AOA) And Bacteria Research Articles

Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils

Unravelling the ecological niche differentiation between comammox Nitrospira, ammonia-oxidizing archaea (AOA) and bacteria (AOB) is essential to understand forest nitrogen dynamics. Although genomic and physiological studies have suggested that comammox Nitrospira may outcompete AOA and AOB under oligotrophic conditions, empirical evidence is lacking in terrestrial ecosystems. Here we investigated the environmental prevalence and functional importance of comammox Nitrospira and their niche differentiation with AOA and AOB in forest soils from eastern Australia. Clade A comammox Nitrospira was widely detected in these forest soils, and their abundance was positively correlated with ammonium, total nitrogen and pH. The ammonium concentration was the most important driver of clade A comammox Nitrospira abundance, based on random forest regression analysis. Clade B comammox Nitrospira was not detected in these forest soils and thus excluded from the downstream analyses. Urea application stimulated the growth of clade A comammox Nitrospira and AOB, but not AOA, during a microcosm incubation. DNA-stable isotope probing revealed that clade A comammox Nitrospira incorporated 13C–CO2 in the incubations, suggesting that clade A comammox Nitrospira may contribute to autotrophic carbon fixation in these forest soils. Taken together, our findings indicate that clade A comammox Nitrospira is prevalent and probably contributing to nitrification in forest soils of eastern Australia.

Levels of heavy metal concentrations and their effect on net nitrification rates and nitrifying archaea/bacteria in paddy soils of Bangladesh

Heavy metal concentrations (HMCs) may alter nitrification activity in soil. However, the levels of HMCs in paddy soil and the relations among HMCs, net nitrification rates, and nitrifying archaea/bacteria in paddy soils of Bangladesh remain unknown. The goal of this study was to determine the effect of HMCs on net nitrification rates and ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in paddy soils. HMCs and net nitrification rates were assayed through an atomic absorption spectrophotometer (AAS) and mass spectrophotometer (MS), respectively, and the abundance of AOA, AOB, and NOB was quantified by q-PCR. According to the contamination factor (Cf), concentrations of Cd were found to be a very severe pollutant in all soils. On the other hand, concentrations of Fe and Cu were found to be moderately contaminated and slightly polluted in paddy soils as compared to control soils. The net nitrification rates (8.67 to 12.75 mg kg−1 h−1) and the abundance of AOA, AOB, and NOB were significantly higher (p < 0.05) in the paddy soils than in the control soils. AOB, AOA, and NOB were correlated positively with net nitrification rates. The relations between net nitrification rates and HMCs (Fe, Pb, and Zn) were correlated significantly and positively (p < 0.05), but the concentration of Cu was correlated negatively with net nitrification rates. To the best of our knowledge, this is the first report that has investigated the effects of HMCs on nitrifying bacteria in paddy soils, which will change the scenario of nitrification in Bangladesh greatly.

Influences of hexafluoropropylene oxide (HFPO) homologues on soil microbial communities

Hexafluoropropylene oxide (HFPO) homologues, as emerging perfluoroalkyl substances (PFASs) to replace legacy PFASs, have wide applications in the organofluorine industry and have been detected in the global environment. However, it is still unclear what effect HFPO homologues will exert on microbial abundance, community structure and function. The objective of this study was to assess potential impacts of HFPO homologue acids on archaea, bacteria, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the soil environment. Grassland soil microcosms were supplemented with low (0.1 mg/kg) or high (10 mg/kg) dosages of dimer, trimer and tetramer acids of HFPO (HFPO-DA, HFPO-TA, and HFPO-TeA), respectively. The amendment of HFPO homologues acids initially decreased the abundance of archaea and bacteria but increased them in the later period. The addition of HFPO homologues acids raised AOA abundance but restrained AOB growth during the whole incubation. AOA and AOB community structures showed considerable variations. Potential nitrifying rate (PNR) showed an increase in the initial period followed by a decline in the later period. HFPO-DA had a lasting and suppressive effect on AOB and PNR even at a nearly environmental level. Overall, HFPO homologues with different carbon chain lengths had different impacts on soil microbial community and ammonia oxidation.

Do soil property variations affect dicyandiamide efficiency in inhibiting nitrification and minimizing carbon dioxide emissions?

Nitrification inhibitors (NIs) are used to retard the nitrification process and reduce nitrogen (N) losses. However, the effects of soil properties on NI efficacy are less clear. Moreover, the direct and indirect effects of soil property variations on NI efficiency in minimizing carbon dioxide (CO2) emissions have not been previously studied. An incubation experiment was conducted for 40 days with two treatments, N (200 mg N-urea kg−1) and N + dicyandiamide (DCD) (20 mg DCD kg−1), and a control group (without the N) to investigate the response of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to DCD application and the consequences for CO2, nitrous oxide (N2O) and ammonia (NH3) emissions from six soils from the Loess Plateau with different properties. The nitrification process completed within 6–18 days for the N treatment and within 30->40 days for the N + DCD treatment. AOB increased significantly with N fertilizer application, while this effect was inhibited in soils when DCD was applied. AOA was not sensitive to N fertilizer and DCD application. The nitrification rate was positively correlated with the clay (p < 0.05) and SOM contents (p < 0.01); DCD was more effective in loam soil with low SOM and high soil pH. Soil pH significantly was decreased with N fertilizer application, while it increased when DCD was applied. Moreover, DCD application decreased CO2 emissions from soils by 22%–172%; CO2 emissions were negatively correlated with the clay and SOM contents. DCD application decreased N2O emissions in each soil by 1.0- to 94-fold compared with those after N fertilizer application. In contrast, DCD application increased NH3 release from soils by 59–278%. NH3 volatilization was negatively correlated with clay (p < 0.05) and SOM (p < 0.01) contents and positively correlated with soil pH (p < 0.01). Therefore, soil texture, SOM and soil pH have significant effects on the DCD performance, nitrification process and gaseous emissions.

Effective nitrogen removal from ammonium-depleted wastewater by partial nitritation and anammox immobilized in granular and thin layer gel carriers

This study investigates the effect of physicochemical conditions on the partial nitritation and anammox treatment by immobilized ammonia oxidizers under ammonium-deplete conditions. The impact of oxygen and temperature was studied by measuring the activity of immobilized aerobic and anaerobic ammonia-oxidizing organisms (Ammonia-oxidizing bacteria (AOB) and archaea (AOA), and Anammox bacteria) embedded in polyvinyl alcohol – sodium alginate (PVA-SA) beads and in thin layer poly-ethylene glycol hydrogels. Beads and flat hydrogels were incubated in a fluidized bed reactor (FBR) and in two flow cells, respectively. Both systems were fed with synthetic wastewater (15 mg N–NH4+/L) at different temperatures (20 °C and/or 30 °C) and different dissolved oxygen (DO) concentrations (0.1, 0.3, 0.5 and/or 1 mg/L) over 152 and 207 days, respectively. The FBR system had a maximum removal rate of 1.7 g-N/m3/d at 0.1 mg O2/L, corresponding to 80% removal efficiency, while a high aerobic ammonia-oxidizing activity but a partial oxygen inhibition of Anammox bacteria were observed at higher DO concentrations. In both flow cells, nitrogen removal efficiency was highest (80%) at 30 °C and 1 mg O2/L while removal was less favorable at lower DO and lower temperature. Our results indicate a potential use of hydrogel beads for an energy efficient technology with reduced aeration demand for treating low ammonia wastewater, while layered hydrogels are a possible first step for biological treatments of wastewater using tangential flow. In addition, we provide blueprint drawings of the flow cells, which may be used to 3D-print the apparatus for other applications.

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (<30cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Biological Nitrification Inhibition (BNI): Phenotyping of a Core Germplasm Collection of the Tropical Forage Grass Megathyrsus maximus Under Greenhouse Conditions.

Modern intensively managed pastures that receive large external nitrogen (N) inputs account for high N losses in form of nitrate (NO3–) leaching and emissions of the potent greenhouse gas nitrous oxide (N2O). The natural plant capacity to shape the soil N cycle through exudation of organic compounds can be exploited to favor N retention without affecting productivity. In this study, we estimated the relationship between biological nitrification inhibition (BNI), N2O emissions and plant productivity for 119 germplasm accessions of Guineagrass (Megathyrsus maximus), an important tropical forage crop for livestock production. This relation was tested in a greenhouse experiment measuring BNI as (i) rates of soil nitrification; (ii) abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA); and (iii) the capacity of root tissue extracts to inhibit nitrification in vitro. We then measured N2O emissions, aboveground biomass and forage nutrition quality parameters. Reductions on nitrification activity ranging between 30 and 70% were found across the germplasm collection of M. maximus. Accessions with low nitrification rates showed a lower abundance of AOB as well as a reduction in N2O emissions compared to accessions of high nitrification rates. The BNI capacity was not correlated to N uptake of plants, suggesting that there may be intraspecific variation in the exploitation of different N sources in this grass species. A group of accessions (cluster) with the most desirable agronomic and environmental traits among the collection was identified for further field validation. These results provide evidence of the ability of M. maximus to suppress soil nitrification and N2O emissions and their relationship with productivity and forage quality, pointing a way to develop N conservative improved forage grasses for tropical livestock production.

Biological-chemical comprehensive effects of goethite addition on nitrous oxide emissions in paddy soils

Iron (Fe) oxides play an important role in regulating nitrification and N2O emissions, but there is very little study on the biological-chemical comprehensive effects of Fe oxides on nitrification and N2O emissions. A laboratory incubation experiment was performed to evaluate the effect of goethite addition on nitrification and N2O emissions from acidic and alkaline paddy soils. The cumulative N2O emissions from alkaline paddy soil were significantly higher than those from acidic paddy soil, no matter whether goethite had been added or not. Adding goethite decreased the average net rate of soil nitrification in acidic paddy soil by 33.2% in comparison with the treatment without adding goethite; however, adding goethite scarcely decreased the average net rate in alkaline paddy soil. Adding goethite increased the maximal N2O emissions by 85.6% in alkaline paddy soil, but had no obvious effect in acidic paddy soil. Adding goethite significantly increased the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) amoA genes in both alkaline and acidic paddy soils. High-throughput pyrosequencing of 16S rRNA gene showed that adding goethite significantly increased the relative abundance of Nitrosomonadaceae in alkaline paddy soil and that the dominant species of AOB and AOA were Nitrosomonadaceae and Nitrososphaeraceae, respectively. N2O emissions in alkaline paddy soil were higher than those in acidic paddy soil. The enhancement of N2O emissions by goethite was more significant in alkaline paddy soil than in acidic paddy soil. Goethite stimulated the abundance of amoA gene (both of AOB and AOA) and participated in nitrification process via chemical reaction with intermediates.

The relative contribution of ammonia oxidizing bacteria and archaea to N2O emission from two paddy soils with different fertilizer N sources: A microcosm study

Ammonia oxidizing bacteria (AOB) and archaea (AOA) have different affinities to different fertilizer N sources; however, there are few studies on the relative contribution of AOB and AOA to N2O emissions under different N fertilizers. In this study, acetylene (0.01%v/v C2H2) and 1-octyne (0.01%v/v) were used to assess the relative contribution of AOB and AOA to N2O emission from paddy soils with different soil pH and N fertilizers application by incubation in microcosms. The results indicated that cumulative N2O emissions from the alkaline paddy soil were significantly higher than those from the acidic paddy soil, and urea-N application promoted more N2O emissions than ammonium-N application. The total relative contribution of AOA and AOB exceeded 60%, so autotrophic nitrification was the main N2O emission process in both soils at 80% water holding capacity (WHC); after N application, their total contribution increased. The relative contribution of 1-octyne-sensitive AOB (>45%) to N2O emissions was significantly higher than that of AOA (<15%) in both tested soils without N application, and its contribution decreased after ammonium-N application in both soils and urea-N application in alkaline soil. The promoting effects of urea-N on N2O yields of AOB were greater than those by ammonium-N; on the contrary, the N2O yields of AOA were more sensitive to ammonium-N application. The main species of nitrifers, Nitrosospira-AOB, Nitrosovibrio-AOB, and Nitrososphaera-AOA, were involved in N2O emissions in both soils.

Imprint of Trace Dissolved Oxygen on Prokaryoplankton Community Structure in an Oxygen Minimum Zone

The Eastern Tropical North Pacific (ETNP) is a large, persistent, and intensifying oxygen minimum zone (OMZ) that accounts for almost half of the total area of global OMZs. Within the OMZ core (~350-700 m depth), dissolved oxygen is typically near or below the analytical detection limit. Steep oxygen gradients above and below the OMZ core lead to vertical structuring of microbial communities that also vary between particle-associated (PA) and free-living (FL) size fractions. Here, we use 16S amplicon sequencing (iTags) coupled with multivariate statistics to analyze the diversity and distribution of prokaryotic populations between FL and PA size fractions and among the range of existing redox conditions. Nonmetric Dimensional Scaling (nMDS) revealed that bacterial and archaeal phylogenetic representations were significantly different between size fractions. Based on analysis of similarities (ANOSIM) and iTag profiles, composition of PA assemblages was less influenced by the prevalent depth-dependent biogeochemical regime than the FL fraction. Trace oxygen concentrations (~0.33 M) were present throughout the OMZ core at our sampling location. Consequently, nitrite accumulations typically reported for OMZ cores were absent. Furthermore, sequences for anammox bacteria (Brocadiales genus Candidatus Scalindua), commonly found at oxic-anoxic boundaries in other systems, were not recovered here. However, ammonia-oxidizing bacteria (AOB) and archaea (AOA) distributions and maximal autotrophic carbon assimilation rates (1.4 µM C d-1) coincided with a pronounced ammonium concentration maximum near the top of the OMZ core. In addition, members of the genus Nitrospina, a dominant nitrite-oxidizing bacteria (NOB) were present suggesting that both ammonia and nitrite oxidation occur at almost undetectable oxygen concentrations. We conclude that the presence of trace oxygen in the OMZ core of this region of the ETNP OMZ is sufficient to support active nitrification.

Effects of reducing chemical fertilizer combined with organic amendments on ammonia-oxidizing bacteria and archaea communities in a low-fertility red paddy field.

Ammonia oxidation process in soil has a great contribution to the emission of nitrous oxide, which is a hot issue in the study of N cycle of rice field ecosystem. Organic amendments which partially substitute chemical nitrogen fertilizer are widely adopted to optimizing N management and reduce the use of chemical nitrogen fertilizers in the paddy ecosystem, but their long-term effects on ammonia-oxidizing archaea (AOA) and bacteria (AOB) were not well understood. Thus, based on a 6-year field trial that comprised four fertilization strategies (CF, chemical fertilizer; PM, pig manure substituting for 20% chemical N; BF, biogas slurry substituting for 20% chemical N; and GM, milk vetch substituting for 20% chemical N) and no N fertilizer application as CK, the abundance and community structure of ammonia oxidizers were examined by using qPCR and Illumina Miseq sequencing approaches based on the functional marker genes (amoA) in a low-fertility paddy field. The results revealed that 6 years of organic-substitute fertilization significantly increased AOA abundance in comparison with NF and CF. However, only CF and PM had a higher AOB abundance than those in NF and no significant difference between CF and organic-substitute treatments was observed. Both AOA and AOB were significantly correlated with soil potential nitrification rate (PNR). Moreover, organic-substitute treatments showed the evident changes in the AOA community, while little were observed in the AOB community. Soil pH was the main predictor for AOA abundance, while NH4+-N and NO3--N were the main predictors for AOB abundance. This study suggests that both AOA and AOB were jointly contributed to the variation of soil potential nitrification rate, while the AOA community was shown to be more responsive to organic-substitute fertilization strategies than AOB in the tested soils.

Temperature decouples ammonia and nitrite oxidation in greenhouse vegetable soils

The influence of temperature on soil ammonia (NH3) and nitrite (NO2−) oxidation and related NO2− accumulation in soils remain unclear. The soil potential NH3 oxidation (PAO) and NO2− oxidation (PNO) rates were evaluated over a temperature gradient of 5–45 °C in six greenhouse vegetable soils using inhibitors. The values of temperature sensitivity traits such as temperature minimum (Tmin), temperature optimum (Topt), and maximum absolute temperature sensitivity (Tm_sens) were also fitted to the square root growth (SQRT) and macromolecular rate theory (MMRT) models. The ammonia-oxidizing archaea (AOA) and bacteria (AOB) were determined by quantifying amoA, and nitrite-oxidizing bacteria (NOB) were determined by quantifying the nxrA and nxrB. Both models identified that Topt for PAO (34.0 °C) was significantly greater than that for PNO (26.0 °C). The Tm_sens (23.4 ± 2.1 °C) and Tmin (1.0 ± 2.0 °C) for PAO were higher than those for PNO (16.8 ± 3.2 °C and − 11.7 ± 6.7 °C). PAO was positively correlated with AOB-amoA at 20–30 °C and with AOA-amoA at 30–35 °C, while PNO was positively correlated with nxrB at 5–30 °C. Additionally, NO2− and N2O were positively correlated with the (AOA + AOB amoA) to (nxrA + nxrB) ratio, and the concentration of N2O was positively correlated with NO2− accumulation. These results highlight that elevated temperatures resulted in the uncoupling of NH3 oxidation and NO2− oxidation, leading to NO2− accumulation, which could stimulate N2O emissions.

Soil N transformation rates are not linked to fertilizer N losses in vegetable soils with high N input

Vegetable soils under plastic shed are characterized by multiple cropping and extremely high rates of nitrogen (N) application, but the N use efficiency (NUE) is generally low and the rate of N loss is often high. The underlying mechanisms behind these N losses following long-term N fertilizer applications remain elusive. Here, a 15N tracing incubation study in conjunction with in-situ monitoring was performed to investigate the effects of different N fertilization regimes on gross N transformations, microbial abundance and N losses via NO3− leaching and N2O emissions in a vegetable soil under plastic shed subjected to 14 years of repeated N fertilization. The field experiment comprised of six treatments: no N fertilization (control, CK), and applications of chicken manure (M), chemical N plus M (CM), CM plus straw (CMS), 42 % of chemical N plus chicken manure (RCM) and RCM plus straw (RCMS). The results showed that the total gross N mineralization rates were significantly higher in CMS, RCMS and M treatments than in CK, CM and RCM treatments. The total gross NH4+ immobilization rates followed the order of CK > CM > CMS > M > RCM ≈ RCMS, indicating a decreasing NH4+ immobilization rate after N application. Gross autotrophic nitrification rate was significantly enhanced by fertilizer application in the order: CK < CM < CMS ≈ RCM < M < RCMS, mainly due to both increased mineralization rates and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB). A significant negative relationship between gross rates of NH4+ immobilization and autotrophic nitrification suggests that higher autotrophic nitrification decreased NH4+ immobilization. Reduced chemical N input alleviated soil acidification, NO3− leaching and N2O emissions. There were significant positive relationships between rates of chemical N input and N loss but no relationships between gross N transformation rates and tomato yields, NO3− leaching losses and N2O emissions. Thus, soil N transformation rates do not reflect rate of fertilizer N losses in vegetable soil managed under plastic shed. We thus suggest that chemical N application rate could be reduced to decrease N losses while sustaining vegetable production.

Interaction type of tetrabromobisphenol A and copper manipulates ammonia-oxidizing archaea and bacteria communities in co-contaminated river sediments

The combined contamination of brominated flame retardants (BFRs) and heavy metals in electronic waste (e-waste) recycling and disposal areas has been a serious concern owing to their environmental persistence and chronic toxicities. Ammonia oxidizers, e.g., ammonia-oxidizing archaea (AOA) and bacteria (AOB) play essential roles in nitrogen cycling and can serve as ideal indicators that reflect the changes in sediment health in response to environmental variables. There is currently very little information available on the combined toxic effects of BFRs and heavy metals on AOA and AOB communities. In this study, two typical e-waste pollutants, tetrabromobisphenol A (TBBPA) and copper (Cu), were selected as target contaminants to investigate the individual and combined effects of both pollutants on AOA and AOB communities in river sediments. Respective treatments of TBBPA (1, 10, and 20 mg/kg wet weight), Cu (100 mg/kg wet weight) and their combined treatments (weight ratios of 1:100, 1:10, and 1:5) were performed in laboratory experiments. High-throughput sequencing was applied to explore the response of ammonia oxidizers to TBBPA and Cu. The interaction types of TBBPA and Cu were calculated by the directional classification system to reveal the individual and combined toxicities of both contaminants to the ammonia oxidizers. On days 15 and 30, the dominant interaction type of TBBPA and Cu was synergistic (62.50%), and the combined contamination exacted selective pressure and inhibition on the AOB and AOA communities. On days 45 and 90, the interaction type shifted to be antagonistic (83.33%), with both the AOB and AOA communities gradually reaching stable population equilibria. The alteration of the interaction type is attributed to the elevated TBBPA/Cu tolerance as the incubation time increased. This study disclosed the interaction types of TBBPA and Cu in contaminated river sediments, and revealed that the combined effect could potentially manipulate AOB and AOA communities.

Crop residue carbon-to-nitrogen ratio regulates denitrifier N2O production post flooding

The response of nitrifier and denitrifier populations and associated N2O emissions to different carbon-to-nitrogen (C/N = 17 or 45) straw amendments was monitored under flooding-drying and non-flooding conditions. A 10-week laboratory mesocosm study was conducted in two soils, (i) a paddy soil with a long history of managed flooding-drying (CN), and (ii) a wheat cropping soil with no previous history of flooding (UK). We measured N2O fluxes and the abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite reductase (nirK and nirS) genes, and nitrous oxide reductase (nosZI and nosZII) genes during flooding (4 weeks) and post-flooding (6 weeks). Straw addition enhanced N2O emissions, with higher fluxes apparent after incorporation of narrow C/N residues. Moreover, the impact of crop amendment on N2O emission was exacerbated when soil was under flooding-drying conditions. The abundances of nirS and nosZI genes in CN soil and AOA gene in UK soil were increased by straw amendment, with highest in narrow C/N straw amendments. Structural equation modeling showed that the impact of denitrifier gene abundance on the N2O flux was stronger than that of nitrifier gene abundance in the two soils, and significant correlations were observed between N2O fluxes and the consumption of DOC and NO3−, indicating that denitrification was the dominant N2O production pathway during the drying phase. The ratio of (nirS + nirK)/(nosZI + nosZII) in the narrow C/N amendment was greater than in the wide C/N treatment after flooding, suggesting that the straw C/N ratio had an effect on the capacity for N2O production via denitrification. We conclude that crop amendments with an appropriate C/N ratio could minimize N2O fluxes through regulating the denitrification process when soils are subjected to regular flooding and drying and also experiencing greater frequencies of flooding.

The rhizosphere and cropping system, but not arbuscular mycorrhizae, affect ammonia oxidizing archaea and bacteria abundances in two agricultural soils

Arbuscular mycorrhizal fungi (AMF) form symbioses with roots that can enhance plant nutrition. While AMF have been shown to have a role in soil nitrogen (N) cycling, it is unclear whether AMF affect N cycling microbes such as ammonia-oxidizing bacteria (AOB) and archaea (AOA), which convert ammonium into nitrite in the first step of nitrification. In this study, we examined the effects of AMF on AOA and AOB abundances within the corn rhizosphere and bulk soil of conventional (corn-soybean rotation with inorganic fertilizer) and diversified (corn-soybean-oats/alfalfa-oats rotation with composted manure) systems. We hypothesized that AMF would decrease AOA and AOB abundances in a cropping-system dependent manner, possibly due to competition for ammonium. We grew corn deficient or proficient in AMF symbiosis in microcosms for 10 weeks. At the end of the experiment, both soils planted with the AMF-proficient corn genotype had higher ammonium and lower nitrate pool sizes compared to the same soils planted with the AMF-deficient corn genotype. Likewise, total plant N was higher in the AMF-proficient genotype compared to the AMF-deficient genotype. Despite changes in soil inorganic N pool sizes, AOA and AOB abundances were unaffected by plant AMF-proficiency. Instead, AOA abundance was greater in the rhizosphere than in the bulk soil regardless of cropping system, and AOB abundance was greater in the conventional than the diversified cropping system soil regardless of proximity to the root. These data indicate that 1) AMF did not affect AOA or AOB abundance in these N-rich soils but other factors such as root proximity and inorganic fertilization did and 2) AOA and AOB have differing ecological niches within rhizosphere and bulk soil that should be considered when managing for nitrogen losses.

Biogeographic distribution of comammox bacteria in diverse terrestrial habitats

Comammox, the microbial group capable of completely oxidizing ammonia to nitrate, challenged the traditional two-step nitrification process where ammonia is oxidized by ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite by nitrite-oxidizing bacteria (NOB). However, the distribution of comammox bacteria in various habitats and their potential environmental drivers remain poorly understood. Using qPCR and high-throughput sequencing approach, we analyzed the abundance and community patterns of comammox from 38 samples taken from five different habitat types including paddy fields in Shaoguan and Antu, the wheat fields, river, and grassland in the Qinghai-Tibet Plateau, and the fringe and central riparian zones of Chaohu Lake of China during winter and summer. Comammox bacteria were detected in all samples, with Ca. N. nitrificans dominating the community, followed by Ca. N. nitrosa. Generally, in paddy fields of Shaoguan and Antu, ammonia (NH4+) was the key factor affecting comammox bacteria. However, in wheat fields, river and grassland of the Qinghai-Tibet Plateau, altitude was the strongest factor affecting comammox bacteria. In Chaohu Lake, comammox bacteria showed temporal heterogeneity, being higher in winter than summer, especially in the fringe riparian zone. Our results suggest that comammox is widespread in diverse habitats and exhibit niche partitioning, and can be affected by different environmental factors that may vary by habitat.

Ammonia oxidizers in river sediments of the Qinghai-Tibet Plateau and their adaptations to high-elevation conditions

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as complete ammonia oxidizers (comammox) aerobically catalyze ammonia oxidation which plays essential roles in riverine nitrogen cycle. However, performances of these ammonia oxidizers in high-elevation river sediments have rarely been documented. This study investigated the abundance, community, and activity of ammonia oxidizers in five high-elevation rivers of the Qinghai-Tibet Plateau (QTP). Comammox were dominant ammonia oxidizers in 23% of studied samples and the clade B was principal comammox type. amoA gene abundances of AOA and AOB in these high-elevation rivers were comparable to those in low-elevation rivers. However, in contrast to most studied low-elevation rivers, AOB amoA gene abundance outnumbered AOA in 92% samples, which might be caused by the lower temperature and more intense solar radiation of the QTP. Potential nitrification rates (PNRs) ranged from 0.02 to 2.95 nmol-N h−1 g−1 dry sediment. Ammonia concentration was the limiting factor to PNRs at some sites, and when ammonia was not limiting, the PNR: ammonia ratio was greater at higher temperatures. There was no apparent variation in ammonia oxidizer community compositions along the elevation gradient due to the high elevation (2687 to 4223 m) of our entire study area. However, compared with low-elevation rivers, the lower temperature, huge diurnal temperature change, and lower nutrient conditions in the QTP rivers shaped distinctive communities for ammonia oxidizers; the unique community characteristics were significantly correlated to PNRs. These results suggest that ammonia oxidizers in the five high-elevation rivers have adapted to high-elevation conditions; more research should be conducted to study their adaptation mechanisms and their roles in riverine nitrogen cycle.

Mineralization and nitrification: Archaea dominate ammonia-oxidising communities in grassland soils

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were <24 h, whilst several days for nitrate. In clay soils, bacterial, archaeal, AOA, and AOB communities were clearly distinct from those in Chalk and Greensand soils. Spatially and temporally, AOA were more abundant than AOB. Notably, Nitrososphaera were predominant, comprising 37.4% of archaeal communities, with the vast majority of AOA found in Chalk and Greensand soils. AOA abundance positively correlated with nitrate concentration, whereas AOB abundance correlated with ammonium and nitrite concentrations, suggesting that these N compounds may be potential drivers for AOA/AOB niche differentiation in these grassland soils.

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

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