Microbial pathways for nitrogen loss in an upland soil

Vertical distribution of Candidatus Methylomirabilis and Methanoperedens in agricultural soils

Candidatus Methylomirabilis-related bacteria conduct anaerobic oxidation of methane (AOM) coupling with NO2- reduction, and Candidatus Methanoperedens-related archaea perform AOM coupling with reduction of diverse electron acceptors, including NO3-, Fe (III), Mn (IV) and SO42-. Application of nitrogen fertilization favors the growth of these methanotrophs in agricultural fields. Here, we explored the vertical variations in community structure and abundance of the two groups of methanotrophs in a nitrogen-rich vegetable field via using illumina MiSeq sequencing and quantitative PCR. The retrieved Methylomirabilis-related sequences had 91.12%-97.32% identity to the genomes of known Methylomirabilis species, and Methanoperedens-related sequences showed 85.49%-97.48% identity to the genomes of known Methanoperedens species which are capable of conducting AOM coupling with reduction of NO3- or Fe (III). The Methanoperedens-related archaeal diversity was significantly higher than Methylomirabilis-related bacteria, with totally 74 and 16 operational taxonomic units, respectively. In contrast, no significant difference in abundance between the bacteria (9.19 × 103-3.83 × 105 copies g-1 dry soil) and the archaea (1.55 × 104-3.24 × 105 copies g-1 dry soil) was observed. Furthermore, the abundance of both groups of methanotrophs exhibited a strong vertical variation, which peaked at 30-40 and 20-30 cm layers, respectively. Soil water content and pH were the key factors influencing Methylomirabilis-related bacterial diversity and abundance, respectively. For the Methanoperedens-related archaea, both soil pH and ammonium content contributed significantly to the changes of these archaeal diversity and abundance. Overall, we provide the first insights into the vertical distribution and regulation of Methylomirabilis-related bacteria and Methanoperedens-related archaea in vegetable soils. KEY POINTS: • The archaeal diversity was significantly higher than bacterial. • There was no significant difference in the abundance between bacteria and archaea. • The abundance of bacteria and archaea peaked at 30-40 and 20-30 cm, respectively.

Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil

Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4+-N, NO3--N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.

Activity and community structure of nitrifiers and denitrifiers in nitrogen-polluted rivers along a latitudinal gradient

Nitrogen (N) cycling in rivers is particularly active and dynamic due to excess nutrient inputs worldwide. However, the multidimensional spatial patterns of the activity and community structure of N-cycling microorganisms in rivers remain unclear, limiting our understanding of river ecological functions, especially N removal capacity. Here, we measured the nitrification and denitrification rates and identified nitrifying and denitrifying microorganisms using high-throughput sequencing of archaeal amoA, bacterial amoA, nirK, and nirS genes in channel sediments, riparian rhizosphere soils, and riparian bulk soils of 30 N-polluted rivers across China. Results showed that in the lateral dimension, nitrification rates in sediments did not differ significantly from those in rhizosphere and bulk soils, but denitrification rates were higher in sediments than in bulk soils. However, the archaeal amoA gene abundance in sediments was considerably lower than that in rhizosphere and bulk soils, and bacterial amoA gene abundance in sediments was greater than that in rhizosphere soils. In the vertical dimension, both nitrification and denitrification rates in riparian bulk soils decreased with soil depth, and topsoils harbored more nitrifying and denitrifying microbes than subsoils. Denitrification but not nitrification rates increased with latitude and altitude but decreased with increasing mean annual temperature and precipitation. Overall, these results provide new insights into the multidimensional spatial patterns of river N cycling at a large scale, which is crucial to evaluating the N removal function of global rivers.

Transformation and migration of Hg in a polluted alkaline paddy soil during flooding and drainage processes

Mercury (Hg) contamination in paddy soils poses a health risk to rice consumers and the environmental behavior of Hg determines its toxicity. Thus, the variations of Hg speciation are worthy of exploring. In this study, microcosm and pot experiments were conducted to elucidate Hg transformation, methylation, bioaccumulation, and risk coupled with biogeochemical cycling of key elements in a Hg-polluted alkaline paddy soil. In microcosm and pot experiments, organic- and sulfide-bound and residual Hg accounted for more than 98% of total Hg, and total contents of dissolved, exchangeable, specifically adsorbed, and fulvic acid-bound Hg were less than 2% of total Hg, indicating a low mobility and environmental risk of Hg. The decrease of pH aroused from Fe(III), SO42-, and NO3- reduction promoted Hg mobility, whereas the increase of pH caused by Fe(II), S2-, and NH4+ oxidation reduced available Hg contents. Moreover, Fe-bearing minerals reduction and organic matter consumption promoted Hg mobility, whereas the produced HgS and Fe(II) oxidation increased Hg stability. During flooding, a fraction of inorganic Hg (IHg) could be transported into methylmercury (MeHg), and during drainage, MeHg would be converted back into IHg. After planting rice in an alkaline paddy soil, available Hg was below 0.3 mg kg-1. During rice growth, a portion of available Hg transport from paddy soil to rice, promoting Hg accumulation in rice grains. After rice ripening, IHg levels in rice tissues followed the trend: root > leaf > stem > grain, and IHg content in rice grain exceed 0.02 mg kg-1, but MeHg content in rice grain meets daily intake limit (37.45 μg kg-1). These results provide a basis for assessing the environmental risks and developing remediation strategies for Hg-contaminated redox-changing paddy fields as well as guaranteeing the safe production of rice grains.

A comprehensive insight into the abundance and community of anammox bacteria in sediments of Hangzhou Bay, China

A total of 13 surface sediments were collected from Hangzhou Bay (HZB) for an investigation into the distribution and influencing factors of anammox bacterial community. The anammox bacterial 16S rRNA and hzo genes ranged between 2.34 × 105 to 9.22 × 105 copies/g and 3.68 × 105 to 1.70 × 106 copies/g, respectively. The results of high throughput sequencing (HTS) revealed that the obtained OTUs were affiliated with five known genera, named Ca. Scalindua, Ca. Jettenia, Ca. Brocadia, Ca. Kuenenia and Ca. Anammoxoglobus. RDA analysis indicated that salinity, pH, and water depth influenced the anammox bacterial community. Furthermore, network analysis identified Ca. Scalindua as a key genus. Neutral community model (NCM) and modified stochasticity ratio (MST) indicated that the deterministic process dominated the anammox bacterial community assembly. Overall, this study offers a more comprehensive understanding of the abundance and community of anammox bacteria in the sediments of HZB.

Nitrogen fixation and diazotroph diversity in groundwater systems

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Unexpectedly high nitrate levels in a pristine forest river on the Southeastern Qinghai-Tibet Plateau

River nitrate (NO₃^-) pollution is a global environmental issue. Recently, high NO₃^- levels in some pristine or minimally-disturbed rivers were reported, but their drivers remain unclear. This study integrated river isotopes (δ¹⁸O/δ¹⁵N-NO₃^- and δD/¹⁸O-H₂O), ¹⁵N pairing experiments, and qPCR to reveal the processes driving the high NO₃^- levels in a nearly pristine forest river on the Qinghai-Tibet Plateau. The river isotopes suggested that, at the catchment scale, NO₃^- removal was prevalent in summer, but weak in winter. The pristine forest soils contributed more than 90 % of the riverine NO₃^-, indicating the high NO₃^- backgrounds. The release of soil NO₃^- to the river was "transport-limited" in both seasons, i.e., the NO₃^- production/stock in the soils exceeded the capacity of hydrological NO₃^- leaching. In summer, this regime and the NO₃^--plentiful conditions in the soils associated with the strong NO₃^- nitrification led to the high riverine NO₃^- levels. While the in-soil nitrification was weak in winter, the leaching of legacy NO₃^- resulted in the consistently high NO₃^- levels. This study provides insights into the reasons for high NO₃^- levels in pristine or minimally-disturbed rivers worldwide and highlights the necessity to consider NO₃^- backgrounds when evaluating anthropogenic NO₃^- pollution in rivers.

Labile carbon and soil texture control nitrogen transformation in deep vadose zone

Understanding transient nitrogen (N) storage and transformation in the deep vadose zone is critical for controlling groundwater contamination by nitrate. The occurrence of organic and inorganic forms of carbon (C) and nitrogen and their importance in the deep vadose zone is not well characterized due to difficulty in sampling and the limited number of studies. We sampled and characterized these pools beneath 27 croplands with different vadose zone thicknesses (6-45 m). We measured nitrate and ammonium in different depths for the 27 sites to evaluate inorganic N storage. We measured total Kjeldahl nitrogen (TKN), hot-water extractable organic carbon (EOC), soil organic carbon (SOC), and δ¹³C for two sites to understand the potential role of organic N and C pools in N transformations. Inorganic N stocks in the vadose zone were 21.7-1043.6 g m^-2 across 27 sites; the thicker vadose zone significantly stored more inorganic N (p < 0.05). We observed significant reservoirs of TKN and SOC at depths, likely representing paleosols that may provide organic C and N to subsurface microbes. The occurrence of deep C and N needs to be addressed in future research on terrestrial C and N storage potential. The increase of ammonium and EOC and δ¹³C value in the proximity of these horizons is consistent with N mineralization. An increase of nitrate, concurrent with the sandy soil texture and the water-filled pore space (WFPS) of 78 %, suggests that deep vadose zone nitrification may be supported in vadose zones with organic-rich layers such as paleosol. A profile showing the decrease of nitrate concentrations, concurrent with the clay soil texture and the WFPS of 91 %, also suggests denitrification may be an important process. Our study shows that microbial N transformation may be possible even in deep vadose zone with co-occurrence of C and N sources and controlled by labile C availability and soil texture.

From Soil to River: Revealing the Mechanisms Underlying the High Riverine Nitrate Levels in a Forest Dominated Catchment

Elevated riverine nitrate (NO₃^-) levels have led to increased eutrophication and other ecological implications. While high riverine NO₃^- levels were generally ascribed to anthropogenic activities, high NO₃^- levels in some pristine or minimally disturbed rivers were reported. The drivers of these unexpectedly high NO₃^- levels remain unclear. This study combined natural abundance isotopes, ¹⁵N-labeling techniques, and molecular techniques to reveal the processes driving the high NO₃^- levels in a sparsely populated forest river. The natural abundance isotopes revealed that the NO₃^- was mainly from soil sources and that NO₃^- removal processes were insignificant. The ¹⁵N-labeling experiments also quantitatively showed that the biological NO₃^- removal processes, i.e., denitrification, dissimilatory NO₃^- reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox), in the soils and sediments were weak relative to nitrification in summer. While nitrification was minor in winter, the NO₃^- removal was insignificant relative to the large NO₃^- stock in the catchment. Stepwise multiple regression analyses and structural equation models revealed that in summer, nitrification in the soils was regulated by the amoA-AOB gene abundances and NH₄⁺-N contents. Low temperature constrained nitrification in winter. Denitrification was largely controlled by moisture content in both seasons, and anammox and DNRA could be explained by the competition with nitrification and denitrification on their substrate (nitrite-NO₂^-). We also revealed the strong hydrological control on the transport of soil NO₃^- to the river. This study effectively revealed the mechanisms underlying the high NO₃^- levels in a nearly pristine river, which has implications for the understanding of riverine NO₃^- levels worldwide.

Anthropogenic impacts on the nitrate pollution in an urban river: Insights from a combination of natural-abundance and paired isotopes

Urban rivers are often characterized by high nitrate (NO₃^-) loadings. High NO₃^- loadings cause water quality and ecological damages, which undermines the sustainable development of cities. To date, the drivers of these high NO₃^- loadings remain unclear. This study, for the first time, integrated natural-abundance isotopes (δ¹⁵ N/δ¹⁸O-NO₃^- and δD/δ¹⁸O-H₂O) and ¹⁵N-pairing techniques to comprehensively reveal the anthropogenic impacts on the NO₃^- pollution in an urban river. Natural-abundance isotopes suggested that in both the wet and dry seasons, the NO₃^- was predominantly from the conservative mixing of different sources, and biological NO₃^- removal was minor. The ¹⁵N-pairing experiments supported the natural-abundance isotope data, quantitatively showing that in-soil nitrification was prevailing, while NO₃^- removal processes (denitrification, anammox, and dissimilatory NO₃^- reduction to ammonium) were weak. A Bayesian isotope-mixing model showed that soil sources (soil organic nitrogen and chemical fertilizer) dominated the NO₃^- in the upper reaches, while in the lower reaches, the impermeable riparian zone short-circuited the access of soils to the river. Here, the wastewater treatment plants became a significant source of NO₃^-. This study quantitatively revealed the drivers of high NO₃^- loadings in an urban river, and generated important clues for effective NO₃^- pollution control and remediation in urban rivers.

Aerobic and denitrifying methanotrophs: Dual wheels driving soil methane emission reduction

The greenhouse gas methane in soils has been considered to be consumed mainly by aerobic methane-oxidizing bacteria for a long time. In the last decades, the discovery of anaerobic methanotrophs greatly complemented the methane cycle, but their contribution rates and ecological significance in soils remain undescribed. In this work, the soil samples from forest, grassland and cropland in four different climatic regions were collected to investigate these conventional and novel methanotrophs. A dual-core microbial methane sink, responsible for over 80 % of soil methane emission reduction, was unveiled. The aerobic core was performed by aerobic methanotrophic bacteria in topsoil, who played important roles in stabilizing bacterial communities. The anaerobic core was denitrifying methanotrophs in anoxic soils, including denitrifying methanotrophic bacteria from NC10 phylum and denitrifying methanotrophic archaea from ANME-2d clade. They were ubiquitous in terrestrial soils and potentially led to around 50 % of the total methane removal. Human activities such as livestock farming and rice cultivation further promoted the contribution rates of these denitrifying methanotrophs. This work elucidated the emission reduction contribution of different methanotrophs in the continental setting, which would help to reduce uncertainties in the estimations of the soil methane emission.

Rhodopseudomonas palustris PSB06 agent enhance pepper yield and regulating the rhizosphere microecological environment

The Rhodopseudomonas palustris (R. palustris) PSB06 can promote crop growth, as it maybe regulates microbial communities in plant root soil, soil physicochemical properties, thus creating a favorable habitat for the crop growth. However, there are few studies on the yields and rhizosphere microbial community of R. palustris PSB06 agent. In the study, the high-throughput sequencing was used to study the changes of rhizosphere soil bacterial community after PSB06 treatment. The results indicated R. palustris PSB06 agent increased the pepper yield by 33.45% when compared to control group, with better effect than other treatments. And it also significantly increased soil nitrogen concentration. R. palustris PSB06 agent had improved pepper rhizosphere bacterial α diversity and changed the community structure. Acidobacteria, Proteobacteria, Actinomycetes and Firmicutes were dominant phyla in all the pepper rhizosphere soil samples. The results showed that soil bacterial community were significantly positively correlated with pH (R = 0.8537, P = 0.001) and total nitrogen (R = 0.4347, P = 0.003). The nine significantly enriched OTU in R.palustris PSB06 treatment (PB) group belong to Nitrososphaera (OTU_109, OTU_14, OTU_18, OTU_8), Lysobacter (OTU_2115, OTU_13), Arenimonas (OTU_26), Luteimonas (OTU_49), and Ramlibacter (OTU_70) were significantly positively correlated with the total yield of pepper (R &gt; 0.5, P &lt; 0.05). Overall, our results provide a theoretical basis for studying the microbial regulation of R.palustris PSB06 on rhizosphere soil.

Feammox is more important than anammox in anaerobic ammonium loss in farmland soils around Lake Taihu, China

Ammonium (NH₄⁺) oxidation is a key step in nitrogen transformation in ecosystems. Prior to the recent discovery of Feammox (anaerobic NH₄⁺ oxidation coupled with iron reduction), anammox (anaerobic NH₄⁺ oxidation coupled with nitrite reduction) was thought of as the only pathway by which anaerobic NH₄⁺ loss (NH₄⁺ directly to N₂) occurs in soils. Experimental evidence has confirmed that both anammox and Feammox contribute to anaerobic NH₄⁺ loss; however, their relative contributions to this process in farmland soils are largely unknown. Therefore, in this study, we examined the seasonal activities of anammox and Feammox in conventional tillage (CT) and no-tillage (NT) soils around Lake Taihu, China. Isotopic tracing experiments showed higher anammox and Feammox rates in summer than in other seasons, and the contribution of Feammox to anaerobic NH₄⁺ loss from the farmland soils (54.6%-69.3%) was higher than that of anammox. Further, the Feammox rates corresponding to the two soil tillage practices were significantly different, whereas their corresponding anammox rates showed no significant differences. Furthermore, molecular analysis showed that the abundance of Geobacteraceae differed significantly with season and tillage practice, whereas the abundance of anammox bacteria showed no significant differences between CT and NT practices. Structural equation modeling also revealed that the anammox rate was directly or indirectly driven by N availability and season, whereas the Feammox rate was driven by soil moisture content, Fe(III) concentration, Fe(III) reduction rates, tillage practice, and season. Overall, this study enhances understanding regarding anaerobic NH₄⁺ oxidation in farmland soils and highlight the importance of Feammox in NH₄⁺ loss in such an ecosystem.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of ¹⁵N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Diverse nirS-type Denitrifying Bacteria Contribute to Vital Nitrogen Loss in Natural Acidic Red Soils

Denitrifying bacteria, playing a key role in nitrogen removal in ecosystem, are highly diverse and complex in their community composition. However, there were few reports on the abundance, community composition, and the contribution to nitrogen loss of denitrifiers in natural acidic red soils. In this study, we investigated the structure and function of nirS-type denitrifying bacteria in ten natural red soil samples collected from nine provinces in southern China, based on quantitative polymerase chain reaction (qPCR) and high-throughput sequencing techniques. Nitrogen loss from microbial denitrification in red soils of southern China was estimated up to 9.86 Tg N per year based on ¹⁵N isotope tracing method. The abundance of nirS-type denitrifiers varied from 8.41 × 10⁵ to 2.55 × 10⁹ copies per gram of dry weight. The community of nirS-type denitrifying bacterial was revealed, which contained 50 dominant OTUs assigned to 9 clusters phylogenetically related to Marinobacter, Rhodobacter, and other uncultured species. pH was the key factor affecting both denitrification rates and community composition. Our results demonstrate that nirS-type denitrifying bacteria have higher abundance, diversity, and contribution to the nitrogen loss in natural acidic red soils of southern China.

Quinolone antibiotics enhance denitrifying anaerobic methane oxidation in Wetland sediments: Counterintuitive results

Denitrifying anaerobic methane oxidation (DAMO) plays an important role in the element cycle of wetlands. In recent years, the content of antibiotics in wetlands has gradually increased due to human activities. However, the impact of antibiotics on the ecological function of DAMO remains unclear. Here we studied the influence of three high-content quinolone antibiotics (QNs) on DAMO in the sediments of the Baiyangdian Wetland. The results show that QNs can significantly promote the potential DAMO rates. Moreover, the enhancement of potential DAMO rates is positively correlated with the dosage of QNs. This promotion effect of QNs on nitrate-DAMO can be attributed to the hormesis phenomenon or their inhibition of substrate competitors. As antibacterial agents, QNs inhibit nitrite-DAMO conducted by bacteria, but greatly promote nitrate-DAMO conducted by archaea. These results suggest that the short-term effect of QNs on DAMO in wetlands is promotion rather than inhibition.

Nitrate Addition Increases the Activity of Microbial Nitrogen Removal in Freshwater Sediment

Denitrification and anammox occur widely in aquatic ecosystems serving vital roles in nitrogen pollution removal. However, small waterbodies are sensitive to external influences; stormwater runoff carrying nutrients and oxygen, flows into waterbodies resulting in a disruption of geochemical and microbial processes. Nonetheless, little is known about how these short-term external inputs affect the microbial processes of nitrogen removal in small waterbodies. To investigate the effects of NO₃⁻, NH₄⁺, dissolved oxygen (DO) and organic C on microbial nitrogen removal in pond sediments, regulation experiments have been conducted using slurry incubation experiments and ¹⁵N tracer techniques in this study. It was demonstrated the addition of NO₃⁻ (50 to 800 μmol L⁻¹) significantly promoted denitrification rates, as expected by Michaelis-Menten kinetics. Ponds with higher NO₃⁻ concentrations in the overlying water responded more greatly to NO₃⁻ additions. Moreover, N₂O production was also promoted by such an addition of NO₃⁻. Denitrification was significantly inhibited by the elevation of DO concentration from 0 to 2 mg L⁻¹, after which no significant increase in inhibition was observed. Denitrification rates increased when organic C was introduced. Due to the abundant NH₄⁺ in pond sediments, the addition demonstrated little influence on nitrogen removal. Moreover, anammox rates showed no significant changes to any amendment.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Environmental heterogeneity determines the response patterns of microbially mediated N-reduction processes to sulfamethoxazole in river sediments

The widespread occurrence of antibiotics in aquatic ecosystems leads to potential ecological risks to organisms, in turn affecting microbially mediated processes. Here, we investigated the response of dominant N-reduction processes to the frequently detected antibiotic sulfamethoxazole (SMX) along the Chaobai River with regional environmental heterogeneity, including denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), and nitrous oxide (N₂O) release. We found two divergent SMX response patterns for denitrification in contrasting scenarios of geochemical properties. In the context of low nitrate and carbon, SMX weakened denitrification with a slightly stimulation first. Whereas SMX directly inhibited denitrification when nitrate and carbon were sufficient. High SMX concentration suppressed anammox (26-72%) and DNRA activities (48-84%) via restraining the activities of anammox and DNRA bacteria. Notably, SMX increased the contribution of denitrification to N-reduction at the expense of DNRA to N-reduction, leading to a shift in nitrogen conversion towards denitrification. Additionally, SMX stimulated N₂O emission (up to 91%) due to superior restraint on process of N₂O reduction to N₂ and an incline for N-reduction towards denitrification, thereby exacerbating greenhouse effect. Our results advance the understanding of how nitrogen cycling is affected by SMX in aquatic ecosystems with environmental heterogeneity.

Variations in nitrogen removal rates and microbial communities over sediment depth in Daya Bay, China

Depth-related variations in the activities, abundances, and community composition of denitrification and anaerobic ammonia oxidation (anammox) bacteria in coastal sediment cores remain poorly understood. In this study, we used ¹⁵N-labelled incubation, quantitative polymerase chain reaction (qPCR), and high-throughput sequencing techniques to reveal the structure and function of denitrifiers and anammox bacteria in sediment cores (almost 100 cm depth) collected in winter and summer from four locations in Daya Bay. The results indicated that the activities and abundances of both denitrifiers and anammox bacteria were detected even in deeper sediments with low concentrations of dissolved inorganic nitrogen (DIN). The potential rates, abundances, and community compositions of denitrifiers and anammox bacteria only varied spatially. In the surface sediment (top 2 cm), denitrifiers had significantly higher activities and abundances than anammox bacteria, but the relative contribution of anammox bacteria to nitrogen loss increased to >60% in the subsurface sediments. Phylogenetic analysis revealed that nirS-type denitrifiers were affiliated to 10 different clusters and Candidatus Scalindua dominated the anammox community in the whole sediments. Furthermore, both denitrification and anammox bacterial communities in the subsurface sediments were distinct from those in the surface sediments. Coupled nitrification and denitrification or anammox may play significant roles in removing fixed N, and the availability of electronic acceptors (e.g. nitrite and nitrate) strongly influenced the N loss activities in the subsurface sediment, emphasising its role as a sink for buried N.

Nitrogen loss through denitrification, anammox and Feammox in a paddy soil

Since the process of anaerobic ammonium oxidation (anammox) coupled with ferric iron reduction (termed Feammox) was discovered, it has been observed in various natural environments. However, besides the vertical distribution of Feammox in paddy soils, its differences and relationships with traditional nitrogen loss processes, including denitrification and anammox, remain unclear. Here, we studied the distribution of nitrogen loss pathways in different layers (0-50 cm) of paddy soil in southeastern China using ¹⁵N isotope tracer technology and molecular analysis. Our study showed that denitrification had a rate of 2.19 ± 0.39 mg N·kg^-1·d^-1, which was the highest activity in the surface layer (0-10 cm). The activities of anammox and Feammox reached peak values in the 10-20 cm (1.13 ± 0.16 mg N·kg^-1·d^-1) and 20-30 cm (0.23 ± 0.02 mg N·kg^-1·d^-1) soil layer, respectively. The nitrogen loss in the surface layer was more serious than that in the deep layer under paddy cultivation. In this study, denitrification was the main nitrogen loss pathway in the surface soil, but Feammox became an important nitrogen loss pathway (up to 26.1%) in the 20-40 cm depth. Overall, our research could improve and perfect the nitrogen cycle pathways in paddy soil.

Influence of Nitrogen Fertilization Rate on Soil Respiration: A Study Using a Rapid Soil Respiration Assay

Efficient nitrogen (N) management is one of the primary objectives of agronomic research as N is expensive and a major environmental pollutant. Soil microbes regulate N cycling and soil respiration (SR) measures soil microbial activity. The Comprehensive Assessment of Soil Health (CASH) soil respiration protocol is a rapid test, and a study was designed to approve this test as a potential tool for corn (Zea mays L.) N management. Five locations were selected around South Dakota (SD) where corn received 0, 45, 90, and 180 kg N ha−1 during summer of 2019. Soil samples were collected before planting and at the V6 corn growth stage to measure SR. We found that N fertilization increased SR and the highest SR was recorded at Ipswich (1.94 mg CO2 g−1) while SR was lowest at Bushnell (1.45 mg CO2 g−1). Higher SR was recorded at the sites where no-till farming was practiced, and soil had higher initial nitrate and organic matter content. SR was weakly correlated with corn grain yield, which indicated a potential area for future research. We concluded that split N application or an additional N application at a later growth stage might boost corn productivity in soil with higher microbial activity.

Abundance and Functional Importance of Complete Ammonia Oxidizers and Other Nitrifiers in a Riparian Ecosystem

The discovery of complete ammonia oxidation (comammox) has altered our understanding of nitrification, which is the rate-limiting process in the global nitrogen cycle. However, understanding the ecological role of comammox or its contribution to nitrification in both natural and artificial ecosystems is still in its infancy. Here, we investigated the community distribution and function of comammox bacteria in riparian ecosystems and analyzed interactions between comammox and other nitrogen cycling microorganisms. The comammox bacterial abundance and rate were higher in summer than in winter and higher in nonrhizosphere soils than in the rhizosphere. Fringe soils in the riparian zone comprise a comammox hotspot, where the abundance (2.58 × 10⁸ copies g^-1) and rate (0.86 mg N kg^-1 d^-1) of comammox were not only higher than at other sampling sites but also higher than those of other ammonia oxidation processes. The comammox rate correlated significantly positively with relative abundance of the comammox species Candidatus Nitrospira nitrificans but not with that of the species Candidatus Nitrospira nitrosa. Analysis of comammox interaction with other ammonia-oxidizing processes revealed ammonia-oxidizing archaea to dominate interface soils, comammox to dominate in fringe soils, and anaerobic ammonium oxidation (anammox) to dominate in interface sediments of the riparian zone. These results indicate that comammox may constitute an important and currently underestimated process of microbial nitrification in riparian zone ecosystems.

Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere

Soil microbes perform important functions in nitrogen and carbon cycling in the biosphere. Microbial communities in the rhizosphere enhance plants' health and promote nutrient turnover and cycling in the soil. In this study, we evaluated the effects of soil fertilization with organic and inorganic fertilizers on the abundances and distribution of carbon and nitrogen cycling genes within the rhizosphere of maize plants. Our result showed that maize plants through rhizosphere effects selected and enriched the same functional genes glnA, gltB, gudB involved in nitrogen cycle as do high compost and low inorganic fertilizer treatments. This observation was significantly different from those of high doses of inorganic fertilizer and low compost manure treated soil. Only alpha amylase encoding genes were selectively enriched by low compost and high inorganic fertilized soil. The other treatments only selected xynB (in Cp8), lacZ (Cp4), bglA, pldB, trpA (N2), uidA (N1) and glgC, vanA (Cn0) carbon cycling genes in the rhizosphere of maize. Also Actinomycetales are selected by high compost, low inorganic fertilizer and control. The control was without any fertilization and the soil was planted with maize. Bacillales are also promoted by low compost and high inorganic fertilizer. This indicated that only microbes capable of tolerating the stress of high dose of inorganic fertilizer will thrive under such condition. Therefore, soil fertilization lowers nitrogen gas emission as seen with the high abundance of nitrogen assimilation genes or microbial anabolic genes, but increases carbon dioxide evolution in the agricultural soil by promoting the abundance of catabolic genes involve in carbon cycling.

Earthworm gut: An overlooked niche for anaerobic ammonium oxidation in agricultural soil

Soil fauna takes an active part in accelerating turnover of nutrients in terrestrial ecosystems. Anaerobic ammonium oxidation (anammox) has been widely characterized, however, whether anammox is active in earthworm gut and the effect of earthworm on anammox in soil remain unknown. In this study, the activity, abundance and community of anammox bacteria in earthworm guts and soils from microcosms were determined using a ¹⁵N-tracing technique, quantitative PCR, and anammox bacterial 16S rRNA gene amplicon sequencing. Results showed that anammox rates in guts ranged between 5.81 and 14.19 nmol N g^-1 dw gut content h^-1, which were significantly (P < 0.01) higher than that in their surrounding soils during 30 day incubation. On the contrary, abundances of hzsB genes encoding subunit B hydrazine synthase in guts were significantly (P < 0.05) lower than those in their surrounding soils. Anammox rates, denitrification N₂ production rates and hzsB genes in soils with earthworms were significantly (P < 0.05) lower than those in control soils. Anammox bacterial compositions differed significantly (P < 0.05) between gut and soil, and earthworm altered anammox bacterial communities in soils. Brocadia, Kuenenia and abundant unclassified anammox bacteria were detected in collected soils and gut contents, in which Brocadia was only detected in guts. These results suggested that microbes in earthworm gut increase, but present of earthworm reduces anammox and denitrification associated N loss by altering the anammox bacterial community compositions in soils.

Insight into the nitrogen accumulation in urban center river from functional genes and bacterial community

Along with urbanization, the intensified nitrogen pollution in urban rivers and the form of black-odor rivers has become one of the biggest concerns. Better understanding of the nitrogen transformations and microbial mechanisms occurring within urban rivers could help to manage their water quality. In this study, pollution characteristics, potential nitrogen removal rate, composition and function of bacterial community, and abundance of functional genes associated with nitrogen transformation were comparatively investigated in a typical urban river (FC) and a suburban river (LH). Compared with LH, FC was characterized by higher content of nutrients, lower potential nitrogen removal rate and lower abundance of functional genes associated with nitrogen transformation in both overlying water and sediment, especially in summer. Sediment dissolved organic matter characterized by excitation−emission matrix (EEM) showed that FC was more severely polluted by high nitrogen organic matter. Our results revealed that anammox was the main nitrogen removal pathway in both rivers and potential nitrogen removal rates decreased significantly in summer. Bacterial community analysis showed that the benthic communities were more severely influenced by the pollutant than aquatic ones in both rivers. Furthermore, the FC benthic community was dominated by anaerobic respiring, fermentative, sulfate reduction bacteria. Quantitatively, the denitrification rate showed a significant positive correlation with the abundance of denitrification genes, whilst the anammox rate was significantly negatively correlated with bacterial diversity. Meanwhile, NH₄⁺-N had a significant negative correlation to both denitrification and anammox in sediment. Taken together, the results indicated that the increased nitrogen pollutants in an urban river altered nitrogen removal pathways and bacterial communities, which could in turn exacerbate the nitrogen pollution to this river.

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China

Mountain riparian zones are excellent buffers for protecting aquatic ecosystems from nutrient runoff in nitrogen deposition processes due to fertilization and manure. Denitrification is a critical process for transferring soil N to the atmosphere. Denitrifying bacterial communities in soil are indicative of the soil quality of a functional ecosystem. We investigated the effects of physicochemical properties of soil on the diversity and activity of denitrifiers in the top-soil and sub-soil of two typical montane riparian meadows: a multi-colored and a flood-plain meadow. Illumina MiSeq 2500 sequencing of nirS showed that the multi-colored meadow had greater diversity and abundance of nirS-type denitrifiers than the flood-plain meadow and that the total N content, ammonium content, and denitrification enzyme activity (DEA) in soil differed significantly between the two types of meadows. The abundances of dominant denitrifiers at phylum and genus levels showed different responses to the two soil layers of the two meadow types. In top-soils, the highest abundance of Firmicutes was recorded in the multi-colored meadow, while in the flood-plain meadow, there was the highest abundance of Proteobacteria. The Actinobacteria abundance was the highest in top-soil and sub-soil of the flood-plain meadow. The abundance of Chloroflexi was the highest in top-soil of the flood-plain meadow and in sub-soil of the multi-colored meadow. The diversity of denitrifying bacteria was strongly influenced by variations of soil properties down the soil profile. Spearman's rank correlation analyses showed that the diversity and community composition of denitrifying bacteria were strongly associated with most of the soil properties. Therefore, physicochemical soil properties, and particularly the organic carbon, nitrate, and ammonium contents, influence the diversity and abundance of denitrifiers in soil.

Comammox bacterial abundance, activity, and contribution in agricultural rhizosphere soils

The newly identified complete ammonia oxidation (comammox), which is capable of oxidizing ammonia directly to nitrate, has complemented our knowledge of nitrification in the global nitrogen (N) cycle. However, understanding the contribution and ecological roles of comammox in complex soil environments is still in its infancy. Here, the community structure and function of comammox and the interactions with other ammonia oxidation processes in rhizosphere and non-rhizosphere soils of four different crop fields (maize, cotton, soybean, and millet) were investigated in summer and winter. The only identified comammox species Candidatus Nitrospira nitrificans was widely distributed in all sampled soils. Comammox bacterial abundance was lower than that of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). The measured comammox potential rate ranged from 0.01 ± 0.002 to 0.40 ± 0.02 mg N kg^-1 d^-1, contributing <19.2 and 22.1% to ammonia oxidation in summer and winter, the remainder being due to AOA and AOB. The potential rate and community composition of comammox bacteria were significantly different on a temporal scale, while crop species and soil types (rhizosphere and non-rhizosphere) showed no obvious influences. In terms of oxidation rates, AOA (1.2 ± 0.7 mg N kg^-1 d^-1) dominated the ammonia oxidation in agricultural soils over AOB (0.31 ± 0.1 mg N kg^-1 d^-1) and comammox (0.2 ± 0.1 mg N kg^-1 d^-1). Both anammox bacterial abundance and activity were below the detection limits, indicating a negligible contribution of anammox in agricultural rhizosphere soils. The identification of comammox bacterial abundance and activity in situ enriches our knowledge of nitrification in agricultural systems.

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil

Nitrate (NO₃^-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO₃^- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g^-1 h^-1and 2.4125-58.682 nmol N g^-1 h^-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO₃^- reduction, hence dominated NO₃^- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO₃^- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments

AIMS

This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors.

METHODS AND RESULTS

We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables.

CONCLUSIONS

Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.

Impact of sand mining on the carbon sequestration and nitrogen removal ability of soil in the riparian area of Lijiang River, China

Riparian areas are widely recognized as the main areas for carbon sequestration and nitrogen pollution removal, while little is known about the effects of the respective sand mining activities on riparian zones. In this study, the effects of sand mining activities on the soil organic carbon (SOC) storage, different N-removal processes (Feammox, anammox, and denitrification), and composition of the relative bacterial community at a depth of 0-40 cm were determined based on investigations in riparian sand mining areas and adjacent forestlands. The SOC density of the sand mining areas (2.59 t ha^-1, depth of 0-40 cm) was lower than that of the riparian forestlands (80.42 t ha^-1). Compared with those of the riparian forestland, the sand mining area exhibited a dramatic reduction in the CO₂-fixed gene abundances (cbbL) and a significant change in the composition of cbbL-containing bacteria. The rates of the Feammox (0.038 ± 0.014 mg N kg^-1 d^-1), anammox (0.017 ± 0.017 mg N kg^-1 d^-1), and denitrification (0.090 ± 0.1 mg N kg^-1 d^-1) processes at a depth of 0-20 cm in the soil layer of the sand mining area were reduced by 70.17%, 91.5%, and 93.62% compared with those of the riparian forestland, respectively. The riparian areas in the study area (approximately 12 ha, depth of 0-40 cm) destroyed by sand mining activities released approximately 933.96 t stored soil carbon, which reduce the annual carbon sequestration potential by 28.8-40.8 t. Moreover, the potential N-removal rates in the riparian forestlands (depth of 0-20 cm) by the Feammox, anammox, and denitrification processes were 1514.21-1530.95 kg N ha^-1 year^-1, whereas the potential N-removal rates in the sand mining area were only 121.2-126.19 kg N ha^-1 year^-1. Therefore, more investigations are necessary for comparing the benefits and damage of sand mining activities in riparian areas before more sand mining activities are approved.

Depth-specific distribution and significance of nitrite-dependent anaerobic methane oxidation process in tidal flow constructed wetlands used for treating river water

Tidal flow constructed wetlands (TF CWs) have been considered an effective approach to treat contaminated river water, as well as a significant role in global matter cycles, especially for carbon and nitrogen. Notably, it has been thought that methane oxidation was completely catalyzed by the aerobic process, ignoring the anaerobic methane oxidation, such as the nitrite-dependent anaerobic methane oxidation (n-damo) process. In our current work, therefore, we used molecular and stable isotopes to investigate the biodiversity, quantity and potential rate of n-damo bacteria in the TF CWs located in the Xisha Wetland Park in the Yangtze River estuary, China. The results revealed that n-damo process was active in the collected soil cores, with a decreasing trend along water depths and rates ranging from 8.48 to 23.45 nmol CO₂ g^-1 dry soil d^-1. The n-damo bacterial contributions to CH₄ oxidation and N₂ production in TF CWs reached 9.49-26.26% and 20.73-47.11%, respectively, suggesting that n-damo bacteria was an important nitrogen and methane sink in the TF CWs, but had been previously overlooked. The copy numbers of total bacterial 16S rRNA and pmoA genes were 1.84-11.21 × 10⁹ and 0.59-2.72 × 10⁶ copies g^-1 ds, respectively, as the higher abundance was found in the soil at lower water levels during tidal submergence. Diverse n-damo bacterial 16S rRNA gene sequences belonged to group B, C and D were measured, and it was found that group B and C were the most frequently measured n-damo clusters in the TF CWs. In addition, nitrite was the key factor regulating the n-damo bacterial distribution in the TF CWs. This study would broaden our horizons and help us better understand the nitrogen and methane cycles in tidal ecosystems.

Preferential flow paths shape the structure of bacterial communities in a clayey till depth profile

Preferential flow paths in subsurface soils serve as transport routes for water, dissolved organic matter and oxygen. Little is known about bacterial communities in flow paths or in subsoils below ∼4 m. We compared communities from preferential flow paths (biopores, fractures and sand lenses) with those in adjacent matrix sediments of clayey till from the plough layer to a depth of 6 m. 16S rRNA gene-targeted community analysis showed bacterial communities of greater abundance and diversity in flow paths than in matrix sediments at all depths. Deep fracture communities contained a higher relative abundance of aerobes and plant material decomposers like Nitrospirae, Acidobacteria and Planctomycetes than adjacent matrix sediments. Similarly, analyses of the relative abundances of archaeal amoA, nirK and dsrB genes indicated transition from aerobic to anaerobic nitrogen and sulphur cycling at greater depth in preferential flow paths than in matrix sediments. Preferential flow paths in the top 260 cm contained more indicator operational taxonomic units from the plough layer community than the matrix sediments. This study indicates that the availability of oxygen and organic matter and downward transport of bacteria shape bacterial communities in preferential flow paths, and suggests that their lifestyles differ from those of bacteria in matrix communities.

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

Purpose

The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result

The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions

The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

Source, contribution and microbial N-cycle of N-compounds in China fresh snow

The importance and contribution of nitrogen compounds and the related microbial nitrogen cycling processes in fresh snow are not well understood under the current research background. We collected fresh snow samples from 21 cities that 80% are from China during 2016 and 2017. Principal component analysis showed that SO₄^2- were in the first principal component, and N-compounds were the second. Furthermore, the main pollutant ions SO₄^2- and NO₃^- were from anthropogenic sources, and SO₄^2- contributed (61%) more to the pollution load than NO₃^- (29%), which were confirmed through a series of precipitation mechanism analysis. We selected five N-cycle processes (consist of oxidation and reduction processes) for molecular biology experiments, including Ammonia-oxidation process, Nitrite-oxidation process, Denitrification process, Anaerobic-ammoxidation process (Anammox) and Dissimilatory nitrate reduction to ammonium process (DNRA). Except ammonia-oxidizing archaeal (AOA) and bacterial (AOB) amoA genes (above 10⁷ copies g^-1), molecular assays of key functional genes in various nitrogen conversion processes showed a belowed detection limit number, and AOB abundance was always higher than AOA. The determination of the microbial transformation rate using the ¹⁵N-isotope tracer technique showed that the potential rate of five N-conversion processes was very low, which is basically consistent with the results from molecular biology studies. Taken together, our results illustrated that microbial nitrogen cycle processes are not the primary biological processes causing the pollution in China fresh snow.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution

The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO₃^-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO₃^- removal. However, the microbial mechanisms regulating NO₃^- reduction in riparian zones are still unclear. In this study, four microbial NO₃^- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO₃^- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO₃^- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO₃^- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO₃^- reducers. As the last line of defense in the interception of terrestrial NO₃^-, these findings contribute to our understanding of NO₃^- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO₃^- pollution.

Denitrification is the main microbial N loss pathway on the Qinghai-Tibet Plateau above an elevation of 5000 m

Soil nitrogen (N) deficiency is the major factor contributing to low primary productivity on the Qinghai-Tibet Plateau. However, most of our understanding of N cycling is still based on human disturbed environments, and the microbial mechanisms governing N loss in low primary productivity environment remain unclear. This study explores three microbial N loss pathways in eight wetland and dryland soil profiles from the Qinghai-Tibet Plateau, at an elevation of above 5000 m with little human activity, using ¹⁵N isotopic tracing slurry technology, quantitative PCR, and high-throughput sequencing. No denitrifying anaerobic methane oxidation was detected. Anammox occurred in two of the wetland (n = 4) and dryland (n = 4) soil profiles, while denitrification widely occurred and was the dominant N loss pathway in all samples. Where denitrification and anammox co-occurred, both abundance and activity were higher in wetland than in dryland soils and higher in surface than in subsurface soils. In comparison with non-anammox sites, nitrate levels initiate anammox-related N cycling. High-throughput sequencing and network analysis of nirK, nirS, nosZ, and hzsB gene communities showed that Bradyrhizobiaceae (a family of rhizobia) may play a dominant role in N loss pathways in this region. Given the geological evolution and relatively undisturbed habitat, these findings strongly suggest that denitrification is the dominant N loss pathway in terrestrial habitats of the Qing-Tibet Plateau with minimal anthropogenic activity.

Methane emissions from aqueous sediments are influenced by complex interactions among microbes and environmental factors: A modeling study

Methane fluxes from aqueous sediments strongly influence global atmospheric methane. However, many questions still puzzle researchers; for example, why are some unstable sediments atmospheric methane sinks? In this study, a biofilm model originally developed for wastewater treatment was modified to simulate the microbial kinetics and substance conversions in aqueous surface sediments. The model was validated by the experimental data and could predict chemical profiles and microbial distributions in sediments. The model revealed complicated interactions between different microbial communities and environmental factors, including competition between aerobic methane-oxidizing bacteria, nitrite-dependent anaerobic methane-oxidizing bacteria, and anaerobic ammonia-oxidizing bacteria. The results of model simulations showed that the effects of environmental factors, especially dissolved oxygen and ammonia in overlying water, on methane fluxes are very complicated. Rapid environmental changes (which can be caused by tide, day-night alternation, or zoobenthic and human activity) and intensive competition between microbes greatly affected methane fluxes and resulted in alternation between atmospheric methane source and sink in unstable sediments. This study extends the application of a wastewater treatment model to ecological studies of microbial interactions in natural sediments and explains some problems that might be difficult to resolve by using experimental methods.

The missing nitrogen pieces: A critical review on the distribution, transformation, and budget of nitrogen in the vadose zone-groundwater system

Intensive agriculture and urbanization have led to the excessive and repeated input of nitrogen (N) into soil and further increased the amount of nitrate (NO₃^-) leaching into groundwater, which has become an environmental problem of widespread concern. This review critically examines both the recent advances and remaining knowledge gaps with respect to the N cycle in the vadose zone-groundwater system. The key aspects regarding the N distribution, transformation, and budget in this system are summarized. Three major missing N pieces (N in dissolved organic form, N in the deep vadose zone, and N in the nonagricultural system), which are crucial for closing the N cycle yet has been previously assumed to be insignificant, are put forward and discussed. More work is anticipated to obtain accurate information on the chemical composition, transformation mechanism, and leaching flux of these missing N pieces in the vadose zone-groundwater system. These are essential to support the assessment of global N stocks and management of N contamination risks.

Global Distribution of Anaerobic Ammonia Oxidation (Anammox) Bacteria - Field Surveys in Wetland, Dryland, Groundwater Aquifer and Snow

The discovery of anaerobic ammonia oxidation (anammox) expanded our knowledge on the microbial nitrogen cycle. Previous studies report that anammox bacteria are distributed in a wide range of habitats and plays significant roles in the global nitrogen cycle. However, most studies focus only on individual ecosystems or datasets from public databases. To date, our understanding of how anammox bacteria respond to environmental properties and are distributed in different habitats on a global scale, remain unclear. To explore the global distribution of anammox bacteria, samples were collected from different habitats at different locations globally, including wetlands, drylands, groundwater aquifers and snow from 10 countries across six continents. We then used high-throughput amplicon sequencing targeting the functional gene hydrazine synthase (HZS) and generated community profiles. Results showed that Candidatus Brocadia is detected as the dominant genus on a global scale, accounting for 80.0% to 99.9% of the retrieved sequences in different habitats. The Jettenia-like sequences were the second most abundant group, accounting for no more than 19.9% of the retrieved sequences in all sites. The samples in drylands, wetlands and groundwater aquifers showed similar community composition and diversity, with the snow samples being the most different. Deterministic processes seem stronger in regulating the community composition of anammox bacteria, which is supported by the higher proportion explained by local-scale factors. Groundwater aquifers showed high gene abundance and the most complex co-occurrence network among the four habitat types, suggesting that it might be the preferred habitat of anammox bacteria. There is little competition between anammox bacterial species based on co-occurrence analysis. Hence, we could infer that environmental factors such as anaerobic and stable conditions, instead of substrate limitations, may be vital factors determining the anammox bacteria community. These results provide a better understanding of the global distribution of anammox bacteria and the ecological factors that affect their community structuring in diverse habitats.

Anaerobic ammonium oxidation is a major N-sink in aquifer systems around the world

Global-scale N-oxide contamination of groundwater within aquifers occurs due to the widespread use of N-bearing fertilizers and chemicals, threatening both human and environmental health. However, the conversion of these pollutants in active nitrogen (N) cycling processes in the subsurface biosphere still remains unclear. This study investigates the global occurrence of anaerobic ammonium oxidation (anammox) in aquifers, where anammox was found to be turned on and off between saturated and unsaturated soil horizons, and contributed 36.8-79.5% to N loss in saturated soil horizons, the remainder being due to denitrification which has traditionally been considered the main pathway for removal of N-pollutants from aquifers. Although anammox activity was undetectable in the unsaturated soil horizons, it could potentially be activated by contact with ascending groundwater. High-throughput pyrosequencing analysis identified Candidatus Brocadia anammoxidans as being the most abundant anammox bacterium in the saturated soils investigated. However, the anammox bacterial abundance was determined by the relative richness of Candidatus Jettenia asiatica. Isotopic pairing experiments revealed that coupling anammox with ammonium oxidation and respiratory ammonification enabled the formation of a revised N cycle in aquifer systems, in which respiratory ammonification acted as an important coordinator. Anammox can therefore contribute substantially to aquifer N cycling and its role in remediation of aquifers contaminated with N-oxides may be of global importance.

Anammox and denitrification separately dominate microbial N-loss in water saturated and unsaturated soils horizons of riparian zones

Fertilized agroecosystems may show considerable leaching of the mobile nitrogen (N) compound NO₃^-, which pollutes groundwater and causes eutrophication of downstream waterbodies. Riparian buffer zones, positioned between terrestrial and aquatic environments, effectively remove NO₃^- and serve as a hotspot for N₂O emissions. However, microbial processes governing NO₃^- reduction in riparian zones still remain largely unclear. This study explored the underlying mechanisms of various N-loss processes in riparian soil horizons using isotopic tracing techniques, molecular assays, and high-throughput sequencing. Both anaerobic ammonium oxidation (anammox) and denitrification activity were maximized in the riparian fringe rather than in the central zones. Denitrifying anaerobic methane oxidation (damo) process was not detected. Interestingly, both contrasting microbial habitats were separated by a groundwater table, which forms an important biogeochemical interface. Denitrification dominated cumulative N-losses in the upper unsaturated soil, while anammox dominated the lower oxic saturated soil horizons. Archaeal and bacterial ammonium oxidation that couple dissimilatory nitrate reduction to ammonium (DNRA) with a high cell-specific rate promoted anammox even further in oxic subsurface horizons. High-throughput sequencing and network analysis showed that the anammox rate positively correlated with Candidatus 'Kuenenia' (4%), rather than with the dominant Candidatus 'Brocadia'. The contribution to N-loss via anammox increased significantly with the water level, which was accompanied by a significant reduction of N₂O emission (∼39.3 ± 10.6%) since N-loss by anammox does not cause N₂O emissions. Hence, water table management in riparian ecotones can be optimized to reduce NO₃^- pollution by shifting from denitrification to the environmentally friendly anammox pathway to mitigate greenhouse gas emissions.

Variation of Feammox following ammonium fertilizer migration in a wheat-rice rotation area, Taihu Lake, China

Feammox is a newly discovered and important anaerobic nitrogen (N) loss pathway, and its variation and role in removing N following the application of N fertilizer and its migration from paddies to other land use types and from surface soils to deep soils have not been thoroughly elucidated to date. In this study, field sampling and slurry incubation experiments were performed to evaluate the Feammox rate between different land use types (paddy, irrigation ditch, riparian zone and lake, 0-10 cm) and different paddy soil depths (0-70 cm) in a wheat-rice rotation area in China. Based on a ¹⁵N-labelled isotope-tracing technique and analysis of microbial communities, it was estimated that the potential Feammox rate ranged from 0.031 to 0.42 mg N kg^-1 d^-1 in this area. In the soil profile of the paddy, the depth of 20-30 cm was the active region of Feammox, with a value of 0.37 ± 0.057 mg N kg^-1 d^-1. Compared with the surface soil (0-10 cm) of the paddy (0.18 ± 0.031 mg N kg^-1 d^-1), the potential Feammox rate of the irrigation ditch soil was not significantly different, but that of the lake riparian soil and lake sediment were decreased by 27.27% and 32.11%, respectively (p < 0.01). Fe(III) content was the best predictor of the Feammox rate and explained the variation of the Feammox rate by 36.00% in the surface soil. At the genus level, the paddy soil at a depth of 20-30 cm had the greatest abundance of the genera in which the Fe reduction bacteria were distributed; and where Bacillus, Geobacter and Anaeromyxobacter had higher proportions. It was estimated that the potential N loss by Feammox was in the range of 7.36 (the lake) ∼43.35 (the paddy) kg N ha^-1 year^-1 in the surface soil of this area. Considering denitrification and the Feammox rate as a whole, we found that denitrification remained to be the main contributor to N loss in the surface soil (94.72-96.89% of N loss), although Feammox dominated N loss in the deep soil (below 0-10 cm).

Resuscitation of anammox bacteria after >10,000 years of dormancy

Water is essential for life on Earth, and an important medium for microbial energy and metabolism. Dormancy is a state of low metabolic activity upon unfavorable conditions. Many microorganisms can switch to a metabolically inactive state after water shortage, and recover once the environmental conditions become favorable again. Here, we resuscitated dormant anammox bacteria from dry terrestrial ecosystems after a resting period of >10 ka by addition of water without any other substrates. Isotopic-tracer analysis showed that water induced nitrate reduction yielding sufficient nitrite as substrate and energy for activating anammox bacteria. Subsequently, dissimilatory nitrate reduction to ammonium (DNRA) provided the substrate ammonium for anammox bacteria. The ammonium and nitrite formed were used to produce dinitrogen gas. High throughput sequencing and network analysis identified Brocadia as the dominant anammox species and a Jettenia species seemed to connect the other community members. Under global climate change, increasing precipitation and soil moisture may revive dormant anammox bacteria in arid soils and thereby impact global nitrogen and carbon cycles.

Anaerobic ammonium oxidation in agricultural soils-synthesis and prospective

Denitrification is considered as the dominant nitrogen (N) removing pathway, however, anaerobic oxidation of ammonium (anammox) also plays a significant part in N loss in agricultural ecosystems. Large N inputs into agricultural soils may stimulate the growth of anammox bacteria, resulting in high activity and diversity of anammox bacteria and subsequent more N loss. In some specific niches, like oxic-anoxic interface, three processes, nitrification, anammox and denitrification couple with each other, and significant anammox reaction could be observed. Soil parameters like pH, dissolved oxygen, salinity, oxidation-reduction potential (ORP), and substrate concentrations impact the anammox process. Here we summarize the current knowledge on anammox activity and contribution to N loss, abundance and diversity of anammox bacteria, factors affecting anammox, and the relationship between anammox and other N loss pathways in agricultural soils. We propose that more investigations are required for (1) the role of anammox to N loss with different agricultural management strategies; (2) microscale research on the coupling of nitrification-anammox-denitrification, that might be a very complex process but ideal model for further studies responsible for N cycling in terrestrial ecosystems; and (3) new methods to estimate differential contributions of anammox, codenitrification and denitrification in total N loss in agricultural ecosystems. New research will provide much needed information to quantify the contribution of anammox in N loss from soils at landscape, ecosystem and global scales.

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands

Excessive nitrogen (N) loadings from human activities have led to increased eutrophication and associated water quality impacts in China's coastal wetlands. Denitrification accounts for significant reduction of inorganic N to nitrous oxide (N₂O) or dinitrogen gas (N₂), and thereby curtails harmful effects of N pollution in coastal and marine ecosystems. However, the molecular drivers and limiting steps of denitrification in coastal wetlands are not well understood. Here, we quantified the abundances of functional genes involved in N cycling and determined denitrification rates using ¹⁵N paring technique in the coastal wetland sediments of Bohai Economic Rim in eastern China. Denitrification accounting for 80.7 ± 12.6% of N removal was the dominant pathway for N removal in the coastal wetlands. In comparison, anaerobic ammonium oxidation (ANAMMOX) removed up to 36.9 ± 7.3% of inorganic N. Structural equation modeling analysis indicated that the effects of ammonium on denitrification potential were mainly mediated by the relative abundances of nosZ/nirS, nirS/(narG + napA) and amoA/nirK. Denitrification was limited by the relative strength of two steps, namely N₂O reduction to N₂ and nitrite (NO₂^-) reduction to nitric oxide (NO). Our results suggest that the relative abundances of functional genes which are more stable than sediment chemical compounds in the context of environmental changes are indictive of denitrification potential in coastal wetlands.