Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

The superiority of hydrophilic polyurethane in comammox-dominant ammonia oxidation during low-strength wastewater treatment

Carriers have been extensively employed to enhance nitrification performance during low-strength wastewater treatment by retaining slow-growing ammonia oxidizing microorganisms (AOMs). Still, there is a dearth of systematic understanding of biofilm properties and microbial community structure formed on different carriers. In this study, hydrophilic polyurethane foam (PUF) carriers were prepared and compared with five widely used commercial carriers, namely Kaldness 3, Biochip, activated carbon, volcanic rock, and zeolite. The results indicated that the biofilms formed on carriers enhanced microbial ammonia oxidation activity. Additionally, the biofilm developed on the PUF demonstrated the most superior performance among all selected carriers, not only exhibiting the highest abundant and the most active AOMs, with amoA gene abundance of 1.41 × 1013 copies/m3 and specific ammonia oxidation rate of 9.84 g NH4+-N/(m3 × h), but also possessing a compact structure, with 3.41 kg VSS/m3 and 46.83 mg extracellular polymeric substances/g VSS. The high-throughput sequencing analysis revealed that the comammox (CMX) Nitrospira dominated on biofilm due to the intrinsically low apparent half-saturation constant for substrate. A unique ecological community structure was established on PUF, characterized by low species diversity and high homogeneity in alignment with community characteristics of CMX. The biofilms on PUF contributed to the proliferation of CMX Nitrospira dominated by Nitrospira nitrosa, achieving the highest proportion among colonial three AOMs at 86.58 %. The appropriate average pore size, superior hydrophilicity, and large specific surface area of PUF carriers provided a robust foundation for the exceptional ammonia oxidation performance of the formed biofilms.

Impact of nutrient deficiency on biological sewage treatment - Perspectives towards urine source segregation

Human urine contains 9 g/L of nitrogen (N) and 0.7 g/L of phosphorus (P). The recovery of N and P from urine helps close the nutrient loop and increase resource circularity in the sewage treatment sector. Urine contributes an average of 80 % N and 50 % P in sewage, whereby urine source segregation could reduce the burden of nutrient removal in sewage treatment plants (STPs) but result in N and P deficiency and unintended negative consequences. This review examines the potential impacts of N and P deficiency on the removal of organic carbon and nutrients, sludge characteristics and greenhouse gas emissions in activated sludge processes. The details of how these impacts affect the operation of STPs were also included. This review helps foresee operational challenges that established STPs may face when dealing with nutrient-deficient sewage in a future where source separation of urine is the norm. The findings indicate that the requirement of nitrification-denitrification and biological P removal processes could shrink at urine segregation above 80 % and 100 %, respectively. Organic carbon, N and biological P removal processes can be severely affected under full urine segregation. The decrease in solid retention time due to urine segregation increases treatment capacity up to 48 %. Sludge flocculation and settleability would deteriorate due to changes in extracellular polymeric substances and induce various forms of bulking. Beneficially, N deficiency reduces nitrous oxide emissions. These findings emphasise the importance of considering and preparing for impacts caused by urine source segregation-induced nutrient deficiency in sewage treatment processes.

Comammox Nitrospira among dominant ammonia oxidizers within aquarium biofilter microbial communities

Nitrification by aquarium biofilters transforms ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Prior to the discovery of complete ammonia-oxidizing ("comammox" or CMX) Nitrospira, previous research revealed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Here, we profiled aquarium biofilter microbial communities and quantified the abundance of all three known ammonia oxidizers using 16S rRNA gene sequencing and quantitative PCR (qPCR), respectively. Biofilter and water samples were each collected from representative residential and commercial freshwater and saltwater aquaria. Distinct biofilter microbial communities were associated with freshwater and saltwater biofilters. Comammox Nitrospira amoA genes were detected in all 38 freshwater biofilter samples (average CMX amoA genes: 2.2 × 103 ± 1.5 × 103 copies/ng) and dominant in 30, whereas AOA were present in 35 freshwater biofilter samples (average AOA amoA genes: 1.1 × 103 ± 2.7 × 103 copies/ng) and only dominant in 7 of them. The AOB were at relatively low abundance within biofilters (average of 3.2 × 101 ± 1.1 × 102 copies of AOB amoA genes/ng of DNA), except for the aquarium with the highest ammonia concentration. For saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. Additional sequencing of Nitrospira amoA genes revealed differential distributions, suggesting niche adaptation based on water chemistry (e.g., ammonia, carbonate hardness, and alkalinity). Network analysis of freshwater microbial communities demonstrated positive correlations between nitrifiers and heterotrophs, suggesting metabolic and ecological interactions within biofilters. These results demonstrate that comammox Nitrospira plays a previously overlooked, but important role in home aquarium biofilter nitrification.

IMPORTANCE

Nitrification is a crucial process that converts toxic ammonia waste into less harmful nitrate that occurs in aquarium biofilters. Prior research found that ammonia-oxidizing archaea (AOA) were dominant over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Our study profiled microbial communities of aquarium biofilters and quantified the abundance of all currently known groups of aerobic ammonia oxidizers. The findings reveal that complete ammonia-oxidizing (comammox) Nitrospira were present in all freshwater aquarium biofilter samples in high abundance, challenging our previous understanding of aquarium nitrification. We also highlight niche adaptation of ammonia oxidizers based on salinity. The network analysis of freshwater biofilter microbial communities revealed significant positive correlations among nitrifiers and other community members, suggesting intricate interactions within biofilter communities. Overall, this study expands our understanding of nitrification in aquarium biofilters, emphasizes the role of comammox Nitrospira, and highlights the value of aquaria as microcosms for studying nitrifier ecology.

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Long-neglected contribution of nitrification to N2O emissions in the Yellow River

Rivers play a significant role in the global nitrous oxide (N2O) budget. However, the microbial sources and sinks of N2O in river systems are not well understood or quantified, resulting in the prolonged neglect of nitrification. This study investigated the isotopic signatures of N2O, thereby quantifying the microbial source of N2O production and the degree of N2O reduction in the Yellow River. Although denitrification has long been considered to be the dominant pathway of N2O production in rivers, our findings indicated that denitrification only accounted for 18.3% (8.2%-43.0%) of the total contribution to N2O production in the Yellow River, with 50.2%-80.2% being concurrently reduced. The denitrification contribution to N2O production (R2 = 0.44, p < 0.01) and N2O reduction degree (R2 = 0.70, p < 0.01) were positively related to the dissolved organic carbon (DOC) content. Similar to urban rivers and eutrophic lakes, denitrification was the primary process responsible for N2O production (43.0%) in certain reaches with high organic content (DOC = 5.29 mg/L). Nevertheless, the denitrification activity was generally constrained by the availability of electron donors (average DOC = 2.51 mg/L) throughout the Yellow River basin. Consequently, nitrification emerged as the primary contributor in the well-oxygenated Yellow River. Additionally, our findings further distinguished the respective contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to N2O emissions. Although AOB dominated the N2O production in the Yellow River, the AOA specie abundance (AOA/(AOA + AOB)) contributed up to 32.6%, which resulted in 25.6% of the total nitrifier-produced N2O, suggesting a significant occurrence of AOA in the oligotrophic Yellow River. Overall, this study provided a non-invasive approach for quantifying the microbial sources and sinks to N2O emissions, and demonstrated the substantial role of nitrification in the large oligotrophic rivers.

Application of single-cell Raman-deuterium isotope probing to reveal the resistance of marine ammonia-oxidizing archaea SCM1 against common antibiotics

Antimicrobial resistance (AMR) in oceans poses a significant threat to human health through the seafood supply chain. Ammonia-oxidizing archaea (AOA) are important marine microorganisms and play a key role in the biogeochemical nitrogen cycle around the world. However, the AMR of marine AOA to aquicultural antibiotics is poorly explored. Here, Raman-deuterium isotope probing (Raman-DIP), a single-cell tool, was developed to reveal the AMR of a typical marine species of AOA, Nitrosopumilus maritimus (designated SCM1), against six antibiotics, including erythromycin, tetracycline, novobiocin, neomycin, bacitracin, and vancomycin. The D2O concentration (30% v/v) and culture period (9 days) were optimized for the precise detection of metabolic activity in SCM1 cells through Raman-DIP. The relative metabolic activity of SCM1 upon exposure to antibiotics was semi-quantitatively calculated based on single-cell Raman spectra. SCM1 exhibited high resistance to erythromycin, tetracycline, novobiocin, neomycin, and vancomycin, with minimum inhibitory concentration (MIC) values between 100 and 400 mg/L, while SCM1 is very sensitive to bacitracin (MIC: 0.8 mg/L). Notably, SCM1 cells were completely inactive under the metabolic activity minimum inhibitory concentration conditions (MA-MIC: 1.6-800 mg/L) for the six antibiotics. Further genomic analysis revealed the antibiotic resistance genes (ARGs) of SCM1, including 14 types categorized into 33 subtypes. This work increases our knowledge of the AMR of marine AOA by linking the resistant phenome to the genome, contributing to the risk assessment of AMR in the underexplored ocean environment. As antibiotic resistance in marine microorganisms is significantly affected by the concentration of antibiotics in coastal environments, we encourage more studies concentrating on both the phenotypic and genotypic antibiotic resistance of marine archaea. This may facilitate a comprehensive evaluation of the capacity of marine microorganisms to spread AMR and the implementation of suitable control measures to protect environmental safety and human health.

Membraneless channels sieve cations in ammonia-oxidizing marine archaea

Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.

Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum

River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.

The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing

The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.

Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans

Introduction

Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions.

Methods

In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria.

Results and Discussion

Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments

Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak.

IMPORTANCE

Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.

Accelerated nitrogen cycling on Mediterranean seagrass leaves at volcanic CO2 vents

Seagrass meadows form highly productive and diverse ecosystems in coastal areas worldwide, where they are increasingly exposed to ocean acidification (OA). Efficient nitrogen (N) cycling and uptake are essential to maintain plant productivity, but the effects of OA on N transformations in these systems are poorly understood. Here we show that complete N cycling occurs on leaves of the Mediterranean seagrass Posidonia oceanica at a volcanic CO2 vent near Ischia Island (Italy), with OA affecting both N gain and loss while the epiphytic microbial community structure remains largely unaffected. Daily leaf-associated N2 fixation contributes to 35% of the plant's N demand under ambient pH, while it contributes to 45% under OA. Nitrification potential is only detected under OA, and N-loss via N2 production increases, although the balance remains decisively in favor of enhanced N gain. Our work highlights the role of the N-cycling microbiome in seagrass adaptation to OA, with key N transformations accelerating towards increased N gain.

Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes

Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.

Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake

Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.

Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands

Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.

Effects of the three amendments on NH3 volatilization, N2O emissions, and nitrification at four salinity levels: An indoor experiment

The marked salinity and alkaline pH of coastal saline soil profoundly impact the nitrogen conversion process, leading to a significantly reduced nitrogen utilization efficiency and substantial gaseous nitrogen loss. The application of soil amendments (e.g. biochar, manure, and gypsum) was proved to be effective for the remediation of saline soils. However, the effects of the three amendments on soil nitrogen transformation in soils with various salinity levels, especially on NH3 volatilization and N2O emission, remain elusive. Here, we reported the effects of biochar, manure, and gypsum on NH3 volatilization and N2O emission under four natural salinity gradients in the Yellow River Delta. Also, high-throughput sequencing and qPCR analysis were performed to characterize the response of nitrification (amoA) and denitrification (nirS, nirK, and nosZ) functional genes to the three amendments. The results showed that the three amendments had little effect on NH3 volatilization in low- and moderate-salinity soils, while biochar stimulated NH3 volatilization in high-salinity soils and reduced NH3 volatilization in severe-salinity soils. Spearman correlation analysis demonstrated that AOA was significantly and positively correlated with the NO3--N content (r = 0.137, P < 0.05) and N2O emissions (r = 0.174, P < 0.01), which indicated that AOA dominated N2O emissions from nitrification in saline soils. Structural equation modeling indicated that biochar, manure, and gypsum affected N2O emission by influencing soil pH, conductivity, mineral nitrogen content, and functional genes (AOA-amoA and nosZ). Two-way ANOVA further showed that salinity and amendments (biochar, manure, and gypsum) had significant effects on N2O emissions. In summary, this study provides valuable insights to better understand the effects of gaseous N changes in saline soils, thereby improving the accuracy and validity of future GHG emission predictions and modeling.

High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay

Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.

A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation

Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown. Here, analyses of carbon isotope composition in a ~ 750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition, with anomalous 14C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology. Microbial community composition and diverse enzyme activities in the upper ~ 27 cm differed from those at lower depths, probably due to sudden sediment deposition and differences in redox condition and organic matter availability. At lower depths, microbial population numbers, and composition remained relatively constant, except at some discrete depths with altered enzyme activity and microbial phyla abundance, possibly due to additional sudden sedimentation events of different magnitude. Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth's deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations. Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00212-y.

Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms

Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.

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.

Effect of carbon and nitrogen mineralization of chitosan and its composites with hematite/gibbsite on soil acidification of an Ultisol induced by urea

Chitosan is a biodegradable polymer with a vast range of applications. Along with its metal composites, chitosan has been applied in the remediation of polluted soils as well as a biofertilizer. However, little attention has been given to the degradation of chitosan composites in soil and how they affect soil respiration rate and other physicochemical parameters. In this study, the degradation of chitosan and its composites with gibbsite and hematite in an acidic Ultisol and the effect on urea (200 mg N kg-1) transformation were investigated in a 70-d incubation experiment. The results showed that the change trends of soil pH, N forms, and CO2 emissions were similar for chitosan and its composites when applied at rates <5 g C kg-1. At a rate of 5 g C kg-1, the C and N mineralization trends suggested that the chitosan-gibbsite composite was more stable in soil and this stability was owed to the formation of a new chemical bond (CH-N-Al-Gibb) as observed in the Fourier-transform infrared spectrum at 1644 cm-1. The mineralization of the added materials significantly increased soil pH and decreased soil exchangeable acidity (P < 0.01). This played an important role in decreasing the amount of H+ produced during urea transformation in the soil. The soil's initial pH was an important factor influencing C and N mineralization trends. For instance, increasing the initial soil pH significantly increased the nitrification rate and chitosan decomposition trend (P < 0.01) and thus, the contribution of chitosan and its composites to increase soil pH and inhibit soil acidification during urea transformation was significantly decreased (P < 0.01). These findings suggest that to achieve long-term effects of chitosan in soils, applying it as a chitosan-gibbsite complex is a better option.

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

Quantifying microbial guilds

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea

Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.

Combined application of Pseudomonas fluorescens and urea can mitigate rapid acidification of cropland Ultisol

Rhizobacteria maintain a healthy soil required for crop growth. This has led to increased interest in the use of bacteria-based biofertilizers in agriculture as they improve soil nutrient content and protect plants against pathogens. However, the effect of bacteria inoculum on N transformation and soil physicochemical properties during urea fertilization remains unexploited. Thus, this study investigated the effect of Pseudomonas fluorescens on urea N transformation in an acidic Ultisol within a 70-d incubation period. The results revealed that (1) soil pH peaked on d 5 (pH 5.58) and 20 (pH 6.23) and rapidly decreased till d 62 (pH 4.10) and 50 (pH 4.93) for urea and urea + bacteria treatments, respectively, and remained constant thereafter. After 70 d, the pH of the bacteria-treated Ultisol remained higher (0.78 pH units) than that of urea-treated Ultisol; (2) the change in soil pH was in agreement with the mineralization trend of N, as the concentration of NH4+-N peaked on d 5 (134.2 mg N kg-1) and 20 (423 mg N kg-1) before decreasing to 62.1 and 276.1 mg N kg-1 on d 70 in urea-treated and bacteria-treated Ultisol, respectively; and (3) P. fluorescens consumed protons produced during nitrification to retard rapid decrease in soil pH, decreased soil exchangeable acidity (33.3 %), increased soil effective cation exchange capacity (32.8 %), and increased the solubility of soil exchangeable base cations (68.4 %, Ca2+ + Mg2+ + K+ + Na+). Thus, bacterial inoculum could promote N mineralization, enhance nutrient solubility, and retard soil acidification during N transformation in soils.

Relative importance between nitrification and denitrification to N2 O from a global perspective

Nitrous oxide (N2 O) is a potent greenhouse gas, and its mitigation is a pressing task in the coming decade. However, it remains unclear which specific process between concurrent nitrification and denitrification dominates worldwide N2 O emission. We snagged an opportunity to ascertain whence the N2 O came and which were the controlling factors on the basis of 1315 soil N2 O observations from 74 peer-reviewed articles. The average N2 O emission derived from nitrification (N2 On ) was higher than that from denitrification (N2 Od ) worldwide. The ratios of nitrification-derived N2 O to denitrification-derived N2 O, hereof N2 On :N2 Od , exhibited large variations across terrestrial ecosystems. Although soil carbon and nitrogen content, pH, moisture, and clay content accounted for a part of the geographical variations in the N2 On :N2 Od ratio, ammonia-oxidizing microorganisms (AOM):denitrifier ratio was the pivotal driver for the N2 On :N2 Od ratios, since the AOM:denitrfier ratio accounted for 53.7% of geographical variations in N2 On :N2 Od ratios. Compared with natural ecosystems, soil pH exerted a more remarkable role to dictate the N2 On :N2 Od ratio in croplands. This study emphasizes the vital role of functional soil microorganisms in geographical variations of N2 On :N2 Od ratio and lays the foundation for the incorporation of soil AOM:denitrfier ratio into models to better predict N2 On :N2 Od ratio. Identifying soil N2 O derivation will provide a global potential benchmark for N2 O mitigation by manipulating the nitrification or denitrification.

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

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.

Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary

In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.

Nitrogen addition stimulates N2O emissions via changes in denitrification community composition in a subtropical nitrogen-rich forest

Microbially driven nitrification and denitrification play important roles in regulating soil N availability and N2O emissions. However, how the composition of nitrifying and denitrifying prokaryotic communities respond to long-term N additions and regulate soil N2O emissions in subtropical forests remains unclear. Seven years of field experiment which included three N treatments (+0, +50, +150 kg N ha-1 yr-1; CK, LN, HN) was conducted in a subtropical forest. Soil available nutrients, N2O emissions, net N mineralization, denitrification potential and enzyme activities, and the composition and diversity of nitrifying and denitrifying communities were measured. Soil N2O emissions from the LN and HN treatments increased by 42.37% and 243.32%, respectively, as compared to the CK. Nitrogen addition significantly inhibited nitrification (N mineralization) and significantly increased denitrification potentials and enzymes. Nitrification and denitrification abundances (except nirK) were significantly lower in the HN, than CK treatment and were not significantly correlated with N2O emissions. Nitrogen addition significantly increased nirK abundance while maintaining the positive effects of denitrification and N2O emissions to N deposition, challenging the conventional wisdom that long-term N addition reduces N2O emissions by inhibiting microbial growth. Structural equation modeling showed that the composition, diversity, and abundance of nirS- and nirK-type denitrifying prokaryotic communities had direct effects on N2O emissions. Mechanistic investigations have revealed that denitrifier keystone taxa transitioned from N2O-reducing (complete denitrification) to N2O-producing (incomplete denitrification) with increasing N addition, increasing structural complexity and diversity of the denitrifier co-occurrence network. These results significantly advance current understanding of the relationship between denitrifying community composition and N2O emissions, and highlight the importance of incorporating denitrifying community dynamics and soil environmental factors together in models to accurately predict key ecosystem processes under global change.

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.

Drug discovery-based approach identifies new nitrification inhibitors

Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.

Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China

Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.

Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil

Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.

Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone

The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.

Differential contribution of nitrifying prokaryotes to groundwater nitrification

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer

Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3  + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1  h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.

A moderately thermophilic origin of a novel family of marine group II euryarchaeota from deep ocean

Marine group II (MGII) is the most abundant planktonic heterotrophic archaea in the ocean. The evolutionary history of MGII archaea is elusive. In this study, 13 new MGII metagenome-assembled genomes were recovered from surface to the hadal zone in Challenger Deep of the Mariana Trench; four of them from the deep ocean represent a novel group. The optimal growth temperature (OGT) of the common ancestor of MGII has been estimated to be at about 60°C and OGTs of MGIIc, MGIIb, and MGIIa at 47°C-50ºC, 37°C-44ºC, and 30°C-37ºC, respectively, suggesting the adaptation of these species to different temperatures during evolution. The estimated OGT range of MGIIc was supported by experimental measurements of cloned β-galactosidase that showed optimal enzyme activity around 50°C. These results indicate that MGIIc may have originated from a common ancestor that lived in warm or even hot marine environment, such as hydrothermal vents.

Kinetic, genomic, and physiological analysis reveals diversity in the ecological adaptation and metabolic potential of Brachybacterium equifaecis sp. nov. isolated from horse feces

Brachybacterium species have been identified in various ecological niches and belong to the family Dermabacteriaceae within the phylum Actinobacteria. In this study, we isolated a novel Brachybacterium equifaecis JHP9 strain from horse feces and compared its kinetic, biochemical, and genomic features with those of other Brachybacterium strains. Moreover, comparative genomic analysis using publicly available Brachybacterium genomes was performed to determine the properties involved in their ecological adaptation and metabolic potential. Novel species delineation was determined phylogenetically through 16S rRNA gene similarity (up to 97.9%), average nucleotide identity (79.5-82.5%), average amino acid identity (66.7-75.8%), and in silico DNA-DNA hybridization (23.7-27.9) using closely related strains. This study also presents the first report of the kinetic properties of Brachybacterium species. Most of the Brachybacterium strains displayed high oxygen (K m(app) =1.6-24.2 µM) and glucose (K m(app) =0.73-1.22 µM) affinities, which may manifest niche adaptations. Various carbohydrate metabolisms under aerobic and anaerobic conditions, antibiotic resistance, mobile genetic elements, carbohydrate-active enzymes, lactic acid production, and the clustered regularly interspaced short palindromic repeats-Cas and bacteriophage exclusion systems were observed in the genotypic and/or phenotypic properties of Brachybacterium species, suggesting their genome flexibility, defense mechanisms, and adaptability. Our study contributes to the knowledge of the kinetic, physiological, and genomic properties of Brachybacterium species, including the novel JHP9 strain, which advocates for their tolerant and thriving nature in various environments, leading to their ecological adaptation. IMPORTANCE Basic physiological and genomic properties of most of the Brachybacterium isolates have been studied; however, the ability of this bacterium to adapt to diverse environments, which may demonstrate its role in niche differentiation, is to be identified yet. Therefore, here, we explored cellular kinetics, metabolic diversity, and ecological adaptation/defensive properties of the novel Brachybacterium strain through physiological and comparative genomic analysis. In addition, we presented the first report examining Brachybacterium kinetics, indicating that all strains of Brachybacterium, including the novel one, have high oxygen and glucose affinity. Furthermore, the comparative genomic analysis also revealed that the novel bacterium contains versatile genomic properties, which provide the novel bacterium with significant competitive advantages. Thus, in-depth genotypic and phenotypic analysis with kinetic properties at the species level of this genus is beneficial in clarifying its differential characteristics, conferring the ability to inhabit diverse ecological niches.

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.

Nitrification and beyond: metabolic versatility of ammonia oxidising archaea

Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.

Role of Nitric Oxide in Hydroxylamine Oxidation by Ammonia-Oxidizing Bacteria

An important role of nitric oxide (NO) as either a free intermediate in the NH3 oxidation pathway or a potential oxidant for NH3 or NH2OH has been proposed for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively. However, tracing NO metabolism at low concentrations remains notoriously difficult. Here, we use electrochemical sensors and the mild NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) to trace apparent NO concentration and determine production rates at low micromolar concentrations in the model AOB strain Nitrosomonas europaea. In agreement with previous studies, we found that PTIO does not affect NH3 oxidation instantaneously in both Nitrosospira briensis and Nitrosomonas europaea, unlike inhibitors for ammonia oxidation such as allylthiourea and acetylene, although it effectively scavenged NO from the cell suspensions. Quantitative analysis showed that NO production by N. europaea amounted to 3.15% to 6.23% of NO2- production, whereas N. europaea grown under O2 limitation produced NO equivalent to up to 40% of NO2- production at high substrate concentrations. In addition, we found that PTIO addition to N. europaea grown under O2 limitation abolished N2O production. These results indicate different turnover rates of NO during NH3 oxidation under O2-replete and O2-limited growth conditions in AOB. The results suggest that NO may not be a free intermediate or remain tightly bound to iron centers of enzymes during hydroxylamine oxidation and that only NH3 saturation and adaptation to O2 limitation may lead to significant dissociation of NO from hydroxylamine dehydrogenase. IMPORTANCE Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria (AOB) is thought to contribute significantly to global nitrous oxide (N2O) emissions and leaching of oxidized nitrogen, particularly through their activity in nitrogen (N)-fertilized agricultural production systems. Although substantial efforts have been made to characterize the N metabolism in AOB, recent findings suggest that nitric oxide (NO) may play an important mechanistic role as a free intermediate of hydroxylamine oxidation in AOB, further implying that besides hydroxylamine dehydrogenase (HAO), additional enzymes may be required to complete the ammonia oxidation pathway. However, the NO spin trap PTIO was found to not inhibit ammonia oxidation in AOB. This study provides a combination of physiological and spectroscopic evidence that PTIO indeed scavenges only free NO in AOB and that significant amounts of free NO are produced only during incomplete hydroxylamine oxidation or nitrifier denitrification under O2-limited growth conditions.

Competitive and substrate limited environments drive metabolic heterogeneity for comammox Nitrospira

Nitrospira has been revealed as a high versatile genus. Although previously considered only responsible for the conversion of nitrite to nitrate, now we know that Nitrospira can perform complete ammonia oxidation to nitrate too (comammox). Comammox activity was firstly reported as dominant in extremely limited oxygen environments, where anaerobic ammonia oxidation was also occurring (anammox). To explain the comammox selection, we developed an Individual-based Model able to describe Nitrospira and anammox growth in suspended flocs assembled in a dynamic nitrogen and oxygen-limiting environment. All known and hypothesized nitrogen transformations of Nitrospira were considered: ammonia and nitrite oxidation, comammox, nitrate-reducing ammonia oxidation, and anaerobic nitrite-reducing ammonia oxidation. Through bioenergetics analysis, the growth yield associated to each activity was estimated. The other kinetic parameters necessary to describe growth were calibrated according to the reported literature values. Our modeling results suggest that even extremely low oxygen concentrations (~1.0 µM) allow for a proportional growth of anammox versus Nitrospira similar to the one experimentally observed. The strong oxygen limitation was followed by a limitation of ammonia and nitrite, because anammox, without strong competitors, were able to grow faster than Nitrospira depleting the environment in nitrogen. These substrate limitations created an extremely competitive environment that proved to be decisive in the community assembly of Nitrospira and anammox. Additionally, a diversity of metabolic activities for Nitrospira was observed in all tested conditions, which in turn, explained the transient nitrite accumulation observed in aerobic environments with higher ammonia availability.

Nitrification in acidic and alkaline environments

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

Simultaneous anaerobic carbon and nitrogen removal from primary municipal wastewater with hydrogel encapsulated anaerobic digestion sludge and AOA-anammox coated hollow fiber membrane

In this study, a one-stage continuous-flow membrane-hydrogel reactor integrating both partial nitritation-anammox (PN-anammox) and anaerobic digestion (AD) was designed and operated for simultaneous autotrophic nitrogen (N) and anaerobic carbon (C) removal from mainstream municipal wastewater. In the reactor, a synthetic biofilm consisting of anammox biomass and pure culture ammonia oxidizing archaea (AOA) were coated onto and maintained on a counter-diffusion hollow fiber membrane to autotrophically remove nitrogen. Anaerobic digestion sludge was encapsulated in hydrogel beads and placed in the reactor to anaerobically remove COD. During the pilot operation at three operating temperature (25, 16 and 10 °C), the membrane-hydrogel reactor demonstrated stable anaerobic COD removal (76.2 ± 15.5 %) and membrane fouling was successfully suppressed allowing a relatively stable PN-anammox process. The reactor demonstrated good nitrogen removal efficiency, with an overall removal efficiency of 95.8 ± 5.0 % for NH₄⁺-N and 78.9 ± 13.2 % for total inorganic nitrogen (TIN) during the entire pilot operation. Reducing the temperature to 10 °C caused a temporary reduction in nitrogen removal performance and abundances of AOA and anammox. However, the reactor and microbes demonstrated the ability to adapt to the low temperature spontaneously with recovered nitrogen removal performance and microbial abundances. Methanogens in hydrogel beads and AOA and anammox on the membrane were observed in the reactor by qPCR and 16S sequencing across all operational temperatures.

Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers

Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km² in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH₄⁺-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.

Phylotype resolved spatial variation and association patterns of planktonic Thaumarchaeota in eastern Chinese marginal seas

The majority of marine ammonia oxidizers belong to Thaumarchaeota, a phylum of Archaea, which is distributed throughout the water column. Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean, but spatial dynamics of the surface-associated lineages are largely unsolved. This study of 120 seawater samples from the eastern Chinese marginal seas identified contrasting distribution and association patterns among thaumarchaeotal phylotypes across different dimensions. Horizontally, Nitrosopumilus-like and Nitrosopelagicus-like phylotypes dominated the surface water (3 m) of the Yellow Sea (YS) and East China Sea (ECS), respectively, along with increased abundance of total free-living Thaumarchaeota in ECS. Similar compositional changes were observed in the surface microlayer. The spatial heterogeneity of particle-attached Thaumarchaeota was less clear in surface microlayers than in surface waters. Vertically, the Nitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS, which led to an increase in the proportion of Thaumarchaeota relative to total prokaryotes. This occurred mainly in the free-living fraction. These results indicate a clear size-fractionated niche partitioning, which is more pronounced at lower depths than in the surface water/surface microlayer. In addition, associations of Thaumarchaeota with other microbial taxa varied between phylotypes and size fractions. Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the Nitrosopelagicus-like phylotype is present in shallow shelf waters.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00169-y.