Genus Nitrospira Research Articles

Achieving stable nitrogen removal through mainstream partial nitrification, anammox and denitrification (SNAD) with a hybrid biofilm-granular reactor.

Simultaneous partial nitrification, anammox, and denitrification (SNAD) process offers a promising method for the effective removal of carbon and nitrogen from wastewater. However, ensuring stability is a challenge. This study investigated operational parameters such as hydraulic retention time (HRT) and biomass retention to stabilize SNAD operation, transitioning from synthetic to anaerobically pre-treated municipal wastewater (APMW) in an upflow hybrid biofilm-granular reactor (UHR). The incorporation of hybrid biomass in the form of biofilms and granules resulted in a significant improvement in ammonium oxidation, increasing the efficiency from 45% to 60%. This outcome underscores the significance of biomass retention as a crucial parameter in achieving optimal performance. Furthermore, extending the HRT resulted in a significant improved nitrogen removal, increasing it from 40% (8h) to 70% (12h), which was attributed to the enhanced specific activities of ammonium-oxidizing bacteria (AOB) and anammox bacteria (AnAOB). Microbial characterization unveiled the emergence of partial denitrifiers (Thauera genus) and the suppression of nitrite-oxidizing bacteria (NOB) (Nitrospira genus) at low aeration rates (0.35 L.min-1.L-1reactor; estimated 0.5 mgDO.L-1). Notably, stable operation persisted throughout the experimental period, primarily due to the consistent nitrite supply from partial nitrification/denitrification. Our findings highlight the potential of innovative hybrid reactor configuration, for achieving stable and efficient SNAD performance in mainstream wastewater treatment.

Effects of pepper–maize intercropping on the physicochemical properties, microbial communities, and metabolites of rhizosphere and bulk soils

BackgroundIntercropping increases land use efficiency and farmland ecological diversity. However, little is understood about whether and how soil biota, metabolites, and nutrients change under interspecific competition among plants. Thus, this study aimed to explore the changes in the physicochemical properties, microbial communities, and metabolites of rhizosphere and bulk soils of pepper monocropping and pepper–maize intercropping systems.ResultsIntercropping significantly increased the contents of available phosphorus (AP) and available potassium (AK), and decreased the pH value, whereas it had little effect on the total nitrogen (TN) and organic matter (OM) in the rhizosphere and bulk soils, compared with those in monocropping pepper. Moreover, the OM content was higher in rhizosphere soil than in bulk soil. The microbial community structures and metabolite profiles also differed between the two systems. The diversity of bacteria and fungi increased in intercropped pepper. The relative abundances of Actinobacteria, Chloroflexi, Cyanobacteria, and Ascomycota were higher while those of Proteobacteria, Planctomycetes, Mucoromycota, and Basidiomycota were significantly lower in the rhizosphere and bulk soils from the intercropping system than in those from the monocropping system. Linear discriminant analysis revealed that the predominant bacteria and fungi in the rhizosphere soil from the intercropping system belonged to the order Sphingomonadales and genera Nitrospira, Phycicoccus and Auricularia, whereas those in the bulk soil from the intercropping system belonged to the phylum Acidobacteria and genera Calocera, Pseudogymnoascus, and Trichosporon. Intercropping promoted the secretion of flavonoids, alkaloids, and nucleotides and their derivatives in the rhizosphere soil and significantly increased the contents of organoheterocyclic compounds in the bulk soil. Furthermore, the AP and AK contents, and pH value had strong positive correlations with bacteria. In addition, co-occurrence network analysis also showed that asebogenin, trachelanthamidine, 5-methyldeoxycytidine, and soil pH were the key factors mediating root-soil-microbe interactions.ConclusionIntercropping can alter microbial community structures and soil metabolite composition in rhizosphere and bulk soils, enhancing soil nutrient contents, enriching soil beneficial microbes and secondary metabolites (flavonoids and alkaloids) of intercropped pepper, and provided a scientific basis for sustainable development in the pepper-maize intercropping system.

Metagenomic Analysis Revealing the Impact of Water Contents on the Composition of Soil Microbial Communities and the Distribution of Major Ecological Functional Genes in Poyang Lake Wetland Soil.

Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland; the results indicate that the three samples have different physicochemical characteristics and their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1 mutually demonstrate prominent roles in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting in that it plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance and their emphatic research value for microbial resistance issues. The results above have preliminarily proved the role of soil microbial communities as indicators predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change.

Comprehensive evaluation of primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia-oxidizing Nitrospira.

Since the discovery of complete ammonia oxidizers (comammox) within the genus Nitrospira, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (amoA) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox Nitrospira or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using in silico analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox Nitrospira. Taken together, our results indicate that few existing comammox amoA primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.IMPORTANCEBacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.

The herbicidal activity of pre-emergence herbicide cinmethylin and its potential risks on soil ecology: pH, enzyme activities and bacterial community

BackgroundThe herbicide cinmethylin, which was originally registered for use in rice fields, has the potential to control grass weeds in wheat fields before the emergence of wheat. However, its herbicidal activity against various troublesome grass weeds that infest wheat fields in China and its relationships with soil pH, soil enzymes and soil bacteria are not well known. Here, the effects of applying cinmethylin on the soil surface were tested on six grass weeds, and its impacts on soil characteristics, including the soil pH, soil enzymes and bacterial community, were evaluated.ResultsAlopecurus aequalis, A. japonicus and A. myosuroides were highly sensitive to cinmethylin, with GR50 values of 78.77, 61.49 and 119.67 g a.i. ha− 1, respectively. The half-lives of cinmethylin at 1-, 10- and 100-fold the recommended rates were estimated at 26.46 − 52.33 d. Cinmethylin significantly increased the soil pH but decreased the activities of soil sucrase and urease. At 10- and 100-fold the recommended rate of cinmethylin, the bacterial abundance and diversity significantly decreased at 30 and 60 days after cinmethylin treatment. Cinmethylin at 100-fold the recommended rates largely promoted bacterial co-occurrence network complexity. Cinmethylin at high concentrations temporarily inhibited the abundance of the Nitrospira genus, as indicated by the copy numbers of the ammonia-oxidising archaea (AOA) amoA and ammonia-oxidising bacteria (AOB) amoA genes. Further analysis revealed that soil pH was negatively related to soil urease, and a significantly positive correlation was detected between soil urease and soil nitrification.ConclusionCollectively, the application of cinmethylin at the recommended field dose had nearly no effect on the soil ecosystem, but its potential risks at high concentrations deserve further attention.

Impact of N loading on Microbial Community Structure and Nitrogen Removal of an Activated Sludge Process with Long SRT for municipal wastewater treatment

Biological nutrient removal process is pivotal in controlling nitrogen and phosphorus from municipal wastewater treatment and reclamation plants in the water environment. The efficiency of municipal wastewater treatment is affected by the fluctuation of influent quality. In this study, the impact of N loading on the removal efficiency and the microbial community structure of activated sludge with long sludge retention time were investigated. The results showed that the effluent NH4+-N and NO2--N concentration were lower than 0.5 mg/L, and the TN removal efficiencies were 79.77% and 65.80%, respectively. The dehydrogenase activity, specific oxygen uptake rate, specific nitrification rate, and specific denitrification rate increased as the N loading increasing. At the phylum level, the most dominant bacterial was affiliated with Proteobacteria in the two systems, accounting for 60.65% and 48.62%, respectively. At the genus level, Acinetobacter, Thauera, and Zoogloea played significant roles in denitrification. The ammonia oxidation bacteria and nitrite-oxidizing bacteria were of the genus Nitrosomonas (r-strategist) and Nitrospira (K-strategist).

Bacterial genera associated with nitrogen cycle in microbial communities of chernozems

BACKGROUND: Reactions associated with the geochemical nitrogen cycle occurring in the soil have a decisive effect on the level of nitrogen availability for green plants. Microorganisms that catalyze them are of interest from the point of view of developing mechanisms for managing soil fertility. In this paper, we focused on bacterial genera associated with nitrogen cycle processes in chernozem soils of the Belgorod Region of Russia. AIM: To determine the list and quantitative ratios of bacterial genera whose representatives are able to participate in the fixation of atmospheric nitrogen, nitrification and denitrification in the chernozems of the forest-steppe zone of the European part of Russia. MATERIALS AND METHODS: Samples of arable and non-arable chernozems of three subtypes were collected in June and August 2022. Microbiological profiling based on high-throughput sequencing of amplicons of V3 and V4 region of the 16S rRNA gene with subsequent computational processing of the results was used in the work. RESULTS: 6 genera of nitrogen-fixing bacteria were found, as well as a group undifferentiated by means of the method used, including genus Rhizobium. 8 genera involved in the first and 5 genera involved in the second stage of nitrification were also found. 7 genera have been found whose representatives are capable of denitrification, without taking into account nitrogen-fixing bacteria, which are also capable of carrying out this process. CONCLUSIONS: Among the bacteria capable of fixing atmospheric nitrogen in the chernozems of the Belgorod region, the genus Bradyrhizobium dominates. Among the nitrifiers performing the first stage of nitrification, Ellin6067 and MND1 from the family Nitrosomonadaceae predominate. The second stage of nitrification is carried out mainly by bacteria of the genus Nitrospira. Of the potential denitrifies, along with nitrogen-fixing genera possessing this ability, representatives of the genera Rubrobacter and Pseudomonas are the most numerous. The study does not claim to give a complete list of organisms that carry out key chemical transformations of nitrogen compounds in chernozems, however, it allows us to name their important participants.

Enhancement the wastewater treatment performance of multistage living machine by underwater lamp

Source separation and decentralized domestic wastewater treatment represent effective strategies to enhance sewage treatment performance and facilitate water reuse economically. The Living Machine (LM) system has gained widespread adoption for decentralized sewage treatment. While underwater light source has been demonstrated to enhance the treatment performance of open aerobic reactors in LM systems, its influence on the treatment efficiency of a fully multistage LM system remains underreported. In this study, an underwater lamp-added LM system (ULLM) with eight reactors was constructed and investigated. The introduction of underwater light source obviously improved the removal capacity of chemical oxygen demand (COD) and NH4+-N, which was 96.1% and 61.6%, respectively. The diversity of algae, zooplankton, and aquatic animals was notably higher in the light-treated reactors than in the control group (CK) without underwater light source, and substantial alteration in the microbial community of the light-treated reactors was observed compared with CK reactors. At the phylum level, Proteobacteria and Nitrospirae enriched in the underwater light-treated reactors, while Bacteroidetes and Actinobacteria exhibited a decrease after light exposure. At the genus level, Nitrospira and Rhodanobacter were enriched in the ULLM system. Importantly, the prevalence of these two dominant genera was sustained until the final operational stage, indicating their potential key roles in enhancing wastewater treatment performance. The addition of underwater light source proves to be an effective strategy for augmenting the treatment efficiency of the multistage living machine systems, resulting in substantial improvements in pollutant removal. These findings contribute valuable insights into optimizing LM systems for decentralized wastewater treatment.

Irons differently modulate bacterial guilds for leading to varied efficiencies in simultaneous nitrification and denitrification (SND) within four aerobic bioreactors

As a novel biological wastewater nitrogen removal technology, simultaneous nitrification and denitrification (SND) has gained increasing attention. Iron, serving as a viable material, has been shown to influence nitrogen removal. However, the precise impact of iron on the SND process and microbiome remains unclear. In this study, bioreactors amended with iron of varying valences were evaluated for total nitrogen (TN) removal efficiencies under aerobic conditions. The acclimated control reactor without iron addition (NCR) exhibited high ammonia nitrogen (AN) removal efficiency (98.9%), but relatively low TN removal (78.6%) due to limited denitrification. The reactor containing zero-valent iron (Fe0R) demonstrated the highest SND rate of 92.3% with enhanced aerobic denitrification, albeit with lower AN removal (84.1%). Significantly lower SND efficiencies were observed in reactors with ferrous (Fe2R, 66.3%) and ferric (Fe3R, 58.2%) iron. Distinct bacterial communities involved in nitrogen metabolisms were detected in these bioreactors. The presence of complete ammonium oxidation (comammox) genus Nitrospira and anammox bacteria Candidatus Brocadia characterized efficient AN removal in NCR. The relatively low abundance of aerobic denitrifiers in NCR hindered denitrification. Fe0R exhibited highly abundant but low-efficiency methanotrophic ammonium oxidizers, Methylomonas and Methyloparacoccus, along with diverse aerobic denitrifiers, resulting in lower AN removal but an efficient SND process. Conversely, the presence of Fe2+/Fe3+ constrained the denitrifying community, contributing to lower TN removal efficiency via inefficient denitrification. Therefore, different valent irons modulated the strength of nitrification and denitrification through the assembly of key microbial communities, providing insight for microbiome modulation in nitrogen-rich wastewater treatment.

Comammox Nitrospira cooperate with anammox bacteria in a partial nitritation–anammox membrane bioreactor treating low-strength ammonium wastewater at high loadings

Research has revealed that comammox Nitrospira and anammox bacteria engage in dynamic interactions in partial nitritation–anammox reactors, where they compete for ammonium and nitrite or comammox Nitrospria supply nitrite to anammox bacteria. However, two gaps in the literature are present: the know-how to manipulate the interactions to foster a stable and symbiotic relationship and the assessment of how effective this partnership is for treating low-strength ammonium wastewater at high hydraulic loads. In this study, we employed a membrane bioreactor designed to treat synthetic ammonium wastewater at a concentration of 60 mg N/L, reaching a peak loading of 0.36 g N/L/day by gradually reducing the hydraulic retention time to 4 hr. Throughout the experiment, the reactor achieved an approximately 80 % nitrogen removal rate through strategically adjusting intermittent aeration at every stage. Notably, the genera Ca. Kuenena, Nitrosomonas, and Nitrospira collectively constituted approximately 40 % of the microbial community. Under superior intermittent aeration conditions, the expression of comammox amoA was consistently higher than that of Nitrospira nxrB and AOB amoA in the biofilm, despite the higher abundance of Nitrosomonas than comammox Nitrospira, implying that the biofilm environment is favorable for fostering cooperation between comammox and anammox bacteria. We then assessed the in situ activity of comammox Nitrospira in the reactor by selectively suppressing Nitrosomonas using 1-octyne, thereby confirming that comammox Nitrospira played the primary role in facilitating the nitritation (33.1 % of input ammonium) rather than complete nitrification (7.3 % of input ammonium). Kinetic analysis revealed a specific ammonia-oxidizing rate 5.3 times higher than the nitrite-oxidizing rate in the genus Nitrospira, underscoring their critical role in supplying nitrite. These findings provide novel insights into the cooperative interplay between comammox Nitrospira and anammox bacteria, potentially reshaping the management of nitrogen cycling in engineered environments, and aiding the development of microbial ecology-driven wastewater treatment technologies.

Effect of linear anionic surfactant (sodium dodecyl sulfate) dosage on nitrogen removal performance of an anammox reactor

AbstractThe impact of sodium dodecyl sulfate (SDS, as model linear anionic surfactant) dosage on overall nitrogen removal performance of anammox reactor alongside its microbial population and sludge properties was investigated. In this study (day 136), an anmmox sequencing batch biofilm reactor was subjected to gradual dosage of SDS from 0 to 20 mg L−1. Intriguingly, results revealed that SDS at ≥7.5 mg L−1 prompted sludge disintegration, evidenced by increased protein and polysaccharide content in the effluent. Nevertheless, reactor's average total nitrogen removal efficiency slightly improved from 83.12% (0 mg L−1) to 86.3% (20 mg L−1). The 16S rRNA gene sequencing revealed that SDS dosing significantly suppressed the unwanted and unavoidable nitrite oxidizing bacteria (NOBs) in the reactor as the abundance of genus Nitrospira declined from 40.68% (day 1) to 19.15% (day 136). The abundance of anammox genus Candidatus Kuenenia significantly improved from 1.86% (day 1) to 40.02% (day 136) as a result of NOB suppression. This study revealed that low concentration of surfactants in wastewater does not affect the anammox bacteria in a biofilm reactor. Furthermore, adding low concentrations of SDS (≥7.5 to 20 mg L−1) to wastewater may effectively suppress notorious NOBs in biofilm‐based anammox systems.

The microbial community, nutrient supply and crop yields differ along a potassium fertilizer gradient under wheat–maize double-cropping systems

Soil microorganisms play critical roles in ecosystem function. However, the relative impact of the potassium (K) fertilizer gradient on the microbial community in wheat-maize double-cropping systems remains unclear. In this long-term field experiment (2008–2019), we researched bacterial and fungal diversity, composition, and community assemblage in the soil along a K fertilizer gradient in the wheat season (K0, no K fertilizer; K1, 45 kg ha−1 K2O; K2, 90 kg ha−1 K2O; K3, 135 kg ha−1 K2O) and in the maize season (K0, no K fertilizer; K1, 150 kg ha−1 K2O; K2, 300 kg ha−1 K2O; K3, 450 kg ha−1 K2O) using bacterial 16S rRNA and fungal internally transcribed spacer (ITS) data. We observed that environmental variables, such as mean annual soil temperature (MAT) and precipitation, available K, ammonium, nitrate, and organic matter, impacted the soil bacterial and fungal communities, and their impacts varied with fertilizer treatments and crop species. Furthermore, the relative abundance of bacteria involved in soil nutrient transformation (phylum Actinobacteria and class Alphaproteobacteria) in the wheat season was significantly increased compared to the maize season, and the optimal K fertilizer dosage (K2 treatment) boosted the relative bacterial abundance of soil nutrient transformation (genus Lactobacillus) and soil denitrification (phylum Proteobacteria) bacteria in the wheat season. The abundance of the soil bacterial community promoting root growth and nutrient absorption (genus Herbaspirillum) in the maize season was improved compared to the wheat season, and the K2 treatment enhanced the bacterial abundance of soil nutrient transformation (genus MND1) and soil nitrogen cycling (genus Nitrospira) genera in the maize season. The results indicated that the bacterial and fungal communities in the double-cropping system exhibited variable sensitivities and assembly mechanisms along a K fertilizer gradient, and microhabitats explained the largest amount of the variation in crop yields, and improved wheat-maize yields by 11.2–22.6 and 9.2–23.8% with K addition, respectively. These modes are shaped contemporaneously by the different meteorological factors and soil nutrient changes in the K fertilizer gradients.

Unveiling the power of COD/N on constructed wetlands in a short-term experiment: Exploring microbiota co-occurrence patterns and assembly dynamics

Constructed wetlands (CWs) are a cost-effective and environmentally friendly wastewater treatment technology. The influent chemical oxygen demand (COD)/nitrogen (N) ratio (CNR) plays a crucial role in microbial activity and purification performance. However, the effects of CNR changes on microbial diversity, interactions, and assembly processes in CWs are not well understood. In this study, we conducted comprehensive mechanistic experiments to investigate the response of CWs to changes in influent CNR, focusing on the effluent, rhizosphere, and substrate microbiota. Our goal is to provide new insights into CW management by integrating microbial ecology and environmental engineering perspectives. We constructed two groups of horizontal subsurface flow constructed wetlands (HFCWs) and set up three influent CNRs to analyse the microbial responses and nutrient removal. The results indicated that increasing influent CNR led to a decrease in microbial α-diversity and niche width. Genera involved in nitrogen removal and denitrification, such as Rhodobacter, Desulfovibrio, and Zoogloea, were enriched under medium/high CNR conditions, resulting in higher nitrate (NO3--N) removal (up to 99 %) than that under lower CNR conditions (<60 %). Environmental factors, including water temperature (WT), pH, and phosphorus (P), along with CNR-induced COD and NO3--N play important roles in microbial succession in HFCWs. The genus Nitrospira, which is involved in nitrification, exhibited a significant negative correlation (p < 0.05) with WT, COD, and P. Co-occurrence network analysis revealed that increasing influent CNR reduced the complexity of the network structure and increased microbial competition. Analysis using null models demonstrated that the microbial community assembly in HFCWs was primarily driven by stochastic processes under increasing influent CNR conditions. Furthermore, HFCWs with more stochastic microbial communities exhibited better denitrification performance (NO3--N removal). Overall, this study enhances our understanding of nutrient removal, microbial co-occurrence, and assembly mechanisms in CWs under varying influent CNRs.

Effect of aeration on low-substrate CANON process

The completely autotrophic nitrogen removal over nitrite (CANON) is a new type of nitrogen removal process developed in recent years. The control of dissolved oxygen (DO) in this process is relatively stringent, especially in low-substrate wastewater treatment. However, the results of studies on the operation of the process in different aeration modes are still controversial, and investigations on biofilm type CANON reactors are limited. In this study, a pilot-scale CANON bioreactor filled with suspended carriers was investigated on the treatment of wastewater at low ammonium concentrations, and the effect of the aeration mode on autotrophic nitrogen removal was evaluated. Seven conditions with various aeration on/off times and DO levels were tested. The results showed that an intermittent aeration with a 20-min/20-min aeration on/off time and DO concentrations of 1.0–1.3 mg/L at the end of the aeration period was appropriate, potentially inhibiting nitrite oxidizing bacteria (NOB) and keeping the total nitrogen (TN) removal rate at a relatively high level of 76.7% ± 2.5%. In the optimal aeration mode, the reactor achieved effluent TN and NH4+-N concentrations of (11.1 ± 3.3) mg/L and (3.6 ± 2.3) mg/L, respectively, with a hydraulic retention time of 12 h and an influent NH4+-N concentration of (48.6 ± 9.4) mg/L at 30.1°C ± 2.2°C. The results of metagenomic sequencing for microorganisms on carriers indicated that the main nitrogen removal bacteria in the reactor were Proteobacteria, Planctomycetes, and Nitrospirae. The NOB genus Nitrospira was completely inhibited by intermittent aeration. Candidatus Kuenenia had strong adaptability to low-concentration wastewater.

An investigation of Nitrospira bacteria in coastal wetlands of China: distribution pattern and related environmental driving factors

Nitrate is mainly converted via aerobic nitrite oxidation during the second step of nitrification, which is catalyzed by nitrite-oxidizing bacteria (NOB) and the recently discovery complete ammonia oxidizers (comammox). Members of the genus Nitrospira are the most diverse and widespread known NOB and comammox. However, the community assembly of Nitrospira in estuary and coastal wetland and the major environmental shaping factors remain understudied. Here in this study, we investigated the geographical distribution pattern of Nitrospira along the large-scale coastal wetlands of China. The results showed that the abundance of Nitrospira ranged from 4.96×106 - 3.88×107 copies/g dry sediment, significantly (more than one order of magnitude) higher than amoA gene of ammonia-oxidizers. The identified Nitrospira belong to Nitrospira lineage IV (50%), lineage I and II. The adaptability of the three lineages to environmental factors (such as temperature, pH, salinity and particle size) are different, which leads to the diversity of its distribution composition in different estuaries. Network analysis showed that the cooperation takes greater portion than competition in the relationship of Nitrospira population. This study revealed the abundance and community composition of Nitrospira bacteria, as well as the major environmental driving factors in coastal wetland ecosystems, which deepens our understanding of the niche separation of Nitrospira with the nitrogen cycling.

Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls

Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.

Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales

Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named “Ca. Nitronereus thalassa”, represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, “Ca. Nitronereus thalassa” harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, “Ca. Nitronereus thalassa” appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.

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.

The ASM2d model with two-step nitrification can better simulate biological nutrient removal systems enriched with complete ammonia oxidizing bacteria (comammox Nitrospira)

The discovery of comammox Nitrospira, a complete ammonia-oxidizing microorganism belonging to the genus Nitrospira, has brought new insights into the nitrification process in wastewater treatment plants (WWTPs). The applicability of Activated Sludge Model No. 2 d with one-step nitrification (ASM2d-OSN) or two-step nitrification (ASM2d-TSN) for the simulation of the biological nutrient removal (BNR) processes of a full-scale WWTP in the presence of comammox Nitrospira was studied. Microbial analysis and kinetic parameter measurements showed comammox Nitrospira was enriched in the BNR system operated under low dissolved oxygen (DO) and long sludge retention time (SRT). The relative abundance of Nitrospira under the conditions of stage I (DO = 0.5 mg/L, SRT = 60 d) was about twice of that under stage II conditions (DO = 4.0 mg/L, SRT = 26 d), and the copy number of the comammox amoA gene for stage I was 33 times higher than that for stage II. Compared to the ASM2d-OSN model, the ASM2d-TSN model simulated the performance of the WWTP under stage I conditions better, and the Theil inequality coefficient values of all the tested water quality parameters were lower than using ASM2d-OSN. These results indicate that an ASM2d model with two-step nitrification is a better choice for the simulation of WWTPs with the presence of comammox.

Ecological distribution and function of comammox Nitrospira in the environment

Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.