Genus Nitrospira Research Articles

Microbial Diversity in the Phyllosphere and Rhizosphere of an Apple Orchard Managed under Prolonged "Natural Farming" Practices.

Microbial diversity in an apple orchard cultivated with natural farming practices for over 30 years was compared with conventionally farmed orchards to analyze differences in disease suppression. In this long-term naturally farmed orchard, major apple diseases were more severe than in conventional orchards but milder than in a short-term natural farming orchard. Among major fungal species in the phyllosphere, we found that Aureobasidium pullulans and Cryptococcus victoriae were significantly less abundant in long-term natural farming, while Cladosporium tenuissimum predominated. However, diversity of fungal species in the phyllosphere was not necessarily the main determinant in the disease suppression observed in natural farming; instead, the maintenance of a balanced, constant selection of fungal species under a suitable predominant species such as C. tenuissimum seemed to be the important factors. Analysis of bacteria in the phyllosphere revealed Pseudomonas graminis, a potential inducer of plant defenses, predominated in long-term natural farming in August. Rhizosphere metagenome analysis showed that Cordyceps and Arthrobotrys, fungal genera are known to include insect- or nematode-infecting species, were found only in long-term natural farming. Among soil bacteria, the genus Nitrospira was most abundant, and its level in long-term natural farming was more than double that in the conventionally farmed orchard.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, “Candidatus Nitrosopumilus”, and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Effects of organic carbon source on the performance and bacterial structure in biofilm processes for source water pretreatment

The operation performance of biofilm system is limited by the oligotrophic quality of source water, especially the bioavailable organics. In this study, two lab-scale biofilm reactors (R1 and R2) feeding different organic carbon sources (OCS) were built up using sediment in drinking water source as bacterial source. Experimental results showed that sediment in biofilm systems enhanced the NH4 +-N removal performance. Using ethanol as OCS was more beneficial to the removal of NH4 +-N with ammonia removal efficiency (ARE) of 87.0 ± 5.4%, which was higher and more stable than that of glucose with ARE of 83.9 ± 13.3%. Organic carbon source changed the bacterial structure in biofilm systems. The dominant phyla in biofilm under ethanol condition were Proteobacteria, Bacteroidetes and Firmicutes with relative abundances (RA) of 29.1%, 32.7% and 22.0%, respectively. The dominant phyla in biofilm exposure to glucose was Proteobacteria with an RA of 63.4%. At genus level, Nitrospira, Lachnospiraceae, Arcobacter and Hyphomicrobium were dominant under ethanol condition (R1) with the total relative abundance of 20.5%. Sphaerotilus was the dominant genus under glucose condition (R2) with RA of 33.72%. These dominant bacteria were basically having the ability for the removal of nitrogen and organic matter.

Coupling Between the Responses of Plants, Soil, and Microorganisms Following Grazing Exclusion in an Overgrazed Grassland.

Grazing exclusion is an effective management practice to restore grassland ecosystem functioning. However, little is known about the role of soil microbial communities in regulating grassland ecosystem functioning during long-term ecosystem restorations. We evaluated the recovery of a degraded semiarid grassland ecosystem in northern China by investigating plant and soil characteristics and the role of soil microbial communities in ecosystem functioning after 22 years of grazing exclusion. Grazing exclusion significantly increased the alpha diversity and changed the community structure of bacteria, but did not significantly affect the alpha diversity or community structure of fungi. The higher abundance of copiotrophic Proteobacteria and Bacteroidetes with grazing exclusion was due to the higher carbon and nutrient concentrations in the soil, whereas the high abundance of Acidobacteria in overgrazed soils was likely an adaptation to the poor environmental conditions. Bacteria of the Sphingomonadaceae family were associated with C cycling under grazing exclusion. Bacteria of the Nitrospiraceae family, and especially of the Nitrospira genus, played an important role in changes to the N cycle under long-term exclusion of grazing. Quantitative PCR further revealed that grazing exclusion significantly increased the abundance of nitrogen fixing bacteria (nifH), ammonia oxidizers (AOA and AOB), and denitrifying bacteria (nirK and nosZ1). Denitrifying enzyme activity (DEA) was positively correlated with abundance of denitrifying bacteria. The increase in DEA under grazing exclusion suggests that the dependence of DEA on the availability of NO3– produced is due to the combined activity of ammonia oxidizers and denitrifiers. Our findings indicate that decades-long grazing exclusion can trigger changes in the soil bacterial diversity and composition, thus modulating the restoration of grassland ecosystem functions, carbon sequestration and soil fertility.

Blended controlled-release nitrogen fertilizer with straw returning improved soil nitrogen availability, soil microbial community, and root morphology of wheat

Microbial activities and nitrogen (N) availability in soil directly affect root morphology and consequently crop yield. These relationships are even more critical at the filling stage of wheat due to the grain formation. The objective of this study was to compare effects of blended controlled-release N fertilizer (CRFS) and conventional urea (BBFS) on soil microflora, soil N content, and root growth of wheat at the filling stage in a field with straw return for seven years. The method of 16 s rRNA and ITS high-throughput sequencing was used to probe soil microbial status, and the in-situ root scanner was used for in-situ observation and monitoring of wheat root morphology during two growing seasons. The results showed that CRFS increased the relative abundance of Penicillium and Aspergillus fungal genera and reduced the operational taxonomic unit of nitrifying bacteria of the genus Nitrospira compared to BBFS treatment. Nitrate, ammonium, total N, and organic matter in soils treated CRFS were 15.8 %, 10 %, 7.5 %, and 11.6 % higher than these in soils treated with BBFS, respectively, while the total root length, root surface area, and root volume from CRFS treatment were 57.6%, 48.8 %, and 54.1 % higher than these from BBFS, respectively. Above-ground growth of wheat showed that CRFS increased plant height by 5.8–12.6 %, net photosynthetic rate by 13.5–22.2 %, N content of stems and spikes by 10.0 % and 64.1 %, respectively compared to BBFS. Wheat yield and economic efficiency were increased by 9.9–46.8 %, 11.6–41.7 %, respectively with CRFS treatments than these with BBFS treatments. Wheat received reduced application rate (2/3) of CRFS had similar availability of N and plant growth as the full rate of BBFS. Therefore, using blended controlled-release N fertilizer is a practically and environmentally feasible approach for wheat production in the straw retuning wheat-corn rotation system.

Evaluation of microbial community shift on the spatial distribution in an innovative anoxic/aerobic device response to performance

Investigating microbial communities will facilitate the evaluation of the applicability of wastewater treating devices. A novel five-section anoxic/aerobic device was proposed and proved its feasibility as the biological unit in bio-ecosystems. Taxonomic diversity and microbial community shift across the sections of this device was investigated in this study. The special structure of this device enabled a gradual change in dissolved oxygen (DO) concentration across different sections. Distinct microbial communities were formed in the different sections. Samples from eight different positions of this device were collected to investigate the microbial community shift via 16S rRNA gene sequencing. Microbial diversity was abundant in all the sections of this device. The phyla Proteobacteria (54.86%), Chloroflexi (8.94%), Acidobacteria (7.72%), Bacteroidetes (5.97%), and Firmicutes (4.31%) were dominant in the anoxic block, whereas the phyla Proteobacteria (45.89%–71.99%), Bacteroidetes (11.88%–21.45%), Nitrospirae (0.57%–23.5%) were dominant in the aerobic block. Ammonia-oxidizing bacteria (genuas Nitrosomonas, 0.63%–8.32%) and nitrite-oxidizing bacteria (genus Nitrospira, 0.57%–14.33%) were abundant in the aerobic block. The shift in microbial communities corresponded with the trend in contaminant removal and DO conditions. The findings of this study revealed that this multi-section device has a diverse microbial community that efficiently removes pollutants. The multi-stage structure of aerobic block is suitable for the nitrification of ammonia in small-scale devices. This device has commercial applications in rural areas where low-strength wastewater needs to be treated.

The pattern of sedimentary bacterial communities varies with latitude within a large eutrophic lake

We investigated the diversity, composition, and assembly processes of sedimentary bacterial communities across Lake Taihu, China, a large, shallow, and eutrophic water body. Amplicon-based 16S rRNA gene high-throughput sequencing identified the composition and phylogenetic structure of the bacterial communities within the 28 collected samples. Diversity analysis revealed that sedimentary bacterial communities demonstrated significant trends with nutrient loading and habitat along latitude. We used network analysis to disentangle the role of keystone taxa in bacterial communities. Most identified keystone species were from the genus Nitrospira (affiliated with Nitrospirae), subphylum Deltaproteobacteria (affiliated with Proteobacteria), subphylum Gammaproteobacteria (affiliated with Proteobacteria), family Rhodocyclaceae (affiliated with Betaproteobacteria), phylum Bacteroidetes, genus Bacillus (affiliated with Firmicutes), and family Anaerolineaceae (affiliated with Chloroflexi) in order of abundance. These keystone taxa play fundamental roles in carbon and nitrogen cycling within Lake Taihu. Phylogenetic structure analysis indicated that the bacterial communities were more phylogenetically clustered than expected by chance and that deterministic processes dominated the assembly of bacterial communities across Lake Taihu. Niche selection was the crucial factor driving the assembly of bacterial communities. This study enhances the understanding of the distribution of sedimentary bacterial communities and their assembly mechanisms across Lake Taihu.

Microbial community response to ciprofloxacin toxicity in sponge membrane bioreactor

This study aims to offer insights into how ciprofloxacin (CIP) impact bacterial community structures in the Sponge-MBR process when CIP is spiked into hospital wastewater. We found that the CIP toxicity decreased richness critical phylotypes such as phylum class ẟ-, β-, ɣ-proteobacteria, and Flavobacteria that co-respond to suppress denitrification and cake fouling to 37% and 28% respectively. Cluster analysis shows that the different community structures were formed under the influence of CIP toxicity. CIP decreased attached growth biomass by 2.3 times while increasing the concentration of permeate nitrate by 3.8 times, greatly affecting TN removal by up to 26%. Ammonia removal was kept stable by inflating the ammonia removal rate (p < 0.003), with the wealthy Nitrospira genus guaranteeing the nitrification activity. In addition, we observed an increasing richness of Chloroflexi and Planctomycetes, which may play a role in fouling reduction in the Sponge-MBR. Therefore, if the amount of antibiotics in hospital wastewater continues to increase, it is so important to extend biomass retention for denitrification recovery.

Ammonium Removal in Aquaponics Indicates Participation of Comammox Nitrospira

Aquaponic systems are sustainable solutions for food production combining fish growth (aquaculture) and production of vegetables (hydroponic) in one recirculating system. In aquaponics, nitrogen-enriched wastewater from fish in the aquaculture serves as fertilizer for the plants in the hydroponics, while the nitrogen-depleted and detoxified water flows back to the aquaculture. To investigate bacterial nitrogen-cycling in such an aquaponic system, measurements of nitrogen species were coupled with time-resolved 16S rRNA gene profiling and the functional capacity of organisms was studied using metagenomics. The aquaponic system was consistently removing ammonia and nitrite below 23 µM and 19 µM, and nitrate to steady-state concentrations of about 0.5 mM. 16S rRNA gene amplicon sequencing of sediments exposed in the pump sump revealed that typical signatures of canonical ammonia-oxidising microorganisms were below detection limit. However, one of the most abundant operational taxonomic units (OTU) was classified as a member of the genus Nitrospira with a relative abundance of 3.8%. For this genus, also genome scaffolds were recovered encoding the only ammonia monooxygenase genes identified in the metagenome. This study indicates that even in highly efficient aquaponic systems, comammox Nitrospira were found to participate in ammonium removal at low steady-state ammonia concentrations.

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.

Weak magnetic field stimulated nitrite oxidizing bacteria and destroyed the SNAD process

Simultaneous partial nitrification, anammox and denitrification (SNAD) process was successfully constructed in a fixed bed reactor. The ammonium and TN removal efficiencies exceeded 90% under the collaboration of ammonium oxidizing bacteria (AOB), anammox and denitrifying bacteria (DNB). However, the well cooperation was interrupted after introducing the weak MF of 3.5 mT, which was reflected directly by the increased nitrite oxidizing bacteria (NOB) activity and decreased AOB, anammox and DNB activities calculated via mass balance. Moreover, drastic microbial community structure changes induced by weak MF were observed. The dominant phylum changed from Proteobacteria (25.6%) to Deferribacteres (35.2%). The weak MF suppressed the growth of AOB (genus Nitrosomanas), anammox (genus Candidatus Brocadia and clone Anammox) and DNB (genus Denitratisoma) while promoted the enrichment of NOB (genus Nitrospira). Moreover, the weakened NH3-NH2OH, NO-N2O and N2O-N2 pathways might explain the deterioration of SNAD process caused by weak MF.

Stress-responses of microbial population and activity in activated sludge under long-term ciprofloxacin exposure

In this study, the effects of ciprofloxacin on activated sludge were evaluated based on the microbial community and metabolic characteristics. The results indicated that the metabolism of chemical oxygen demand (COD) and nitrogen were inhibited with ciprofloxacin at mg/L level compared to the control experiment, and the concentration of ciprofloxacin was slightly decreased. High-throughput sequencing (HTS) results showed that ciprofloxacin greatly shaped the microbial communities in activated sludge, especially for the Nitrospirae phylum and Nitrospira genus. High concentrations of ciprofloxacin stimulated the enrichment of Zoogloea, thus reducing the stability of the activated sludge. Moreover, quinolone resistance proteins in Aeromonas were enriched, which demonstrates their competitive advantage in these enrichment incubations. Finally, the functional profiles were predicted through Tax4Fun, which revealed the adaption to microbes in activated sludge to the ciprofloxacin selective pressure. This work demonstrates the influence of ciprofloxacin on the activated sludge process, and can provide a useful reference for the assessment of the ecological security of ciprofloxacin.

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification

The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named “Candidatus Nitrospira kreftii”, and performed a detailed genomic and physiological characterization. The complete genome of “Ca. N. kreftii” allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of “Ca. N. kreftii” indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant.

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7–78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3–12.8 g salt/l), highly alkaline (pH 8.9–10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils.

In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.

Evaluating responses of nitrification and denitrification to the co-selective pressure of divalent zinc and tetracycline based on resistance genes changes

The responses of nitrification and denitrification to the divalent zinc (Zn(II)) and tetracycline (TC) co-selective pressure were evaluated in a sequencing batch reactor (SBR). The removal rates of organics and nitrogen, nitrifying and denitrifying enzymatic activity, and microbial diversity and richness at the Zn(II) and TC co-selective pressure were higher than those at the alone Zn(II) selective pressure, while were lower than those at the individual TC selective pressure. The Zn(II) and TC co-selective pressure induced the TC resistance genes abundance increase and the Zn(II) resistance genes levels decrease, and enhanced bacterial enzymatic modification resistance to TC and bacterial outer membrane resistance to Zn(II). The network analysis showed that the genera Nitrospira and Nitrosomonas of nitrifiers and the genera Ferruginibacter, Dechloromonas, Acidovorax, Rhodobacter, Thauera, Cloacibacterium, Zoogloea and Flavobacterium of denitrifiers were the potential hosts of antibiotics resistance genes (ARGs) and/or heavy metals resistance genes (HMRGs).

Contribution of influent rivers affected by different types of pollution to the changes of benthic microbial community structure in a large lake.

As a microbial group in watershed ecosystems, the bacterial community is a sensitive indicator of external environmental fluctuations. However, the effects of different sources of exogenous pollution on the diversity and structure of bacterial communities in inflow rivers and lakes have not been studied in depth. In this study, we used 16S rRNA gene sequencing technology to study the diversity and composition of bacterial communities in rivers affected by different types of pollution. The results showed that the composition of the bacterial communities in rivers with different exogenous pollution sources was different. For example, the genus Arenimonas, which belongs to the Gamma-proteobacteria, is extensively enriched in IDPR (industrially and domestically polluted rivers) and ADPR (agriculturally and domestically polluted rivers) (KW, p<0.05), while the genus Micromonospora is a more unique genus found in APR (agriculturally polluted rivers). When exploring the topology and classification characteristics of river microbial symbiosis models, it was found that the bacterial community symbiosis network is divided into six modules under different exogenous pollution regimes, and the nodes in the different modules perform different functions, such as the IDPR-dominated module I. In the network, the relatively abundant the genus Flavobacterium and the genus Nitrospira are the key factors driving the nitrogen cycle in the watershed where the samples were collected. In addition, our research indicates that communities in lake environments may be more susceptible to disturbances of various physiological or functional redundancies, thus retaining their original community structure. Overall, this study emphasizes that adaptive changes in the bacterial community structure of the sediments in the catchment and the occurrence of interactions are responses to different exogenous pollution sources.

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.