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Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea , Nitrosospira multiformis , Nitrosospira tenuis , Nitrosospira briensis ) and archaea (AOA, Nitrososphaera viennensis ), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis , while others showed antagonism against N. europaea , N. multiformis , and N. viennensis . Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are crucial for N sub(2)O emission as they carry out the key step of nitrification. Dicyandiamide (DCD) and acetylene (C sub(2)H sub(2)) are typical nitrification inhibitors (NIs), while the comparative effects of these NIs on N sub(2)O production and ammonia oxidizers' (AOB and AOA) growth are unclear. Four treatments including a control, urea, urea + DCD, and urea + C sub(2)H sub(2) were set up to investigate their effect of inhibiting soil nitrification, nitrification-related N sub(2)O emission as well as the growth of ammonia oxidizers with a fluvo-aquic soil using microcosms for 28 days. N sub(2)O emission and net nitrification rate increased after the application of urea, but were significantly restrained in urea + NI treatments, while C sub(2)H sub(2) was more effective in reducing N sub(2)O emission and nitrification rate than DCD. The abundance of AOB, which was significantly correlated with N sub(2)O emission and net nitrification rate, was more inhibited by C sub(2)H sub(2) than DCD. Furthermore, the application of urea in all the soils had little impact on the AOA community, while obvious shifts of AOB community structure were found compared with the control. All AOB sequences fell within Nitrosospira cluster 3, and the AOA community was clustered to group 1.1b. Collectively, it indicated that application of urea combined with NIs (DCD or C sub(2)H sub(2)) could potentially alter N sub(2)O emission, mainly through regulating the growth of AOB but not AOA in this fluvo-aquic soil.

The objective of this study was to demonstrate the feasibility of novel, Horizontal Flow Biofilm Reactor (HFBR) technology for the treatment of ammonia (NH sub(3))-contaminated airstreams. Three laboratory-scale HFBRs were used for remediation of an NH sub(3)-containing airstream at 10 degree C during a 90-d trial to test the efficacy of low-temperature treatment. Average ammonia removal efficiencies of 99.7 % were achieved at maximum loading rates of 4.8 g NH sub(3) m super(3) h super(-1). Biological nitrification of ammonia to nitrite (NO sub(2) super(-)) and nitrate (NO sub(3) super(-)) was mediated by nitrifying bacterial and archaeal biofilm populations. Ammonia-oxidising bacteria (AOB) were significantly more abundant than ammonia-oxidising archaea (AOA) vertically at each of seven sampling zones along the vertical HFBRs. Nitrosomonas and Nitrosospira, were the two most dominant bacterial genera detected in the HFBRs, while an uncultured archaeal clone dominated the AOA community. The bacterial community composition across the three HFBRs was highly conserved, although variations occurred between HFBR zones and were driven by physicochemical variables. The study demonstrates the feasibility of HFBRs for the treatment of ammonia-contaminated airstreams at low temperatures; identifies key nitrifying microorganisms driving the removal process; and provides insights for process optimisation and control. The findings are significant for industrial applications of gas oxidation technology in temperate climates.

Purpose This study aimed at elucidating the biotic components of crop decline affecting kiwifruit ( Actinidia deliciosa ) orchards. Methods The study was carried out on soil samples originating from an over twenty-year-old orchard showing typical yield decline (Old), one in full production phase (Adult), one fallow after a kiwifruit cultivation (Fallow), an abandoned one (Virgin). Soil health of those soil samples was assessed with an in-pot growth assay using kiwifruit plantlets in which root endophytic fungi and rhizosphere bacteria communities were assessed using qPCR and NGS analysis. Results Plant growth in the Old field was significantly lower than the others, in line with the crop decline of that field. The Old treatment differed from the others in the following soil features: i. a great reduction of total bacteria, Pseudomonas , actinomycetes and Bacillus compared to the Adult orchard; ii. a significant increase of Nitrosospira and other nitrifying bacteria which persisted in kiwifruit rhizosphere even under the optimal conditions; iii. a reduction of potentially beneficial genera among which Massilia , Rubrobacter and Kaistobacter . Old, Adult and Fallow were similar in root fungal community composition, with Dactylonectria as dominant genus (about 50%); whilst in the Virgin prevailed saprophytic non-pathogenic fungi. Conclusions Bacterial communities in over-30-year-old kiwifruit orchards were greatly reduced and modified, thus suggesting being a cause of the reduced ability of soil to support plant growth. In addition, kiwifruit manifested a legacy effect on soil-borne fungal communities, including root endophytes.

Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76 T exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196 T . In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis , but not of N. multiformis , was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N 2 O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N 2 O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N 2 O emissions.

Nitrous oxide (N sub(2)O) emissions from grazed pastures are a product of microbial transformations of nitrogen and the prevailing view is that these only occur in the soil. Here we show this is not the case. We have found ammonia-oxidising bacteria (AOB) are present on plant leaves where they produce N sub(2)O just as in soil. AOB (Nitrosospira sp. predominantly) on the pasture grass Lolium perenne converted 0.02-0.42% (mean 0.12%) of the oxidised ammonia to N sub(2)O. As we have found AOB to be ubiquitous on grasses sampled from urine patches, we propose a 'plant' source of N sub(2)O may be a feature of grazed grassland.

Nitrification is a major process within the nitrogen (N) cycle leading to global losses of N, including fertiliser N, from natural and agricultural systems and producing significant nitrous oxide emissions. One strategy for the mitigation of these losses involves nitrification inhibition by plant-derived biological nitrification inhibitors (BNIs). Cultivation-based studies of BNIs, including screening for new compounds, have predominantly investigated inhibition of a single ammonia-oxidising bacterium (AOB), Nitrosomonas europaea, even though ammonia oxidation in soil is usually dominated by ammonia-oxidising archaea (AOA), especially in acidic soils, and AOB Nitrosospira sp., rather than Nitrosomonas, in fertilised soils. This study aimed to assess the sensitivity of ammonia oxidation by a range of AOA and AOB pure cultures to BNIs produced by plant roots (methyl 3-(4-hydroxyphenyl) propionate, sakuranetin and 1,9-decanediol) and shoots (linoleic acid, linolenic acid and methyl linoleate). AOA were generally more sensitive to BNIs than AOB, and sensitivity was greater to BNIs produced by shoots than those produced by roots. Sensitivity also varied within AOA and AOB cultures and between different BNIs. In general, N. europaea was not a good indicator of BNI inhibition, and findings therefore highlight the limitations of use of a single bioassay strain and suggest the use of a broader range of strains that are more representative of natural soil communities.

Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N 2 O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N 2 O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis , the first pure culture of AOA from soil, to produce N 2 O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil . N. viennensis produced N 2 O at a maximum yield of 0.09% N 2 O per molecule of nitrite under oxic growth conditions. N 2 O production rates of 4.6±0.6 amol N 2 O cell −1  h −1 and nitrification rates of 2.6±0.5 fmol NO 2 − cell −1  h −1 were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N 2 O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In 15 N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N 2 O formation to the N 2 O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N 2 O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting.

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira ) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15 N-urea incubation has not been totally clarified. The 15 N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C 2 H 2 almost completely inhibited NO 3 − -N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15 N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS ( Nitrososphaerales )-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT ( Ca. Nitrosotaleales)-Alpha), and AOB ( Nitrosospira ) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15 N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. Key points • 15 N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different. Graphical Abstract

Aims Traditional tillage represents a serious threat to the stability of soil ecosystems. Understanding the response mechanisms of soil microbial community assembly to different tillage practices is a major topic of soil ecological research. Methods Here, we investigated the bacterial community structures and assembly in bulk and rhizosphere soils of soybeans grown under traditional tillage (moldboard plow, MP) and two conservation tillage practices, namely, no-tillage (NT) and ridge tillage (RT), using high-throughput sequencing methods. Results Compared with MP, NT and RT increased the relative abundances of nitrifying bacteria of Nitrosospira sp . and the nitrogen-fixing bacteria of Mesorhizobium sp . , Bradyrhizobium sp . and Burkholderia sp . , but decreased the abundance of carbon-degrading bacteria, especially Blastococcus sp . , Streptomyces sp . and Sphingomonas sp. The altered functional bacteria were mostly affiliated with biomarkers and keystone taxa in the NT and RT networks. For the results of network properties and assembly processes, we found that NT and RT habited a more stable bacterial network structure and a lower homogenizing dispersal value. Soil pH was the primary factor regulating both the bacterial community structures and assembly processes under the three tillage practices. Conclusions The soil bacterial community structures and assembly processes were profoundly altered by tillage practices. The changes in functional bacteria indicated that conservation tillage might contribute to soil carbon sequestration, while stimulating nitrogen fixation and nitrification.