Ammonia-oxidizing Archaea Research Articles

Unveiling the nitrogen and phosphorus removal potential: Comparative analysis of three coastal wetland plant species in lab-scale constructed wetlands

It is well accepted that tidal wetland vegetation performs a significant amount of water filtration for wetlands. However, there is currently little information on how various wetland plants remove nitrogen (N) and phosphorus (P) and how they differ in their denitrification processes. This study compared and investigated the denitrification and phosphorus removal effects of three typical wetland plants in the Yangtze River estuary wetland (Phragmites australis, Spartina alterniflora, and Scirpus mariqueter), as well as their relevant mechanisms, using an experimental laboratory-scale horizontal subsurface flow constructed wetland (CW). The results showed that all treatment groups with plants significantly reduced N pollutants as compared to the control group without plants. In comparison to S. mariqueter (77.2–83.2%), S. alterniflora and P. australis had a similar total nitrogen (TN)removal effectiveness of nearly 95%. With a removal effectiveness of over 99% for ammonium nitrogen (NH4+-N), P. australis outperformed S. alterniflora (95.6–96.8%) and S. mariqueter (94.6–96.5%). The removal of nitrite nitrogen (NO2−-N)and nitrate nitrogen (NO3−-N)from wastewater was significantly enhanced by S. alterniflora compared to the other treatment groups. Across all treatment groups, the removal rate of PO43--P was greater than 95%. P. australis and S. alterniflora considerably enriched more 15N than S. mariqueter, according to the results of the 15N isotope labeling experiment. While the rhizosphere and bulk sediments of S. alterniflora were enriched with more simultaneous desulfurization-denitrification bacterial genera (such as Paracoccus, Sulfurovum, and Sulfurimonas), which have denitrification functions, the rhizosphere and bulk sediments of P. australis were enriched with more ammonia-oxidizing archaea and ammonia-oxidizing bacteria. As a result, compared to the other plants, P. australis and S. alterniflora demonstrate substantially more significant ability to remove NH4+-N and NO2−-N/NO3−-N from simulated domestic wastewater.

How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal.

Innovation in decarbonizing wastewater treatment is urgent in response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic wastewater is the key to reconciling carbon-neutral management of wastewater treatment with sustainable development. Nitrite availability is the prerequisite of the anammox reaction, but how to achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on the recent advances in nitrite supply for mainstream anammox, paying special attention to available pathways (forward-going (from ammonium to nitrite) and backward-going (from nitrate to nitrite)), key controlling strategies, and physiological and ecological characteristics of functional microorganisms involved in nitrite supply. First, we comprehensively assessed the mainstream nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning to technologies possessing multiple selective pressures (such as intermittent aeration and membrane-aerated biological reactor), integrating side stream treatment (such as free ammonia/free nitrous acid suppression in recirculated sludge treatment), and maintaining high activity of ammonia-oxidizing bacteria and anammox bacteria for competing oxygen and nitrite with nitrite-oxidizing bacteria. We then highlight emerging strategies of nitrite supply, including the nitrite production driven by novel ammonia-oxidizing microbes (ammonia-oxidizing archaea and complete ammonia oxidation bacteria) and nitrate reduction pathways (partial denitrification and nitrate-dependent anaerobic methane oxidation). The resources requirement of different mainstream nitrite supply pathways is analyzed, and a hybrid nitrite supply pathway by combining partial nitrification and nitrate reduction is encouraged. Moreover, data-driven modeling of a mainstream nitrite supply process as well as proactive microbiome management is proposed in the hope of achieving mainstream nitrite supply in practical application. Finally, the existing challenges and further perspectives are highlighted, i.e., investigation of nitrite-supplying bacteria, the scaling-up of hybrid nitrite supply technologies from laboratory to practical implementation under real conditions, and the data-driven management for the stable performance of mainstream nitrite supply. The fundamental insights in this review aim to inspire and advance our understanding about how to provide nitrite robustly for mainstream anammox and shed light on important obstacles warranting further settlement.

Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.

Mathematical modeling and experimental validation of a novel Circulating Oxygenation Biofilm Equipment (COBE) for the management of decentralized wastewater treatment

The difficulties of management were the key barriers to the promotion of decentralized wastewater treatment in remote areas. In this study, a novel decentralized Circulating Oxygenation Biofilm Equipment (COBE) and its remote management potential based on mathematical modeling were investigated. The COBE is an integrated biofilm reactor that employs drippage aeration and enables oxygenation, filtration, and effluent processes to be controlled, thus providing convenience for controlling. The model for the COBE describing drippage aeration, comprehensive ammonia-related microbes, and corncob carbon source release process was studied to uncover the impacts of operational conditions on decentralized wastewater treatment in the COBE system. The equipment regulation parameter (circulating oxygenation ratio) was found to be linearly correlated with the oxygen mass transfer coefficient. This discovery enabled highly accurate prediction of COD, NH4–N, and TN concentrations in the equipment effluent at various scenarios. The comprehensive ammonia oxidation biological model indicated that the model could duplicate the actual situation of the succession of ammonia metabolizing related microorganisms. Comammox and ammonia-oxidizing archaea (AOA) dominated ammonia metabolism in this equipment rather than conventional ammonium-oxidizing bacteria (AOB). This study could contribute to the Internet of Things system construction of decentralized wastewater treatment equipment, and provide a solution for timely decentralized equipment management in remote areas.

Visualizing small-scale subsurface NH3 and pH dynamics surrounding nitrogen fertilizer granules and impacts on nitrification activity

In agricultural soils, nitrogen (N) fertilizer is typically applied as ammonium salts or urea, and undergoes microbially mediated oxidation. However, insights regarding substrate concentrations nitrifiers are exposed to in the zones immediately surrounding N fertilizer granules remain unexamined, as well as how this affects the activity or inhibition of nitrifier groups adapted to different ranges of ammonia (NH3) concentrations. To examine millimeter scale changes in soil chemistry after sub-surface fertilizer granule application with high spatiotemporal resolution, we applied a newly developed NH3 and pH planar optical sensor (optode) system. With this system, we visualized in situ subsurface NH3 production, diffusion, and associated pH shifts in an agricultural soil following the application (from 5 min up to 65.5 h) of ammonium chloride (NH4Cl) or urea granules in a laboratory study. Ammonia from both NH4Cl and urea granules diffused up to 1.5 and 2 cm and reached maximum concentrations of >49 and >130 ppmv, respectively. Spatially informed destructive subsampling (0.5–2 cm from granules) revealed that nitrate accumulation was greatest closest (0.5–1 cm) to the ammonium chloride granules, while nitrite was not detected. In contrast, urea application resulted in both nitrite and nitrate accumulation, with the highest concentrations detected furthest (1.5–2 cm) from urea granules. Urea hydrolysis also caused a significant localized pH increase, while ammonium chloride caused a circular elevated pH zone migrating outwards leaving a decreased pH at the center. Transcription of the ammonia-oxidizing bacterial amoA gene was highest in areas furthest (1.5–2 cm) from the urea granules, while there were no significant differences in amoA transcription with increasing distance from the NH4Cl granules. Ammonia-oxidizing archaea and comammox amoA transcripts were not detected. This study is the first to directly visualize small-scale subsurface changes in NH3 concentration and pH after fertilizer granule application and relate these to nitrification activity.

The abundance of comammox bacteria was higher than that of ammonia-oxidizing archaea and bacteria in rhizosphere of emergent macrophytes in a typical shallow lake riparian.

Complete ammonia oxidation (comammox) bacteria can complete the whole nitrification process independently, which not only challenges the classical two-step nitrification theory but also updates long-held perspective of microbial ecological relationship in nitrification process. Although comammox bacteria have been found in many ecosystems in recent years, there is still a lack of research on the comammox process in rhizosphere of emergent macrophytes in lakeshore zone. Sediment samples were collected in this study from rhizosphere, far-rhizosphere, and non-rhizosphere of emergent macrophytes along the shore of Lake Liangzi, a shallow lake. The diversity of comammox bacteria and amoA gene abundance of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in these samples were measured. The results showed that comammox bacteria widely existed in the rhizosphere of emergent macrophytes and fell into clade A.1, clade A.2, and clade B, and clade A was the predominant community in all sampling sites. The abundance of comammox amoA gene (6.52 × 106-2.45 × 108 copies g-1 dry sediment) was higher than that of AOB amoA gene (6.58 × 104-3.58 × 106 copies g-1 dry sediment), and four orders of magnitude higher than that of AOA amoA gene (7.24 × 102-6.89 × 103 copies g-1 dry sediment), suggesting that the rhizosphere of emergent macrophytes is more favorable for the growth of comammox bacteria than that of AOB and AOA. Our study indicated that the comammox bacteria may play important roles in ammonia-oxidizing processes in all different rhizosphere regions.

Biochar Amendment in Vermi-Wetland for Enhancing Nitrification during Excess Sludge Recycling

Vermi-wetland is a sustainable technology for recycling excess sludge in small-town areas. Although biochar (BC) amendment into the vermi-wetland could considerably boost the effectiveness of treating sludge, its impact on the nitrogen transformation in vermi-wetland remains unclear. Hence, this study aimed to explore the mechanism and performance of BC amendment into the vermi-wetland for enhancing nitrogen transformation during excess sludge recycling. The semi-aquatic plant Acorus calamus and the earthworm Eisenia fetida were planted in the designed vertical vermi-reactor, with corncob BC added to the upper and lower layers of one vermi-reactor, in comparison with the vermi-reactor without BC. The vermi-reactor with BC significantly lowered (p < 0.05) ammonia nitrogen (NH4+-N) and nitrite nitrogen (NO2−-N) in the effluent by 1.63 and 4.85-fold, respectively, and increased considerably nitrate nitrogen (NO3−-N) in the effluent by 1.5-fold. The numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in the vermi-reactor with BC were greatly enriched by 6 and 1.42-fold, compared with their counterparts (p < 0.05). Moreover, nirS and nirK gene copies in the vermi-reactor with BC were considerably improved (p < 0.05) by 2.03 and 1.82-fold, respectively. BC significantly enhanced the growth of earthworms by 6.92-fold and promoted plant growth by 1.28-fold. In addition, the AOB members like Nitrosomonas and Nitrosospira and the AOA members like Crenarchaeota and Thaumarchaeota cohabited in BC. Overall, these results suggest that a vermi-reactor amended with BC could enhance the nitrification processes of excess sludge, thereby improving the treatment performance of vermi-wetland.

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade’s ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.

Sustainable Use of Organic Seaweed Fertilizer Improves the Metagenomic Function of Microbial Communities in the Soil of Rice Plants

The frequent use of chemical fertilizers in agricultural practices has developed into a serious environmental concern which urgently needs a solution to restrain their use in agricultural systems. Hence, there is an urgent need to investigate potential organic fertilizers from various natural resources to decrease the use of chemical fertilizers. Seaweed is among the natural resources with potential sustainability value. Our previous work has shown the effectiveness of seaweed fertilizer for increasing plant growth and soil beneficial microbiota. This study aims to evaluate the functional genes present in the soil of rice plants treated with seaweed fertilization. It involves amendments with reduced concentrations of chemical fertilizer in three groups: CF (only chemical fertilizer), CFSF1 (50% dose of CF + seaweed fertilizer 1 ton/ha), and CFSF2 (50% dose of CF + seaweed fertilizer 2 ton/ha). The rice plants supplemented with CFSF1 and CFSF2 were taller and faster to mature compared to CF. In addition, the primary macronutrients nitrogen (N), phosphorus (P), and potassium (K) were also significantly higher in soil supplemented with SF. Our findings showed increased ammonia-oxidizing archaea Crenarchaeota abundance in increasing SF treatments. The PICRUSt analyses indicated enriched functional genes and proteins in relation to amino acid, nucleotide, protein, and carbohydrate metabolism based on the KEGG, BioCyc, and PFAM databases. The current outcomes enhanced our understanding regarding the importance of microbial community for soil quality. Furthermore, seaweed supplementation has shown improvement in soil fertility, which significantly increases rice plant growth and productivity.

Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China.

Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.

Epiphytic microorganisms of submerged macrophytes effectively contribute to nitrogen removal

Submerged macrophytes play important roles in nutrient cycling and are widely used in ecological restoration to alleviate eutrophication and improve water quality in lakes. Epiphytic microbial communities on leaves of submerged macrophytes might promote nitrogen cycling, but the mechanisms and quantification of their contributions remain unclear. Here, four types of field zones with different nutrient levels and submerged macrophytes, eutrophic + Vallisneria natans (EV), eutrophic + V. natans + Hydrilla verticillata, mesotrophic + V. natans + H. verticillata, and eutrophic without macrophytes were selected to investigate the microbial communities that involved in nitrification and denitrification. The alpha diversity of bacterial community was higher in the phyllosphere than in the water, and that of H. verticillata was higher compared to V. natans. Bacterial community structures differed significantly between the four zones. The highest relative abundance of dominant bacterioplankton genera involved in nitrification and denitrification was observed in the EV zone. Similarly, the alpha diversity of the epiphytic ammonia-oxidizing archaea and nosZI-type denitrifiers were highest in the EV zone. Consist with the diversity patterns, the potential denitrification rates were higher in the phyllosphere than those in the water. Higher potential denitrification rates in the phyllosphere were also found in H. verticillata than those in V. natans. Anammox was not detected in all samples. Nutrient loads, especially nitrogen concentrations were important factors influencing potential nitrification, denitrification rates, and bacterial communities, especially for the epiphytic nosZI-type taxa. Overall, we observed that the phyllosphere harbors more microbes and promotes higher denitrification rates compared to water, and epiphytic bacterial communities are shaped by nitrogen nutrients and macrophyte species, indicating that epiphytic microorganisms of submerged macrophytes can effectively contribute to the N removal in shallow lakes.

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3−-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge

In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.

Comammox bacteria and ammonia oxidizing archaea are major drivers of nitrification in glacier forelands

This study investigated the abundance of comammox bacteria and canonical ammonia-oxidizing bacteria (AOB) and archaea (AOA), and their relative contribution to nitrification along a chronosequence of deglaciated forelands. The results showed that nitrification related gene abundance tended to increase with glacier retreat, with comammox bacteria and AOA appearing to be the most critical drivers for soil nitrification rates. These findings provide new evidence for the presence of comammox bacteria in glacier forelands and enhance our understanding of the niche differentiation of canonical nitrifier and comammox bacteria.

Database of nitrification and nitrifiers in the global ocean

Abstract. As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen – ammonium–ammonia (NH4+–NH3) – into the oxidized species nitrite (NO2-) and nitrate (NO3-). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023).

How does biochar influence soil nitrification and nitrification-induced N2O emissions?

Nitrification is a major pathway of N2O production, especially in aerobic soils. The amendment of soils with biochar has been suggested as a promising solution to regulate soil N cycle and reduce N2O emissions. However, there is a lack of comprehensive and quantitative understanding of biochar impacts on soil nitrification and nitrification-induced N2O emissions. In this study, a meta-analysis was conducted using data compiled across 95 peer-reviewed studies. Results showed that biochar in general significantly increased soil nitrification rate by 56 %, with overall no significant effect on nitrification-induced N2O emissions, suggesting that biochar likely restricted the fraction of nitrified N emitted as N2O emissions. The abundance of ammonia-oxidizing bacteria (AOB) was significantly increased by 37 % following biochar addition, but that of ammonia-oxidizing archaea (AOA) did not change significantly, indicating that the impact of biochar on AOB rather than AOA may play an important role in soil nitrification. The impacts of biochar on soil nitrification processes were heterogeneous depending on soil properties. Biochar increased soil nitrification rate and AOB abundance to a larger extent in poorly pH-buffered soils such as those with acidic pH (<5), low organic carbon (<10 g kg−1), or poor texture (rich in either sand or clay), which may be attributed to the liming and structural effects of biochar that regulate soil pH and water-air status. The overall no significant effect of biochar on nitrification-induced N2O emissions was due to a positive effect in acidic soils, a negative effect in alkaline soils, and little effect in neutral soils. This study provides a comprehensive insight into how different factors mediate the response of soil nitrification processes to biochar amendment, which contributes to a new understanding of biochar function in regulating soil N2O emissions, and can assist in designing biochar projects that would benefit soil N cycle while minimizing undesirable side effects.

Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.

Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains.

Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.

Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica.

Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.

Microbial gene abundance mirrors soil nitrogen mineralization intensity across an age gradient in Chinese-fir plantations

Stand development affects soil properties, nitrogen (N) dynamics, and soil microbial community composition, but the question remains whether differences in N mineralization rates are mirrored by the abundance of relevant functional genes. In this study, we used the 15N pool-dilution method to estimate N mineralization (i.e., ammonification and nitrification) rates across a Chinese fir (Cunninghamia lanceolata) chronosequence, with stands aged 7, 16, 29, 36, and >80 years. Gene copy numbers of bacteria (16S rRNA), fungi (ITS), ammonia-oxidizing archaea (AOA) and bacteria (AOB) (amoA), denitrifiers (nirS, nirK), N2 fixers (nifH) and organic N decomposers (chiA) were quantified by qPCR. Gross ammonification and nitrification rates increased linearly with stand age in the topsoil (0–5 cm depth) and were strongly positively correlated with the abundance of the bacterial 16S rRNA gene and AOA amoA, respectively. Higher net nitrification but lower NO3− immobilization rates in older stands (32 and > 80 years) drove higher N availability for vegetation than in young stands (7 years). Older stands also had higher rates of NH4+ consumption than younger stands due to the increased fungal ITS abundance and higher microbial biomass N (MBN), and AOA amoA was more abundant and active than AOB amoA due to the more acid conditions characteristic of mature forests. Redundancy analysis showed that functional gene abundance was strongly affected by soil properties such as pH, NH4+-N content, and MBN. We also found that microbial N storage potential was lower, and the NO3−-N leaching and gaseous N loss potential were higher in older stands than in younger stands. Collectively, stand developmental stage gave rise to the observed spatial gradient of gross ammonification and nitrification rates by altering the abundance of microbial functional genes, which affected plantation productivity via its modulation of the supply of bioavailable N.