Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding

COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4+ to NO3- alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.

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.

Effects of different aeration strategies and ammonia-nitrogen loads on nitrification performance and microbial community succession of mangrove constructed wetlands for saline wastewater treatment

In highly salinized environments, nitrification is the process that limits the rate of nitrogen transformation and removal. Therefore, this study concentrated on the impacts of different aeration strategies and NH4+-N loads on the nitrification performance of mangrove constructed wetlands (CWs), as well as investigating the succession mechanism of ammonia-oxidizing microorganisms (AOMs). The results showed that both the CW with continuous aeration (CA-CW) and intermittent aeration (IA-CW) achieved a nitrification efficiency of more than 98% under an NH4+-N loading of 1.25-4.7 g/(m2·d). However, the total nitrogen removal rates of IA-CW under low and high ammonia-nitrogen loads (LAL, 20.09 ± 4.4% and HAL, 8.77 ± 1.35%, respectively) were higher than those of CA-CW (16.11 ± 4.7% and 3.32 ± 2.3%, respectively), especially under HAL (p < 0.05). Pearson correlation analysis showed that under different operating conditions, the differential secretion of Kandelia candel rhizosphere organic matter had a certain regulatory effect on nitrification and denitrification groups such as Candidatus Nitrocosmicus, Nitrancea, Truepera, Pontibacter, Halomonas, and Sulfurovum in the wetland root layer. The quantitative polymerase chain reaction revealed that the NH4+-N load rate was the primary factor driving the succession of the AOMs, with different aeration strategies exacerbating this process. Overall, this study revealed that the dominant AOMs in mangrove CWs could be significantly altered by regulating the aeration modes and pollution loads to adjust the rhizosphere organic matter in situ, thereby resulting in more efficient nitrification.

Effects of straw returning combined with earthworm addition on nitrification and ammonia oxidizers in paddy soil

Introduction

Soil ammonia oxidation, which acts as the first and rate-limiting step of nitrification, is driven by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox, amoA gene of clade-A and clade-B). Straw returning, widely used ecological technology in China, is an effective measure for promoting straw decomposition and soil nutrient cycling when combined with earthworm addition. However, the effects of straw returning combined with earthworm addition on soil ammonia oxidizers remain poorly understood.

Methods

A 2-year plot experiment was conducted with 5 treatments: no fertilizer (CK); regular fertilization (RT); straw returning (SR); earthworm addition (W); straw returning + earthworm addition (SRW). The AOA, AOB, comammox clade-A and clade-B community microbial diversities and structures were investigated by high-throughput sequencing.

Results

The results showed that (1) compared to RT treatment, W, SR, and SRW treatments all significantly increased the richness of AOA and comammox clade-A and clade-B (p < 0.05), and the richness of AOB was only significantly promoted by SRW treatment (p < 0.05). However, only SRW had a higher comammox clade-B diversity index than RT. (2) The ammonia oxidizer community structures were altered by both straw returning and earthworm addition. Soil NH4 +-N was the critical environmental driver for altering the ammonia oxidizer community structure. (3) Compared with RT treatment, the soil potential nitrification rate (PNR) of W and SRW treatments increased by 1.19 and 1.20 times, respectively. The PNR was significantly positively correlated with AOB abundance (path coefficient = 0.712, p < 0.05) and negatively correlated with clade-B abundance (path coefficient = -0.106, p < 0.05).

Discussion

This study provides scientific support for the application of straw returning combined with earthworm addition to improve soil nitrification with respect to soil ammonia-oxidizing microorganisms.

PM2.5 drives bacterial functions for carbon, nitrogen, and sulfur cycles in the atmosphere

Airborne bacteria may absorb the substance from the atmospheric particles and play a role in biogeochemical cycling. However, these studies focused on a few culturable bacteria and the samples were usually collected from one site. The metabolic potential of a majority of airborne bacteria on a regional scale and their driving factors remain unknown. In this study, we collected particulates with aerodynamic diameter ≤2.5 μm (PM_2.5) from 8 cities that represent different regions across China and analyzed the samples via high-throughput sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) analysis, and functional database prediction. Based on the FAPROTAX database, 326 (80.69%), 191 (47.28%) and 45 (11.14%) bacterial genera are possible to conduct the pathways of carbon, nitrogen, and sulfur cycles, respectively. The pathway analysis indicated that airborne bacteria may lead to the decrease in organic carbon while the increase in ammonium and sulfate in PM_2.5 samples, all of which are the important components of PM_2.5. Among the 19 environmental factors studied including air pollutants, meteorological factors, and geographical conditions, PM_2.5 concentration manifested the strongest correlations with the functional genes for the transformation of ammonium and sulfate. Moreover, the PM_2.5 concentration rather than the sampling site will drive the distribution of functional genera. Thus, a bi-directional relationship between PM_2.5 and bacterial metabolism is suggested. Our findings shed light on the potential bacterial pathway for the biogeochemical cycling in the atmosphere and the important role of PM_2.5, offering a new perspective for atmospheric ecology and pollution control.

Comparison of Bacterial Community Structure in PM2.5 within Broiler Houses under Different Rearing Systems in China

Background: In intensive poultry farming, high concentrations of indoor particulate matter (PM) impact production performance and welfare. In this study, PM2.5 level and bacterial community diversity were investigated in a multilayer cage house rearing system (CH) and a net flooring house rearing system (FH) during different growth stages to clarify the effects of the rearing systems on the diversity of airborne bacteria and help improve health management. Methods: The IC and high-throughput sequencing were used for ion composition and bacterial diversity analysis of PM2.5 collected from CH and FH. Results: The concentrations of NH3, CO2 and PM2.5 in CH were significantly lower than FH (p < 0.001) in both middle and late rearing stages. PM concentrations gradually increased with broiler growth only in FH. The water-soluble ions of PM2.5 samples had no significant difference between the two systems (p > 0.05). Firmicutes, Actinobacteria and Proteobacteria were the most abundant phyla in both the atmosphere and the broiler houses, but the composition was significantly different. The bacterial community in the broiler houses had strong correlations with temperature, humidity and PM of extremely high concentrations. Ions had stronger correlations with microbial community structure. Conclusions: The superiority of CH in environmental control over FH indicates that improved techniques in environmental control and breeding management can greatly reduce farming air pollution and improve the health management of broiler houses.

High time-resolved characterization of airborne microbial community during a typical haze pollution process

Variations of bioaerosol characteristics during the process of haze pollution have rarely been explored. In this study, high time-resolved variations of the community structures of bacteria, fungi, and ammonia-oxidizing microorganisms (AOMs) were assessed during a typical haze pollution process. The impacts of meteorological factors, water-soluble inorganic ions (WSII), and organic dicarboxylic acids (DCA) on the airborne microbial community were systematically evaluated. The results showed that the bacterial community varied greatly during the formation stages of haze pollution, and tended to stabilize with the further development of haze pollution. Nevertheless, variations of the fungal community lasted throughout the whole haze pollution process. Furthermore, Nitrososphaera absolutely dominated the ammonia-oxidizing archaea (AOA) and declined as PM_2.5 burst. Network analysis identified relatively weak interactions and co-occurrence patterns between dominant fungal genera. Importantly, dust source ions and PM_2.5 acidity exerted the most significant impacts on bacterial and fungal communities. These results identify the high time-resolved variations of airborne microbial communities during the formation and development of haze pollution process, and provide valuable data to better understand the interaction between bioaerosols and haze pollution.

Efficient Nitrification and Low-Level N2O Emission in a Weakly Acidic Bioreactor at Low Dissolved-Oxygen Levels Are Due to Comammox

Nitrification is an essential process for nutrient removal from wastewater and an important emission source of nitrous oxide (N2O), which is a powerful greenhouse gas and a dominant ozone-depleting substance. In this study, nitrification and N2O emissions were tested in two weakly acidic (pH 6.3 to 6.8) reactors: one with dissolved oxygen (DO) at over 2.0 mg/liter and the other with DO at approximately 0.5 mg/liter. Efficient nitrification was achieved in both reactors. Compared to that in the high-DO reactor, N2O emission in the low-DO reactor decreased slightly, by 20%, and had insignificant correlation with the fluctuations of DO (P = 0.935) and nitrite (P = 0.713), indicating that N2O might not be produced mainly via nitrifier denitrification. Based on quantitative PCR (qPCR), quantitative fluorescent in situ hybridization (qFISH), and functional gene amplicon and metagenome sequencing, it was found that complete ammonia oxidizers (comammox), i.e., Nitrospira organisms, significantly outnumbered canonical ammonia-oxidizing bacteria (AOB) in both weakly acidic reactors, especially in the low-DO reactor with the comammox/AOB amoA gene ratio increasing from 6.6 to 17.1. Therefore, it was speculated that the enriched comammox was the primary cause for the slightly decreased N2O emission under long-term low DO in the weakly acidic reactor. This study demonstrated that the comammox Nitrospira can survive well under the weakly acidic and low-DO conditions, implying that achieving efficient nitrification with low N2O emission as well as low energy and alkalinity consumption is feasible for wastewater treatment.IMPORTANCE Nitrification in wastewater treatment is an important process for eutrophication control and an emission source for the greenhouse gas N2O. The nitrifying process is usually operated at a slightly alkaline pH and high DO (>2 mg/liter) to ensure efficient nitrification. However, it consumes a large amount of energy and chemicals, especially for wastewater without sufficient alkalinity. This paper demonstrates that comammox can adapt well to the weakly acidic and low-DO bioreactors, with a result of efficient nitrification and low N2O emission. These findings indicate that comammox organisms are significant for sustainable wastewater treatment, which provides an opportunity to achieve efficient nitrification with low N2O production as well as low energy and chemical consumption simultaneously.

Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants

The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.

Efficient nitrification and low N2O emission in a weakly acidic bioreactor at low dissolved oxygen levels are due to comammox

Nitrification is an essential process for nutrient removal from wastewater and an important emission source of nitrous-oxide (N₂O), which is a powerful greenhouse gas and a dominant ozone-depleting substance. In this study, nitrification and N₂O emissions were tested in two weakly acidic (pH = 6.3-6.8) reactors: one with dissolved oxygen (DO) over 2.0 mg/L and the other with DO approximately 0.5 mg/L. Efficient nitrification was achieved in both reactors. Compared to the high-DO reactor, N₂O emission in the low-DO reactor decreased slightly by 20% and had insignificant correlation with the fluctuations of DO (P = 0.935) and nitrite (P = 0.713), indicating that N₂O might not be mainly produced via nitrifier denitrification. Based on qPCR, qFISH, functional gene amplicon and metagenome sequencing, it was found that complete ammonia oxidizer (comammox) Nitrospira significantly outnumbered canonical ammonia-oxidizing bacteria (AOB) in both weakly acidic reactors, especially in the low DO reactor with the comammox/AOB amoA gene ratio increasing from 6.6 to 17.1. Therefore, it was speculated that the enriched comammox was the primary cause for the slightly decreased N₂O emission under long-term low DO in weakly acidic reactor. This study demonstrated that comammox Nitrospira can survive well under the weakly acidic and low-DO conditions, implying that achieving efficient nitrification with low N₂O emission as well as low energy and alkalinity consumption is feasible for wastewater treatment.ImportanceNitrification in wastewater treatment is an important process for eutrophication control and an emission source for greenhouse gas of N₂O. The nitrifying process is usually operated at a slightly alkaline pH and high DO (>2 mg/L) to ensure efficient nitrification. However, it consumes a large amount of energy and chemicals especially for wastewater without sufficient alkalinity. This manuscript demonstrated that comammox can adapt well to the weakly acidic and low-DO bioreactors, with a result of efficient nitrification and low N₂O emission. These findings indicate that comammox are significant for sustainable wastewater treatment, which provides an opportunity to achieve efficient nitrification with low N₂O production as well as low energy and chemical consumption simultaneously.

N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers

Nitrous oxide (N₂O) and NO_y (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO₂)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N₂O and NO_y emissions_. Yet, little is known about HONO and NO₂ production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N₂O and NO_y production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NO_y production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N₂O based on results from NH₂OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH₂OH) and NO transformation enzymatic activities may lead to a buildup of NH₂OH/NO which can abiotically react to N₂O ; iv) collectively confirm restrained N₂O and NO_y emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA

Microorganisms are abundant in the near surface atmosphere and make up a significant fraction of organic aerosols with implications on both human health and ecosystem services. Despite their importance, studies investigating biogeographical patterns of the atmospheric microbiome between urban and suburban areas are limited. Urban and suburban locations (including their microbial communities) vary considerably depending on climate, topography, industrial activities, demographics and other socio-economic factors. Hence, we need more location-specific data to make informed decision affecting air quality, human health, and the implication of a changing climate and policy decisions. The objective of this study was to describe how the atmospheric microbiome varies in composition and function between urban and suburban sites. We used high-throughput sequencing to analyze microbial communities collected at different times from PM_2.5 samples collected by active sampling method (using a pump and an impactor) and dust settling of TSP collected by passive sampling method (no pump and no impactor) from an urban and suburban site. We found diverse communities unique in composition at both sites with equivalent functional potential. Taxonomic composition varied significantly with Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Other phyla in greater relative abundance at the urban site. In contrast, Cyanobacteria, Tenericutes, Fusobacteria, and Deinococcus, were enriched at the suburban site. Community diversity also demonstrated a high degree of temporal variation within site. We identified over one-third of the communities as potentially pathogenic taxa (urban: 47.52% ± 14.40%, suburban: 34.53% ± 14.60%) and determined the majority of organisms come from animal-associated host or are environmental non-specific. Potentially pathogenic taxa and source environments were similar between active- and passive- sampling method results. Our research is novel it adds to the underrepresented set of studies on atmospheric microbial structure and function across land types and is the first to compare suburban and urban atmospheric communities.

Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils

The recent discovery of complete ammonia oxidation (comammox) process in a single organism challenged the division of labor between two functional groups in the classical two-step nitrification model. However, the distribution and activity of comammox bacteria in various environments remain largely unknown. This study presented a large-scale investigation of the geographical distribution, phylogenetic diversity, and activity of comammox Nitrospira in typical agricultural soils. Among the 23 samples harvested across China, comammox Nitrospira clade A was ubiquitously detected at 4.14 × 10⁴-1.65 × 10⁷amoA gene copies/g dry soil, with 90% belonging to the subclade A2. The abundance of comammox Nitrospira clade B was two orders of magnitude lower than clade A. In all samples, comammox Nitrospira were 1-2 orders of magnitude less abundant than canonical nitrifiers, and soils with slightly high pH and C/N tended to enrich more comammox Nitrospira. Unlike canonical nitrifiers, comammox Nitrospira had sustained amoA gene transcription regardless of external ammonia supply, indicating their competitive advantage over other nitrifiers under low-ammonia conditions. When fed with 1 mM ammonium for 15 days, comammox Nitrospira in tested soils were enriched 2.36 times higher than those enriched by the same amount of nitrite, indicating their preference to utilizing ammonia as the substrate. DNA-SIP further confirmed the in situ nitrification activity of comammox Nitrospira. This study provided new insights into the broad distribution and diversity of comammox Nitrospira in agricultural soils, which could potentially play an important role in the microbial nitrogen cycle in soils.

Diversity and abundance of comammox bacteria in the sediments of an urban lake

AIMS

Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia-oxidizing microbe exists in urban lakes and to determine the factors influencing its existence.

METHODS AND RESULTS

This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia-oxidizing micro-organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co-existed with ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 10⁸ , 1·07 × 10⁸ , 3·24 × 10⁷ and 3·21 × 10¹¹ copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria.

CONCLUSIONS

Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

Structural Characteristics and Functional Implications of PM2.5 Bacterial Communities During Fall in Beijing and Shanghai, China

Air pollution characterized by fine particulate matter (PM_2.5) frequently has occurred in China, and has posed threats to human health. The physiochemical characteristics of airborne PM_2.5 have been extensively studied, but its bacterial structures and functions have not yet been well studied. Herein, we focused on the structural characteristics and functional implications of airborne bacteria under different pollution levels in Beijing and Shanghai. The α- and β-diversities showed no obvious difference in two cities (p > 0.05). The dominant phyla Proteobacteria, Firmicutes, and Actinobacteria with total abundance of over 92% were found in all PM_2.5 samples. The results of weighted unifrac non-metric multidimensional scaling (NMDS) suggested that air pollution was no obviously correlated with bacterial community but dispersed disorderly. Furthermore, canonical correlation analysis (CCA) and permutation test indicated that NH4+, SO42-, and wind speed were the key factors that associated with airborne bacterial community structure. Chemical components of particulate matter played more important role in structuring bacterial community than meteorological conditions based on the result of partial CCA. In addition, the annotation of metabolic pathway suggested that the predominant genus Pseudomonas was obviously correlated with disease infections. Several dominant species might contribute to organic degradation, nitrogen cycles, and ice-nuclei activities in environments. Overall, this work enhanced our understanding of functions of airborne bacteria and highlighted their potential role in atmospheric chemical progresses.

More obvious air pollution impacts on variations in bacteria than fungi and their co-occurrences with ammonia-oxidizing microorganisms in PM2.5

Based on long-term systematic sampling, information is currently limited regarding the impacts of different air pollution levels on variations of bacteria, fungi and ammonia-oxidizing microorganisms (AOMs) in fine particulate matter (PM_2.5), especially their interactions. Here, PM_2.5 samples were weekly collected at different air pollution levels in Beijing, China during one-year period. Microbial composition was profiled using Illumina sequencing, and their interactions were further investigated to reveal the hub genera with network analysis. Diversity of bacteria and fungi showed obvious seasonal variations, and the heavy- or severe-pollution levels mainly affected the diversity and composition of bacteria, but not fungi. While, the community structure of both bacteria and fungi was influenced by the combination of air pollution levels and seasons. The most abundant bacterial genera and some genera with highest abundance in heavy- or severe-pollution days were the hub bacteria in PM_2.5. Whereas, only the dominant fungi in light-pollution days in winter were the hub fungi in PM_2.5. The complex positive correlations of bacterial or fungal pathogens would aggravate the air pollution effects on human health, despite of their low relative abundances. Moreover, the strong co-occurrence and co-exclusion patterns of bacteria and fungi in PM_2.5 were identified. Furthermore, the hub environmental factors (e.g., relative humidity and atmospheric pressure) may play central roles in the distributions of bacteria and fungi, including pathogens. Importantly, AOMs showed significant co-occurrence patterns with the main bacterial and fungal genera and potential pathogens, providing possible microbiological evidences for controlling ammonia emissions to effectively reduce PM_2.5 pollution. These results highlighted the more obvious air pollution impacts on bacteria than fungi, and the complex bacterial-fungal interactions, as well as the important roles of AOMs in airborne microbial interactions webs, improving our understanding of bioaerosols in PM_2.5.

The association of PM2.5 with airway innate antimicrobial activities of salivary agglutinin and surfactant protein D

Fine particulate matter ≤2.5 μm (PM_2.5) is a prominent global public health risk factor that can cause respiratory infection by downregulating the amounts of antimicrobial proteins and peptides (AMPs). Both salivary agglutinin (SAG) and surfactant protein D (SPD) are important AMPs in respiratory mucosal fluid, providing protection against airway pathogen invasion and infection by inducing microbial aggregation and enhancing pathogen clearance. However, the relationship between PM_2.5 and these AMPs is unclear. To better understand the relationship between PM_2.5 and airway innate immune defenses, we review the respiratory antimicrobial activities of SAG and SPD, as well as the adverse effects of PM_2.5 on airway innate antimicrobial defense. We speculate there exists a dual effect between PM_2.5 and respiratory antimicrobial activity, which means that PM_2.5 suppresses respiratory antimicrobial activity through downregulating airway AMPs, while airway AMPs accelerate PM_2.5 clearance by inducing PM_2.5 microbial aggregation. We propose further research on the relationship between PM_2.5 and these AMPs.

Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling

The new discovery of complete ammonia oxidizers (comammox), single organisms capable of oxidizing ammonia into nitrate, redefined the traditional view of nitrification. However, little is known about the relative contributions of comammox and other nitrifiers to nitrification, particularly in agricultural soils with long-term intensive input of nutrients. Herein, we investigated the communities of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and comammox Nitrospira in agricultural soils under nutrients input gradient of nitrogen (0-675 kg N ha^-1 year^-1), phosphorus (0-405 kg P₂O₅ ha^-1 year^-1), and potassium (0-675 kg K₂O ha^-1 year^-1) fertilizers for 19 years. The results showed that N and K fertilizers input significantly (P < 0.05) increased the AOB-amoA gene abundance, while AOA were not as sensitive as AOB. The comammox-amoA gene copies were increased in all fertilizer treatments and was significantly correlated (P < 0.05) with the amount of N fertilizer added. Terminal restriction fragment length polymorphism (T-RFLP) combined with clone-library assays of comammox-amoA gene showed that increasing gradient of nutrients input increased the relative abundance of 73 bp T-RF (assigned to Clade A) but decreased the relative abundance of 198 bp T-RF (representing Clade B). Correlation analyses and stepwise linear regression analyses demonstrated that AOB were the dominate contributors to soil potential nitrification, while comammox Nitrospira did not play a significant role (P > 0.05). This study provided insights into the adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations and their relative contributions to potential nitrification in arable soils.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.

A review on airborne microorganisms in particulate matters: Composition, characteristics and influence factors

Airborne microorganisms (AM), vital components of particulate matters (PM), are widespread in the atmosphere. Since some AM have pathogenicity, they can lead to a wide range of diseases in human and other organisms, meanwhile, some AM act as cloud condensation nuclei and ice nuclei which let them can affect the climate. The inherent characteristics of AM play critical roles in many aspects which, in turn, can decide microbial traits. The uncertain factors bring various influences on AM, which make it difficult to elaborate effect trends as whole. Because of the potential roles of AM in environment and potent effects of factors on AM, detailed knowledge of them is of primary significance. This review highlights the issues of composition and characteristics of AM with size-distribution, species diversity, variation and so on, and summarizes the main factors which affect airborne microbial features. This general information is a knowledge base for further thorough researches of AM and relevant aspects. Besides, current knowledge gaps and new perspectives are offered to roundly understand the impacts and application of AM in nature and human health.

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources. By contrast, compared to canonical Nitrospira, comammox Nitrospira harbor a higher diversity of urea transporters and copper homeostasis genes and lack cyanate hydratase genes. Additionally, the two comammox clades differ in their ammonium uptake systems. Contrary to β-AOB, comammox Nitrospira genomes have single copies of the two central ammonia oxidation pathway operons. Similar to ammonia oxidizing archaea and some oligotrophic AOB strains, they lack genes involved in nitric oxide reduction. Furthermore, comammox Nitrospira genomes encode genes that might allow efficient growth at low oxygen concentrations. Regarding the evolutionary history of comammox Nitrospira, our analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from β-AOB to comammox Nitrospira. We postulate that the absence of comammox genes in other sublineage II Nitrospira genomes is the result of subsequent loss.

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve

Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon forest reserve that are probably caused by more than one environmental factors such as rhizosphere and soil depth.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Impacts of particulate matter (PM2.5) on the behavior of freshwater snail Parafossarulus striatulus

Fine particulate (PM2.5) is a severe problem of air pollution in the world. Although many studies were performed on examining effects of PM2.5 on human health, the understanding of PM2.5 influence on aquatic organisms is limited. Due to wet deposition, the pollutants in PM2.5 can enter aquatic ecosystems and affect aquatic organisms. This study tested the hypothesis that PM2.5 will negatively affect the behavior of freshwater snail Parafossarulus striatulus (Benson, 1842). Along with PM2.5, a number of components (Al, Pb, and Zn) that are commonly present in PM2.5 were also tested for their effects on the snail's behavior. The snail behavior was scored using the Behavioral State Score (BSS), ranging from 0 (no movement) to 5 (active locomotion and fully extended body). The result shows that high PM2.5 concentration dose (7.75 mg/L) induced a significant decrease in snails' movement behavior, and such reduced movement. The same behavior was also observed for treatments with chemical components related to PM2.5, including aluminum and acidity (pH 5.0). In contrast, a low concentration of PM2.5 (3.88 mg/L), lead, and zinc did not significantly affect snails' behavior. The results suggest that high PM2.5 deposition in water bodies, associated with acidification and some metals, can have an adverse effect on aquatic organisms.