each compound on the growth of AOB (Nitrosomonas europaea, Nitrosospira multiformis), ammonia-oxidizing archaea (AOA; “Candidatus Nitrosocosmicus franklandus,” “Candidatus Nitrosotalea sinensis”), and a nitrite-oxidizing bacterium (NOB; Nitrobacter sp. NHB1), all being soil isolates, were determined in liquid culture over a range of concentrations by measuring nitrite production or consumption and qPCR of amoA and nxrB genes, respectively. The degradation of NIs in the liquid cultures was also determined. In all cultures, EQ was transformed to the short-lived QI (major derivative) and the persistent EQNL (minor derivative). They all showed significantly higher inhibition activity of AOA compared to AOB and NOB isolates. QI was the most potent AOA inhibitor (EC50 = 0.3–0.7 μM) compared to EQ (EC50 = 1–1.4 μM) and EQNL (EC50 = 26.6–129.5 μM). The formation and concentration of QI in EQ-amended cultures correlated with the inhibition patterns for all isolates suggesting that it was primarily responsible for inhibition after application of EQ. DCD and DMPP showed greater inhibition of AOB compared to AOA or NOB, with DMPP being more potent (EC50 = 221.9–248.7 μM vs EC50 = 0.6–2.1 μM). NP was the only NI to which both AOA and AOB were equally sensitive with EC50s of 0.8–2.1 and 1.0–6.7 μM, respectively. Overall, EQ, QI, and NP were the most potent NIs against AOA, NP, and DMPP were the most effective against AOB, while NP, EQ and its derivatives showed the highest activity against the NOB isolate. Our findings benchmark the activity range of known and novel NIs with practical implications for their use in agriculture and the development of NIs with broad or complementary activity against all AO.

Potato is considered a nitrogen (N) intensive plant with a low N use efficiency (NUE). The current study introduced an excellent approach by combining dicyandiamide (DCD), moringa seed oil (MSO), or zeolite (ZE), with N fertilizer for maximizing potato tuber yields and NUE as well as minimizing tubers nitrate (NO3−) accumulation. The impact of these materials on soil N availability and gaseous emissions (NH3, and N2O) was investigated under incubation conditions. A 2-year field experiment were carried out with seven treatments [without N (control), N fertilizer (350 kg N-urea ha−1 as a recommended dose; UreaRD), 75% of N recommended dose with DCD (Urea75%RD+DCD), Urea75%RD with 2% MSO (Urea75%RD+MSO2%), Urea75%RD with 4% MSO (Urea75%RD+MSO4%), Urea75%RD with 0.5 Mg ZE ha−1 (Urea75%RD+ZER1), and Urea75%RD with 1.0 Mg ZE ha−1 (Urea 75%RD+ZER2)]. We also conducted a 40-days incubation trial with the same treatments; however, urea was added at the rate of 200 mg N kg−1 soil for all treatments, excluding the control. The addition of DCD, MSO, and ZE with urea under incubation conditions delayed the nitrification process, thereby causing a rise in NH4+-N content and a decrease in NO3−-N content. Ammonia-oxidizing bacteria (AOB) was inhibited (p ≤ 0.01) in treatments Urea+DCD, Urea+MSO4%, and Urea+ZER2. The highest NUE indexes were recorded in treatment Urea75%RD+DCD. The highest NO3- accumulation (567 mg NO3− kg−1) in potato tubers was recorded in treatment UreaRD. Whilest, the lowest NO3- content (81 mg NO3− kg−1) was in treatment Urea75%RD+DCD. The lowest cumulative N2O emissions and highest cumulative NH3 volatilization were observed in the treatment Urea+DCD under incubation conditions. Our findings demonstrated that N fertilizer rate could be reduced by 25%, while the tuber yields increased with an acceptable limit of NO3− content, resulting in economical, agronomical, and environmental benefits.

This research explored the effects of eukaryotic predation on nitrifying membrane-aerated biofilm reactor (MABR) biofilms. Past research on heterotrophic MABR biofilms showed that predation could create internal voids that promoted sloughing. However, the no past research addressed the effects of predation on nitrifying MABRs, even though nitrification is the most common MABR application. Nitrifying biofilms are typically denser, and ammonia oxidizing bacteria (AOB) form large, dense clusters within the biofilm. This could affect their susceptibility to predation. Nitrifying biofilms were grown in flat-sheet MABRs. Images of the biofilm were captured using optical coherence tomography (OCT). For detachment tests, an increased shear flow (Re≅140) was used, and a shear rheometer was used to measure the biofilm mechanical properties. The nitrifying community was analyzed with fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR). Predation increased internal void ratios from 54 ± 5 % to 69 ± 6 %. Biofilms were weakened by predation, with a storage modulus (G′) and loss modulus (G′′) of 242 ± 135 and 1,649 ± 853 Pa with predation and 3,644 ± 1,857 and 23,334 ± 11,481 Pa for the control with suppressed predation. Predation increased the relative biofilm detachment from 4 ± 5 to 18 ± 12 %, decreased the amount of biomass, i.e., the average biofilm thickness, from 502 ± 150 to 266 ± 54 µm, and decreased the nitrification flux from 1.00 to 0.61 g NH4+-N/m2day. Also, predation decreased the abundance of nitrite oxidizing bacteria (NOB) relative to AOB, consistent with the observed nitritation. These results show that predation can significantly impact the structural stability, bacterial community and removal rates of nitrifying MABR biofilms. Lumping the effects of predation into the detachment or decay coefficients of biofilm models may not accurately reflect the behavior of nitrifying MABR biofilms.

Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.

In this study, a membrane bioreactor (MBR) was used to achieve both nitrogen and carbon removal by a simultaneous partial nitrification, anammox and denitrification (SNAD) process. During the entire experiment, the intermittent aeration (non-aerobic time : aeration time, min min −1 ) cycle was controlled by a time-controlled switch, and the aeration rate was controlled by a gas flowmeter, and the optimal operating parameters as determined by response surface methodology (RSM) were a C/N value of 1.16, a DO value of 0.84 mg l −1 and an aerobic time ( T ae ) of 15.75 min. Under these conditions, the SNAD process achieved efficient and stable nitrogen and carbon removal; the total inorganic nitrogen removal efficiency and chemical oxygen demand removal efficiency were 92.31% and 95.67%, respectively. With the formation of granular sludge, the membrane fouling rate decreased significantly from 35.0 Pa h −1 at SNAD start-up to 19.9 Pa h −1 during stable operation. Fluorescence in situ hybrid analyses confirmed the structural characteristics and the relative ratio of aerobic ammonia-oxidizing bacteria, anaerobic ammonia-oxidizing bacteria and denitrifying bacteria in the SNAD system.

Background The niche differentiation between ammonia-oxidizing archaea (AOA) and bacteria (AOB) has been believed to primarily stem from their disparities in substrate affinity and tolerance threshold for ammonia, such that the latter group dominates in ammonium-rich neutral-alkaline soils. However, recent surveys indicate that direct competition between them might be of importance in driving this phenomenon. As such, diverse AOA lineages might grow in ammonium-rich alkaline arable soils if AOB growth was suppressed. To test this hypothesis, a microcosm study using three alkaline arable soils differing substantially in biogeochemical properties was established in which high ammonium concentration (200 μg N g -1 dry soil) was maintained by routinely replenishing urea, and activities of AOB were selectively inhibited by 1-octyne or 3, 4-dimethylpyrazole phosphate (DMPP). The dynamics of AOA and AOB population were monitored throughout the incubation. Results Our results suggested that amendment with either 1-octyne or DMPP retarded the growth of AOB to varying extents, but AOA proliferation accelerated in both treatments; this fitted well with the magnitude to which AOB growth was inhibited. Unexpectedly, nearly identical AOA OTUs were enriched by high-ammonium amendment across the soils tested, and they were taxonomically related to Nitrososphaera sp. JG1, N. viennensis EN76, and N. garnensis . These phylotypes have been previously demonstrated to be sensitive to high ammonia concentrations adopted here. Besides, the changed OTUs in the same lineage of AOA showed a similar response pattern to a given treatment across soils. Conclusions Our results demonstrate that some AOA phylotypes occupy a wider niche than previously believed, and it is the competitiveness for ammonia rather than disparities in substrate affinity and tolerance threshold for ammonia that drives niche differentiation between these AOA and AOB in ammonium-rich alkaline soils. These results further expand our understanding of microbial nitrogen cycling in the terrestrial environment.

The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.

The ultrasonic treatment of sludge has been considered as an effective method to facilitate the partial nitritation of municipal sewage. This study aims to reveal the effects of ultrasound on ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). The impact factors including ultrasonic irradiation time and intensity, sludge concentration, thermal effect and released free radicals were studied. The maximized difference between the changes in AOB and NOB activities were obtained with 10 g mixed liquor suspended solids (MLSS)/L, using 0.9 kJ/mL ultrasonic energy density and 12 h interval time. The increased ultrasonic intensity destroyed the floc structure of activated sludge, increased the microbial death, and decreased the cellular ATP level. Further, the mechanism exploration indicated that the mechanical shearing could be a critical factor in achieving the nitritation with inhibitory effect on nitrite oxidation.

Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.

Composting of cattle manure was conducted under four ventilation strategies, i.e., no-aeration (A-00), continuous aeration (B-44), non-aeration for 14 d and then aeration for 42 d (C-04), aeration for 14 d and then no-aeration for 42 d (D-40). Physicochemical parameters and potential ammonia oxidation (PAO) indicated that continuous and intermittent ventilation provide favourable conditions for ammonia-oxidizing bacteria (AOB) and archaea (AOA) to oxidize ammonia. Quantitative PCR (qPCR) analysis showed AOB amoA gene abundance of all treatments on every sampling day ranged from 2.25 × 105 to 2.76 × 109copies/g, was significantly lower than that of archaeal amoA gene from 2.71 × 108 to 9.05 × 1011copies/g. There was also a significantly positive relationship between PAO rates and AOB (r2 ≥ 0.066, p < 0.05) and AOA (r2 ≥ 0.300, p < 0.05) abundance. These data suggested that ammonia oxidation is driven by both AOA and AOB in cattle manure composting.

Recently, partial nitrification has been adopted widely as a first step of both nitrite shunt and deammonification processes towards efficient and economical nitrogen removal from wastewater. Effective partial nitrification relies on stimulating the first step of nitrification while inhibiting the second step and by consequence accumulating ammonia-oxidizing bacteria (AOB). Successful AOB accumulation depends upon the knowledge of their microbial characteristics and kinetics parameters as well as the main parameters that can selectively inhibits NOBs’ growth or allow AOBs to outcompete them. Several bioreactors configurations either in suspended or attached growth have been used towards achieving partial nitrification using different inhibition conditions. This review aims to illustrate an up to date version of the metabolism and factors affecting AOB growth and summarize the current bioreactors configurations in all lab-scale and full-scale applications for AOB. Moreover, successful partial nitrification attempts in the literature in suspended and attached growth systems have been complied. Additionally, the possibility of improving the current applications of AOB and the integration into the operation of existing WWTPs in order to transform into water resources recovery facility has been presented.

RESUMO A quantificação de bactérias nitrificantes é de extrema importância para o monitoramento de sistemas biológicos de tratamento que promovam a nitrificação. Neste trabalho, 15 amostras de efluentes coletadas em sistema de tratamento por lodos ativados (LA) foram analisadas de modo a quantificar bactérias nitrificantes por meio de duas técnicas: tubos múltiplos ou técnica do número mais provável (NMP); e hibridação in situ fluorescente (FISH). Os resultados sugerem que houve uma tendência de se obter valores diferentes para bactérias oxidadoras de amônia por meio da NMP em comparação com a FISH. Não obstante, a análise estatística revelou que a diferença de quantificação encontrada entre as técnicas não foi significativa, indicando que ambas podem ser usadas. Para as oxidadoras de nitrito, não foi possível realizar comparação, uma vez que os gêneros que estavam sendo determinados em cada uma das técnicas provavelmente eram diferentes. Sendo assim, as técnicas NMP e FISH se mostraram métodos relativamente simples e adequados para quantificação de microrganismos nitrificantes, com vantagens e limitações inerentes a cada uma. ABSTRACT The quantification of nitrifying bacteria is of utmost importance for monitoring biological treatment systems designed to promote nitrification. In this study, 15 activated sludge samples were analyzed in order to quantify nitrifying bacteria by two different methods: the most-probable number (MPN); and the fluorescence in situ hybridization (FISH). The results suggest that there was a tendency to obtain different values for ammonia-oxidizing bacteria by MPN compared to FISH. However, statistical analysis of these data revealed that the difference found between the two techniques was not significant, indicating that both can be used for quantification of ammonia-oxidizing bacteria. For nitrite-oxidizing bacteria it was not possible to make this comparison, since the bacterial genera that were being determined in each technique were likely different. Thus, MPN and FISH techniques proved to be relatively simple and suitable for quantification of nitrifying microorganisms in sludge samples, each of them with advantages and limitations.

Detailed ecological information on ammonia-oxidizing bacteria (AOB) in activated sludge of wastewater treatment plants (WWTPs) is very important to improve the efficiency of wastewater treatment. In this study, activated sludge samples were collected from seven municipal WWTPs located in seven cities in China, and real-time quantitative polymerase chain reaction (qPCR), as well as construction of clone libraries combined with correlation-based data analysis was performed. Further, the effect of geographic distribution and some water quality parameters on the ecological distribution of AOB in activated sludge from WWTPs were investigated. The geographic distribution, the influent concentration of total nitrogen (TN) and ammonia nitrogen (NH4+-N) had significant effects on the abundance of AOB (P < 0.05). However, the community structure of AOB were not significantly affected by geographic distribution, but by water quality parameters including the concentrations of TN and NH4+-N. N. oligotropha lineage was the dominant AOB group in the wastewater treatment systems. The results obtained in this study provide useful information to understand some aspects of the ecological information and influencing factors of AOB in geographically distributed WWTPs.

Solarization makes a great impact on the abundance of ammonia oxidizers and nitrifying activity in soil. To elucidate fluctuations in the abundance of ammonia oxidizers and nitrification in solarized soil, copy numbers of amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA), viable number of ammonia oxidizers and inorganic nitrogen contents were investigated in greenhouse experiments. The copy number of amoA gene and the viable number of ammonia oxidizers were determined by the quantitative polymerase chain reaction and most probable number methods, respectively. Abundance of AOB based on the estimation of amoA gene copy numbers and viable counts of ammonia oxidizers was decreased by the solarization treatment and increased during the tomato (Solanum lycopersicum L.) cultivation period following the solarization. Effect of solarization on the copy number of amoA gene of AOA was less evident than that on AOB. The proportion of nitrate in inorganic nitrogen contents was declined by the solarization and increased during the tomato cultivation period following the solarization. Positive correlations were found between the proportion of nitrate in inorganic nitrogen content and the copy number of bacterial or archaeal amoA gene or the viable number of ammonia oxidizers; the copy number of bacterial amoA gene showed a strong correlation with the viable number of ammonia oxidizers. The present study revealed influences of solarization on the fluctuation in the abundance of ammonia oxidizers and dynamics of inorganic nitrogen contents in soil and the results indicate that the determination of amoA gene of AOB is possibly a quick and useful diagnostic technique for evaluating suppression and restoration of nitrification following solarization., ファイル公開日: 2018/08/18

This study aims at investigating the relationship between the nitric oxide (NO) and nitrous oxide (N2O) production rates with the ammonia oxidation rate (AORsp) in an enriched AOB culture. Different concentrations of ammonia were applied in a sequential batch reactor (SBR) performing partial nitritation in order to determine the effect of AORsp on N2O and NO production rates. Results showed that NO linearly correlates with the AORsp whereas N2O presents an exponential relationship. The effect of changes on the dissolved oxygen (DO) concentration on the overall NO and N2O emissions was assessed by increasing and decreasing the DO maintaining a constant pH at 7. When DO decreased the AORsp was maintained at the level achieved with the starting DO and led to lower NO and N2O emissions than when DO was increased. Finally, the effect of pH on N2O and NO was also tested by maintaining the DO at 1.5–2 mg O2/L while pH was gradually decreased from 8 to 6.5. Results show that NO was chemically produced due to the addition of HCl when decreasing the pH whereas N2O was only produced biologically and was not affected by the addition of HCl This study was funded by the Spanish Government (MINECO) (CTM 2011-27163 and CTM 2015-66892-R) and the European Commission (FP7-PEOPLE-2011-CIG 303946). ). M. Pijuan and A. Ribera-Guardia acknowledge the Ramon y Cajal research fellowship (RYC-2009-04959) and the FPI PhD grant (BES-2012-052753) respectively provided by the Spanish Government

The proper use of selective ammonia-oxidizing archaea (AOA) and/or ammonia-oxidizing bacteria (AOB) inhibitors is critical to distinguish AOA and AOB contribution. In this research, three inhibitors including ampicillin, dicyandiamide (DCD), and allylthiourea (ATU) were examined mainly focusing on inhibiting dosage, adaptability, and effects. The results showed that the optimized inhibitory dosage of ampicillin, DCD, and ATU was separately 1.5 g L-1, 1 mM, and 25 μM. Among the three inhibitors, ATU exhibited the strongest and persistent inhibition effects and resulted in up to 90% inhibition in the AOB-enriched culture. The seemingly weakening inhibiting effects of ATU in the simulated river systems can be attributed to the involved role of AOA, the uneven spatial distribution of ATU, and protection by sediment structure in complex malodorous rivers. The high-throughput pyrosequencing analysis showed the AOB-related genus Nitrosomonas and Nitrosococcus were mostly affected by ATU in the enrichments and the river systems, respectively. The inhibition of ATU was realized mainly by reducing the abundance and activity of AOB. The decrease of the ratio of AOB/AOA amoA gene copy numbers after addition of ATU further confirmed the inhibiting effectiveness of ATU in complex microbial community of malodorous rivers.

To quantify the spatial distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and to determine nitrification activity in soil aggregates along a landscape, soil samples were collected from three landscape positions (shoulder, backslope, and toeslope) at two pasture sites with contrasting climatic conditions. The abundance of AOB and AOA was estimated by quantifying their respective bacterial and archaeal amoA gene copies using real-time polymerase chain reaction. Soil organic C (SOC), total N (TN), and the potential nitrification rate (PNR) were measured in aggregate size ranges (4–1, 1–0.25, and 0.25–0.05 mm). At site 1, a decreasing trend in PNR was observed as the size of aggregates decreased. Both bacterial and archaeal amoA genes were higher in the macroaggregates (4–1 and 1–0.25 mm) than in the microaggregates (0.25–0.05 mm) along the landscape. At site 2, PNR was higher in the smallest size of aggregates. In the 0.25–0.05-mm fraction, the abundance of bacterial and archaeal amo...

© 2016 Elsevier Ltd In the present study, a novel seasonal plant collocation system (SPCS), specifically the Potamogeton crispus and Phragmites australis series system, was investigated to enhance the performance of surface flow constructed wetlands (SFCWs) at low temperature. Results of a year-round experiment showed that SPCS conquered the adverse effect of low temperature and achieved sustainable nutrients removal. In addition, during winter, removal efficiencies of NH4-N, TP, COD, and TN in SPCS were 18.1%, 17.6%, 10.1% and 5.2% higher than that in the control, respectively. P. crispus and P. australis complemented each other in terms of plant growth and plant uptake during the experiment period. Furthermore, it emerged that P. crispus could increase the quantity of ammonia oxidizing bacteria by 10.2%, due to its high oxygen enrichment ability. It is suggested that seasonal plant collocation has a promising future in SFCWs of areas being affected by climate change, e.g. northern China.

We investigated the effects of free ammonia (FA) and free nitrous acid (FNA) concentrations on the predominant ammonia-oxidizing bacteria (AOB) and the emission of nitrous oxide (N2O) in a lab-scale sequencing batch reactor for partial nitrification. The reactor was operated with stepwise increases in the NH4 + loading rate, which resulted in a maximum FA concentration of 29.3 mg-N/L at pH 8.3. Afterwards, FNA was increased by a gradual decrease of pH, reaching its maximum concentration of 4.1 mg-N/L at pH 6.3. Fluorescence in situ hybridization indicated that AOB remained predominant during the operation, achieving specific nitrification rates of 1.04 and 0.99 g-N/g-VSS/day at the highest accumulations of FA and FNA, respectively. These rates were in conjunction with partial nitrification efficiencies of >84%. The N2O emission factor of oxidized NH4 + was 0.90% at pH 7.0, which was higher than those at pH 8.3 (0.11%) and 6.3 (0.12%), the pHs with the maximum FA and FNA concentrations, respectively. High-throughput sequencing of 16S ribosomal RNA genes showed that increases in FNA drastically changed the predominant AOB species, although increased FA produced no significant changes. This study demonstrates that the FNA concentration and pH are the main drivers that determine the predominant AOB species and N2O-emission in a partial nitrifying bioreactor.

To elucidate the importance and mechanisms of particle-attached microorganisms on ammonia oxidation, we conducted a controlled simulation experiment with samples collected from the Shunao River, an ammonia-rich hypereutrophic urban river in eastern China. The effects of particle concentration, ammonia concentration, organic carbon source and concentration, dissolved oxygen concentration and pH were investigated on ammonia transformation rate (ammonia removal rate and NO2 - +NO3 - accumulation rate) and abundance of particle-attached ammonia-oxidizing bacteria (AOB) and archaea (AOA). All these factors significantly influenced ammonia transformation rates. Our results provided direct evidence that microorganisms attached on riverine suspended particles were associated with ammonia oxidation. Sequencing revealed that the AOA genus Nitrososphaera, and the AOB genus Nitrosomonas were the most dominant in particle-attached ammonia-oxidizing microbial communities. Further analysis showed that AOB communities had higher species richness and diversity compared to AOA communities. Additionally, AOB amoA genes were ~10-100 times more abundant than AOA amoA genes, and AOB abundance was more strongly correlated with ammonia transformation rates than AOA abundance in most experiments, indicating that particle-attached AOB were more important than AOA in the hypereutrophic urban river. This study adds to our knowledge of particle-attached microorganism oxidation of ammonia. This article is protected by copyright. All rights reserved.

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale. This research is supported by the Australian Research Council projects (DP170104634 and DP190103714), by the European Research Council (BIOCOM project, ERC Grant agreement n°242658) and by the Spanish Ministerio de Economía y Competitividad (BIOMOD project, ref. CGL2013-44661-R). M.D-B. acknowledges support from the Marie Sklodowska-Curie Actions of the Horizon 2020 Framework Programme H2020-MSCA-IF-2016 under REA grant agreement n°702057. FTM acknowledges support from the European Research Council (BIODESERT project, ERC Grant agreement n°647038).

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.

The study investigates low temperature attached growth rates and nitrifying biofilm, biomass, and microbiome responses down to 1 °C. Two moving bed biofilm reactors (MBBR) were acclimatized from 10 °C to 1 °C by incremental decreases in temperatures. A non-linear decline in nitrification with decreasing temperatures was recorded with a kinetic threshold temperature delineated between 4 °C and 2 °C, at which a significant decline in efficiency of 22.47% occurred. An increase in biofilm thickness of 25.47% occurs between 10 °C and 4 °C, followed by lesser increases of 6.55% and 9.60% at 2 °C and 1 °C. Biofilm density decreases between 10 °C and 1 °C. An increase in embedded viable cells of 24.01% occurs between 10 °C and 4 °C, followed by lesser non-statistically relevant increases at 2 °C and 1 °C. No statistically significant change in the number of estimated species is observed; however, β-diversity analysis indicates greater microbial community shifts above the kinetic threshold followed by lesser shifts between 2 °C and 1 °C. Nitrosomanadacea and Nitrosopira are the ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) families in the biofilm with relative abundances of 3.43 ± 0.51% and 0.94 ± 0.44% respectively at 10 °C. A change in NOB relative abundance occurred between the temperatures of 10 °C and 1 °C, decreasing to 0.19 ± 0.10% above the kinetic threshold. The estimation of nitrifiers per carrier in the bioreactors, based on biofilm thickness, biomass viability and relative abundances shows an increase of 30.2% in AOB/carrier above the kinetic threshold temperature (> 4 °C) followed by lesser increases down to 1 °C.