Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations

Density-Based Separation of Microbial Functional Groups in Activated Sludge

Mechanistic understanding of how activated sludge (AS) solids density influences wastewater treatment processing is limited. Because microbial groups often generate and store intracellular inclusions during certain metabolic processes, it is hypothesized that some microorganisms, like polyphosphate-accumulating organisms (PAOs), would have higher biomass densities. The present study developed a density-based separation approach and applied it to suspended growth AS in two full-scale domestic water resource recovery facilities (WRRFs). Incorporating quantitative real-time PCR (qPCR) and fluorescence in situ hybridization (FISH) analyses, the research demonstrated the effectiveness of density-based separation in enriching key microbial functional groups, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and PAOs, by up to 90-fold in target biomass fractions. It was observed that WRRF process functionalities have significant influence on density-based enrichment, such that maximum enrichments were achieved in the sludge fraction denser than 1.036 g/cm³ for the enhanced biological phosphorus removal (EBPR) facility and in the sludge fraction lighter than 1.030 g/cm³ for the non-EBPR facility. Our results provide important information on the relationship between biomass density and enrichment of microbial functional groups in AS, contributing to future designs of enhanced biological treatment processes for improved AS settleability and performance.

Characterizing community dynamics and exploring bacterial assemblages in two activated sludge systems

Bacterial communities in the activated sludge (AS) determine the wastewater treatment performance in the municipal wastewater treatment plants (WWTPs). Aiming at identifying the affecting factors and the variation patterns of the bacterial assemblages in AS, a 2-year time-series AS samples were collected from two separated WWTPs and metagenomic sequencing was conducted. Obvious seasonal shift and succession of the bacterial community were observed in both WWTPs on the genus and species levels, especially for the persistent taxa, implying that temperature was a decisive factor for maintaining bacterial assemblage patterns in long-term period. Taxa abundance distribution (TAD) concerning occurrence frequency and average abundance were found fitting for exponential formulations, and the approximately equal total abundance of persistent taxa suggested that stable and high abundance (~ 90%) of core functional bacterial groups would help to maintain wastewater treatment performance. Drastic changes of environmental factors were found causing temporally significant bacterial structure variation, while the innate correlations between bacterial species could recover the community gradually and maintain relative stability of the AS system. Delayed correlations between environmental factors and abundant (persistent or intermittent) bacterial species were observed widely, while synchronous biotic interactions were identified more frequently. Besides, bacterial species with similar functions were prone to cluster together and shared the same seasonal variation pattern, implicating that the cooperation of functional correlated taxa played the most dominant role in shaping the bacterial assemblages. Furthermore, rare bacterial groups were to be explored for removing emerging pollutants with lower concentrations. The results of this study would assist dealing with operational defect and optimize the treatment system in WWTPs.

Immobilizing partial denitrification biomass and redox mediators to integrate with the anammox process for nitrogen removal

In this study, immobilizing partial denitrification biomass and redox mediators to integrate with the anammox process for nitrogen removal was investigated. Three redox mediators (RMs), namely, 2-methyl-1,4-naphthoquinone (ME), anthraquinone (AQ) and 1-dichloroanthraquinone (1-AQ) were catalyzed to reduce nitrate to only nitrite by denitrification to integrate with the anammox process for nitrogen removal. First, our experimental results showed that there were 35.8, 42.2 and 53.0 mg-N L⁻¹ nitrite accumulation values with the addition of ME, AQ and 1-AQ, respectively, at the dose of 75 µM by the denitrification process at C/N = 2, which were 25.6%, 48.2% and 86.1% higher than that of the control without the addition of any RMs. Nitrate reductase activities were higher than that of nitrite reductase affected by RMs, which was the main reason for nitrite accumulation and further maintenance of the anammox process. Second, owing to the stable nitrite production by the partial denitrifying biomass with the addition of 1-AQ, the nitrogen removal rate of the reactor that integrated the partial denitrification and anammox process reached 1788.36 g-N m⁻³ d⁻¹ only using ammonia and nitrate as the influent nitrogen resource in the long-term operation. Third, the 16S rDNA sequencing results demonstrated that Yersinia frederiksenii and Thauera were the primary groups of the denitrifying biomass, which were considered the dominant partial denitrification species.

In this study, immobilizing partial denitrification biomass and redox mediators to integrate with the anammox process for nitrogen removal was investigated.

Biogas upgrading with hydrogenotrophic methanogenic biofilms

Hydrogen produced from periodic excess of electrical energy may be added to biogas reactors where it is converted to CH₄ that can be utilized in the existing energy grid. The major challenge with this technology is gas-to-liquid mass transfer limitation. The microbial conversions in reactors designed for hydrogenotrophic methanogenesis were studied with microsensors for H₂, pH, and CO₂. The H₂ consumption potential was dependent on the CO₂ concentration, but could partially recover after CO₂ depletion. Reactors with 3-dimensional biofilm carrier material and a large gas headspace allowed for a methanogenic biofilm in direct contact with the gas phase. A high density of Methanoculleus sp. in the biofilm mediated a high rate of CH₄ production, and it was calculated that a reactor filled with 75% carrier material could mediate a biogas upgrading from 50 to 95% CH₄ within 24 h when an equivalent amount of H₂ was added.

High-rate nitrification of saline wastewaters using fixed-bed reactors

Fixed-bed reactor (FBR) is a promising technology for realising robust high-rate nitrification. Only a few studies have investigated the effect of salinity on these systems. In this research work, the effect of gradual stepwise increase in chloride concentration (NaCl content) on the performance of high-rate nitrifying FBRs was studied at loading rates of about 1 kg NH₄⁺-N∙m^-3∙d^-1 at 25 °C. Two lab-scale FBRs having stable biofilms (adapted to 4 g Cl^-/L) grown on commercial media - plastic carrier fed with nanofiltration (NF) permeate of a landfill leachate concentrate, and clay beads fed with synthetic saline wastewater, respectively - were operated using up-flow velocities (u) of about 12 and 8 m/h, respectively, for a period of about 100 days, wherein the chloride content of the feed water was increased from 4 to 16 g/L (electrical conductivity: 13-45 mS/cm). On an average, the FBR packed with plastic carriers (u ≈ 12 m/h) offered ammonia removal percentages greater than 97%, whereas the FBR filled with clay beads due to its low bed porosity (and therefore, u ≈ 8 m/h only) gave nitrification efficiencies of about 70% only. The organic compounds contained in the NF permeate were found to temporarily inhibit the nitrifiers (causing nitrite accumulation), whereas the ammonia removed in the clay beads-packed FBR was transformed almost entirely into nitrate. Increase in chloride content did not have any observable detrimental effect on the performance of the reactors.

Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan

Bacteria and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.

High Dissolved Oxygen Selection against Nitrospira Sublineage I in Full-Scale Activated Sludge

A single Nitrospira sublineage I OTU was found to perform nitrite oxidation in full-scale domestic wastewater treatment plants (WWTPs) in the tropics. This taxon had an apparent oxygen affinity constant lower than that of the full-scale domestic activated sludge cohabitating ammonium oxidizing bacteria (AOB) (0.09 ± 0.02 g O₂ m^-3 versus 0.3 ± 0.03 g O₂ m^-3). Thus, nitrite oxidizing bacteria (NOB) may in fact thrive under conditions of low oxygen supply. Low dissolved oxygen (DO) conditions selected for and high aeration inhibited the NOB in a long-term lab-scale reactor. The relative abundance of Nitrospira sublineage I gradually decreased with increasing DO until it was washed out. Nitritation was sustained even after the DO was lowered subsequently. The morphologies of AOB and NOB microcolonies responded to DO levels in accordance with their oxygen affinities. NOB formed densely packed spherical clusters with a low surface area-to-volume ratio compared to the Nitrosomonas-like AOB clusters, which maintained a porous and nonspherical morphology. In conclusion, the effect of oxygen on AOB/NOB population dynamics depends on which OTU predominates given that oxygen affinities are species-specific, and this should be elucidated when devising operating strategies to achieve mainstream partial nitritation.

Sources of anammox granular sludge and their sustainability in treating low-strength wastewater

Anaerobic ammonium oxidation (anammox) has been widely applied in the treatment of high-strength nitrogen wastewaters. However, few engineering practices were reported to treat low-strength nitrogen wastewaters. In this study, three types of anammox granular sludge (GS) were separately collected from the expanded granular sludge bed (EGSB) reactors treating nitrogen wastewaters at high (H-), moderate (M-) and low (L-) nitrogen loading rates (NLRs), and employed for the treatment of low-strength nitrogen wastewater in sequencing batch advanced nitrogen removal (ANR) systems. The ANR system with M-GS (namely M-ANR system) was most useful. At the initial biomass concentration of 2.43 g-VSS·L^-1, cycle length of 8 h and influent total nitrogen (TN) concentration of less than 15 mg·L^-1, the performance data were as follows: effluent TN of less than 1 mg·L^-1, TN removal efficiency of more than 92.8%, the nitrogen removal rate (NRR) of 0.039 kg-N·m^-3·d^-1. The efficient performance lasted as long as 46 cycles, indicating the sustainability of the M-ANR system. The advanced microscopic analysis and metagenomic analysis were applied to reveal the successful but non-permanent treatment by the M-ANR system. The long-time lag between biomass decay and sludge activity decay provided a window period for the good performance of M-ANR system. However, the weak support of oligotrophic habitat for anaerobic ammonium oxidizing bacteria community was doomed to the degradation of anammox GS, resulting in gradual loss of their activities. A periodic addition of fresh M-GS or a periodic rejuvenation cultivation in the eutrophic habitat is necessary to achieve a permanent performance.

A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to Escherichia coli cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.

Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing

Insight to nitrogen transformation and cycling during composting is vital in developing management strategies that improve nitrogen content and quality of the end product. In this study, a positive ventilation device was constructed and used to elucidate nitrogen transformation and microbial community structures during the composting of cow manure and rice straw. Bacterial community successions were analyzed during the composting process by examining the change in their structural dynamics using high-throughput sequencing technique. The results revealed that dominant phyla, included Acidobacter, Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Actinobacteria. Furthermore, a positive strong correlation was observed between the key bacterial communities and nitrogen transformation. Analyses of functional genera, Spearman correlation and Path showed that Thermomonospora_curvata_DSM_43183 followed by Luteimonas and Simiduia, Brevundimonas and Tamlana, Pseudomonas followed by Brevundimonas and Flavobacterium were the key bacterial communities affecting NH₄⁺-N, NO₃^--N, and NO₂^--N transformation, respectively. Thauera followed by Pseudomonas_putida_NBRC_14164 played a dominant role in N₂O transformation.

Towards mainstream anammox: lessons learned from pilot-scale research at WWTP Dokhaven

The aim of this research was to study the biological feasibility of the Partial Nitritation/Anammox (PN/A) technology to remove nitrogen from municipal mainstream wastewaters. During stable process operations at summer temperatures (23.2 ± 1.3°C), the total nitrogen removal rate was 0.223 ± 0.029 kg N (m³d)^-1 while at winter temperatures (13.4 ± 1.1°C) the total nitrogen removal rate was 0.097 ± 0.016 kg N (m³ d)^-1. Nitrite-oxidizing bacteria (NOB) suppression was successfully achieved at the complete temperature range of municipal mainstream wastewater. Despite the presence of NOB as observed in activity tests, their activity could be successfully suppressed due to a relative low dissolved oxygen concentration. An overcapacity of ammonia-oxidizing bacteria and anammox activity was always present. Long-term stability is a focus point for future research, especially in relation to the stability of the biological oxygen demand removing step, preceding the PN/A reactor.

Low Temperature and Neutral pH Define "Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii

Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.

Impact of current density on the function and microbial community structure in electro-bioreactors

The assessment of bacterial communities in wastewater electro-bioreactors has garnered attention to improve efficiency of wastewater treatment plant (WWTP) processes. This study evaluated the effects of applying different current densities on the function and microbial community structure of an electro-bioreactor by measuring nutrient removal efficiency and analyzing 16S rRNA gene high-throughput sequencing. The electro-bioreactors at current density of 3, 5 and 7 A/m² resulted in an enrichment of operational taxonomic units belonging to distinct functional bacterial families such as (Nitrospiraceae: 8.5, 12.5 and 12.6% relative abundance, respectively) and (Rhodocyclaceae: 8.1, 8.8 and 9.7% relative abundance, respectively), leading to efficient N-removal (>98%) and P-removal (>98%) higher than the control bioreactor (9.6 and 5.0%, respectively). Applying different electric currents proved to affect microbial community composition in electro-bioreactors. The results reported here could prove to be valuable for process control, optimization and improving WWTPs design and operation.

Impact of solids residence time on community structure and nutrient dynamics of mixed phototrophic wastewater treatment systems

Suspended growth, mixed community phototrophic wastewater treatment systems (including high-rate algal ponds and photobioreactors) have the potential to achieve biological nitrogen and phosphorus recovery with effluent nutrient concentrations below the current limit-of-technology. In order to achieve reliable and predictive performance, it is necessary to establish a thorough understanding of how design and operational decisions influence the complex community structure governing nutrient recovery in these systems. Solids residence time (SRT), a critical operational parameter governing growth rate, was leveraged as a selective pressure to shape microbial community structure in laboratory-scale photobioreactors fed secondary effluent from a local wastewater treatment plant. In order to decouple the effects of SRT and hydraulic retention time (HRT), nutrient loading was fixed across all experimental conditions and the effect of changing SRT on microbial community structure, diversity, and stability, as well as its impact on nutrient recovery, was characterized. Reactors were operated at distinct SRTs (5, 10, and 15 days) with diurnal lighting over long-term operation (>6 SRTs), and in-depth examination of the eukaryotic and bacterial community structure was performed using amplicon-based sequencing of the 18S and 16S rRNA genes, respectively. In order to better represent the microalgal community structure, this study leveraged improved 18S rRNA gene primers that have been shown to provide a more accurate representation of the wastewater process-relevant algal community members. Long-term operation resulted in distinct eukaryotic communities across SRTs, independent of the relative abundance of Operational Taxonomic Units (OTUs) in the inoculum. The longest SRT (15 days, SRT 15) resulted in a more stable algal community along with stable bacterial nitrification, while the shortest SRT (5 days, SRT 5) resulted in a less stable, more dynamic community. Although SRT was not strongly associated with overall bacterial diversity, the eukaryotic community of SRT 15 was significantly less diverse and less even than SRT 5, with a few dominant OTUs making up a majority of the eukaryotic community structure in the former. Overall, although longer SRTs promote stable bacterial nitrification, short SRTs promote higher eukaryotic diversity, increased functional stability, and better total N removal via biomass assimilation. These results indicate that SRT may be a key factor in not only controlling microalgal community membership, but community diversity and functional stability as well. Ultimately, the efficacy and reliability of NH₄⁺ removal may be in tension with TN removal in mixed phototrophic systems given that lower SRTs may achieve better total N removal (via biomass assimilation) through increased eukaryotic diversity, biomass productivity, and functional stability.

Effect of Selected Stilbenoids on Human Fecal Microbiota

Dietary phenolics or polyphenols are mostly metabolized by the human gut microbiota. These metabolites appear to confer the beneficial health effects attributed to phenolics. Microbial composition affects the type of metabolites produced. Reciprocally, phenolics modulate microbial composition. Understanding this relationship could be used to positively impact health by phenolic supplementation and thus create favorable colonic conditions. This study explored the effect of six stilbenoids (batatasin III, oxyresveratrol, piceatannol, pinostilbene, resveratrol, thunalbene) on the gut microbiota composition. Stilbenoids were anaerobically fermented with fecal bacteria from four donors, samples were collected at 0 and 24 h, and effects on the microbiota were assessed by 16S rRNA gene sequencing. Statistical tests identified affected microbes at three taxonomic levels. Observed microbial composition modulation by stilbenoids included a decrease in the Firmicutes to Bacteroidetes ratio, a decrease in the relative abundance of strains from the genus Clostridium, and effects on the family Lachnospiraceae. A frequently observed effect was a further decrease of the relative abundance when compared to the control. An opposite effect to the control was observed for Faecalibacterium prausnitzii, whose relative abundance increased. Observed effects were more frequently attributed to resveratrol and piceatannol, followed by thunalbene and batatasin III.

Feasible and effective reuse of municipal sludge for vegetation restoration: physiochemical characteristics and microbial diversity

The large volume of municipal sludge causes environmental problems in cities worldwide. In this study, municipal sludge, mixed with construction waste residue, was used as substrate to plant Ailanthus altissima. The growth of A. altissima, the substrate characteristics, and substrate microbial diversity were measured to investigate potential recycling and reusing pathways of municipal sludge. The obtained results showed that compared to garden soil, the mixed substrate was weakly alkaline, and had higher nutrient contents, which is beneficial for A. altissima, and results in better growth in mixed substrate. Although the contents of the main heavy metals in the mixed substrate were significantly higher than in garden soil, the values met the criterion of Class II soil in the Environmental Quality Standard for the Soils of China (GB15618-1995). Different substrates showed a variety of microbial diversities. Proteobacteria was the top microbial phylum in all samples, and higher relative abundances were found in samples containing municipal sludge. After growing A. altissima, the relative abundances of Acidobacteria and Gemmatimonadetes increased in the mixed substrate. Therefore, addition of construction waste residue and growth of A. altissima caused a difference. The microbial communities in the mixed substrate with A. altissima are both plant friendly and environmentally friendly. These results suggest this mixed substrate as a potentially feasible and effective pathway for the reuse and recycling of municipal sludge for vegetation restoration.

Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae)

Background

The nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported.

Method

In order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments.

Results

Methylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10.

Discussion

Our results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.

Natural continuous influent nitrifier immigration effects on nitrification and the microbial community of activated sludge systems

Two sequencing batch reactors (SBRs) were operated for 100days under aerobic conditions, with one being fed with unsterilized municipal wastewater (USBR), and the other fed with sterilized municipal wastewater (SSBR). Respirometric assays and fluorescence in situ hybridization (FISH) results show that active nitrifiers were present in the unsterilized influent municipal wastewater. The maximum ammonia utilization rate (AUR) and nitrite utilization rate (NUR) of the unsterilized influent were 0.32±0.12mg NH₄⁺-N/(L·hr) and 0.71±0.18mg NO₂^--N/(L·hr). Based on the maximum utilization rates, the estimated seeding intensity for the ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) of the USBR was 0.08g AOB/(g AOB·day) and 0.20g NOB/(g NOB·day) respectively. The fraction of nitrifiers/total bacteria in the influent was 5.35%±2.1%, the dominant AOB was Nitrosomonas spp., Nitrosococcus mobilis hybridizated with Nsm156, and the dominant NOB was Nitrospira hybridizated with Ntspa662. The influent nitrifiers potentially seeded the activated sludge of the bioreactor and hence demonstrated a mitigation of the acclimatization times and instability during start-up and early operation. The AUR and NUR in the USBR was 15% and 13% higher than the SSBR respectively during the stable stage, FISH results showed that nitrifiers population especially the Nitrospira in the USBR was higher than that in the SSBR. These results indicate that the natural continuous immigration of nitrifiers from municipal influent streams may have some repercussions on the modeling and design of bioreactors.

The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge

The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of "Nitrospira lenta" strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of "N. lenta" has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the "N. lenta" core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and "N. defluvii", despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of "N. lenta" provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.

Quorum Sensing and Spoilage Potential of Psychrotrophic Enterobacteriaceae Isolated from Milk

The 16S rDNA of six psychrotrophic Enterobacteriaceae isolated from cold raw milk were sequenced and the isolate 039 was identified as Pantoea sp., isolates 059, 068, and 071 were identified as Hafnia alvei, 067 was identified as Enterobacter sp., and 099 was identified as Aeromonas hydrophila. They presented different spoilage potentials in milk with A. hydrophila 099 being the most deteriorative. Only Pantoea sp. 039 was not able to induce the quorum sensing monitor strains of acyl homoserine lactones (AHLs). The halI gene, which encodes the AHL synthase in H. alvei, was identified in the isolates 059, 067, 068, and 071. After initial sequencing characterization and cloning, this gene showed its function by the heterologous synthesis of N-hexanoyl-DL-homoserine lactone and N-3-oxohexanoyl-L-homoserine lactone in Escherichia coli. In addition to producing AHLs, A. hydrophila 099 produced AI-2 in higher level than the assay's positive control Vibrio harveyi BB120. Therefore, Enterobacteriaceae strains isolated from cooled raw milk produce a rich array of signaling molecules that may influence bacterial traits in the milk environment.

Methane-generating ammonia oxidizing nitrifiers within bio-filters in aquaculture tanks

The discovery of aerobic and anammox bacteria capable of generating methane in bio-filters in freshwater aquaculture systems is generating interest in studies to understand the activity, diversity, distribution and roles of these environmental bacteria. In this study, we used microbial enrichment of bio-filters to assess their effect on water quality. Profiles of ammonia-oxidizing bacterial communities generated using nested PCR methods and DGGE were used to assess the expression of 16S rRNA genes using DNA sequencing. Five dominant ammonia-oxidizing bacterial strains-clones; KB.13, KB.15, KB.16, KB.17 and KB.18-were isolated and identified by phylogenetic analysis as environmental samples closely related to genera Methylobacillus, Stanieria, Nitrosomonas, and Heliorestis. The methyl ammonia-oxidizing microbes thereby found suggest a biochemical pathway involving electron donors and carbon sources, and all strains were functional in freshwater aquaculture systems. Environmental parameters including TN (2.69-20.43); COD (9.34-31.47); NH4+-N (0.44-11.78); NO2-N (0.00-3.67); NO3-N (0.05-1.82), mg/L and DO (1.47-10.31 µg/L) assessed varied in the ranges in the different tanks. Principal component analysis revealed that these water quality parameters significantly influenced the ammonia oxidizing microbial community composition. Temperature rises to about 40 °C significantly affected environmental characteristics-especially DO, TN and NH4+-N-and directly or indirectly affected the microbial communities. Although the nested PCR design was preferred due to its high sensitivity for amplifying specific DNA regions, a more concise method is recommended, as an equimolar mixture of degenerate PCR primer pairs, CTO189f-GC and CTO654r, never amplified only 16S rRNA of ammonia-oxidizing bacteria.

Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture

Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture ( Nitrobacter sp.) and an AOB ( Nitrosomonas europaea)/NOB ( Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.

Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria

Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus "Candidatus Nitrotoga" are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure "Ca Nitrotoga" culture was available. Here we obtained the first "Ca Nitrotoga" isolate from activated sludge. This organism, "Candidatus Nitrotoga fabula," prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous "Ca Nitrotoga" enrichments, which were described as cold-adapted NOB. "Ca Nitrotoga fabula" also showed an unusually high tolerance to nitrite (activity at 30 mM NO2-) and nitrate (up to 25 mM NO3-). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of "Ca Nitrotoga fabula" were reconstructed from the closed genome. "Ca Nitrotoga fabula" possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in "Ca Nitrotoga" and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, "Ca Nitrotoga fabula" uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable "Ca Nitrotoga fabula" to survive nitrite depletion and colonize new niches.IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus "Candidatus Nitrotoga" and performed a detailed physiological and genomic characterization of this organism ("Candidatus Nitrotoga fabula"). Differences between key phenotypic properties of "Ca Nitrotoga fabula" and those of previously enriched "Ca Nitrotoga" members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that "Ca Nitrotoga" are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in "Ca Nitrotoga fabula" expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.

Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools

The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes.

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH₄⁺ and NO₂^- biochemically to form N₂ gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.

Diversity of Ochrobactrum species in food animals, antibiotic resistance phenotypes and polymorphisms in the blaOCH gene

Twenty-six lactose non-fermenting, oxidase, urease and citrate-positive Gram-negative rods, isolated from broiler chickens, pigs and cattle at slaughter, were subjected to the matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and 16S rDNA sequencing for identification. Susceptibility to 14 antimicrobials was determined by the disc diffusion method. Ochrobactrum isolates resistant to third-generation cephalosporins were PCR-screened for the presence of the Ochrobactrum anthropi ampC gene (blaOCH). A 547-bp internal segment of blaOCH in the Ochrobactrum spp isolates was amplified with a newly designed primer set, and a phylogenetic reconstruction based on the complete amino acid sequence of blaOCH obtained from nine Ochrobactrum strains in our collection and 20 O. anthropi available in the GenBank was undertaken. All the Ochrobactrum isolates were resistant to the expanded-spectrum beta-lactams and streptomycin. None of the isolates was resistant to imipenem while 41.7% to 50.0% of them were resistant to fluoroquinolones. The blaOCH gene was detected in 16 (66.7%) and 20 (83.3%) of the 24 Ochrobactrum isolates (O. intermedium/O. tritici species), using primers designed for O. anthropi and the newly designed primer set, respectively. Six blaOCH variants grouped into two divergent clusters were identified. This is the first report of the complete nucleotide sequence of the blaOCH gene in non-antropi Ochrobactrum species.

Microbial pathways for nitrogen loss in an upland soil

The distribution and importance of anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) have been identified in aquatic ecosystems; their role in agricultural upland soils however has not yet been well investigated. In this study, we examined spatio-temporal distributions of anammox and n-damo bacteria in soil profiles (300 cm depth) from an agricultural upland. Monitoring nitrogen (N) conversion activity using isotope-tracing techniques over the course of one year showed denitrification (99.0% N-loss in the winter and 85.0% N-loss in the summer) predominated over anammox (1.0% N-loss in the winter and 14.4% N-loss in the summer) and n-damo (0.6% N-loss in the winter) in surface soils (0-20 cm). While below 20 cm depth, N-loss was dominated by anammox (79.4 ± 14.3% in the winter and 65.4 ± 12.5% in the summer) and n-damo was not detected. Phylogenetic analysis showed that Candidatus Brocadia anammoxidans dominated the anammox community in the surface soil and Candidatus Brocadia fulgida dominated below 20 cm depth. Dissimilatory nitrate reduction to ammonium (DNRA), another nitrite reduction process, was found to play a limited role (4.9 ± 3.5%) in the surface soil compared with denitrification; below 80 cm DNRA rates were much higher than rates of anammox and denitrification. Ammonium oxidation was the main source of NO2- above 80 cm (70.9 ± 23.3%), the key influencing factor on anammox rates, and nitrate reduction (100%) was the main NO2- source below 80 cm. Considering the anammox, n-damo and denitrification rates as a whole in the sampled soil profile, denitrification is still the main N-loss process in upland soils.

Effect of hydraulic retention time on microbial community structure in wastewater treatment electro-bioreactors

The impact of hydraulic retention time (HRT) on the performance and microbial community structure of control and electro-bioreactors was investigated. Control bioreactors and electro-bioreactors were operated at HRT ranging between 6 and 75 hr. The total bacterial counts in addition to the removal efficiency of NH₄⁺ -N, sCOD, and PO₄^3- -P was assessed in all the reactors tested. In addition, Illumina sequencing was performed to determine the microbial communities that developed in these reactors under each HRT condition. Phylogenetic analysis showed that Proteobacteria and Bacteroidetes were the dominant phyla in those reactors. In addition, Nitrospira sp. and Pseudomonas sp. were found to be present in electro-bioreactors with higher relative abundance than in control bioreactors. The results presented here are the first to determine what different microbial communities in wastewater electro-bioreactors due to the application of an electric current under different HRTs.

Integrating anammox with the autotrophic denitrification process via electrochemistry technology

In this study, an autotrophic denitrification process was successfully coupled with anammox to remove the nitrate by-product via electrochemical technology. When the voltage applied to the combined electrode reactor was 1.5 V, the electrode reaction removed nitrate by using the autotrophic denitrification biomass without affecting the anammox biomass. The nitrogen removal efficiency of the combined electrode reactor reached 99.1% without detectable nitrate at an influent NO₂^--N/NH₄⁺-N ratio of 1.5. On day 223, using the model calculations based on reaction equations, 19.7% of total nitrogen was removed via the autotrophic denitrification process, while the majority of nitrogen removal (approximately 79.4%) was attributed to the anammox reaction. Small variations of the population numbers and community structure of artificial bacteria according to electron microscopy predicted that the anammox and autotrophic denitrifying biomasses could coexist in the electrode reactor. Then, 16S rRNA analysis determined that the anammox biomass group was always dominant in mixed flora during continuous cultivation.

Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace

Rice paddies are a significant source of the greenhouse gas methane, which mainly originates from microbial activity. Methane generation in anaerobic systems involves complex interactions of multiple functional microbial groups. Rice paddies installed in hilly terrain are often terraced, providing multiple quasi-independent plots differing primarily in their elevation up a hillside. This represents an excellent study site to explore the influence of environmental factors on microbial communities and interactions among microbial populations. In this study, we used a combination of geochemical analyses, high-throughput amplicon sequencing, and statistical methods to elucidate these interactions. Sulfate, total nitrogen, total iron, and total organic carbon were determined to be critical factors in steering the ecosystem composition and function. Sulfate-reducing bacteria predominated in the rice terrace microbial communities, and Fe(III)-reducing and methane-oxidizing bacteria were abundant as well. Biotic interactions indicated by co-occurrence network analysis suggest mutualistic interactions among these three functional groups. Paddy-scale methane production may be affected by competition among methanogens and sulfate- and Fe(III)-reducing bacteria, or by direct methane oxidation by methane-oxidizing bacteria.

CAPSULE

Microbial communities were characterized in rice terrace. The environment- and microbe-microbe interactions indicated the mitigation of sulfate and Fe on methane production.

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment

Cheese ripening involves the succession of complex microbial communities that are responsible for the organoleptic properties of the final products. The food processing environment can act as a source of natural microbial inoculation, especially in traditionally manufactured products. Austrian Vorarlberger Bergkäse (VB) is an artisanal washed-rind hard cheese produced in the western part of Austria without the addition of external ripening cultures. Here, the composition of the bacterial communities present on VB rinds and on different processing surfaces from two ripening cellars was assessed by near full length 16S rRNA gene amplification, cloning and sequencing. Non-inoculated aerobic bacteria dominated all surfaces in this study. VB production conditions (long ripening time, high salt concentration and low temperatures) favor the growth of psychro- and halotolerant bacteria. Several bacterial groups, such as coryneforms, Staphylococcus equorum and Halomonas dominated VB and were also found on most environmental surfaces. Analysis of OTUs shared between different surfaces suggests that VB rind bacteria are inoculated naturally during the ripening from the processing environment and that cheese surfaces exert selective pressure on these communities, as only those bacteria better adapted flourished on VB rinds. This study analyzed VB processing environment microbiota and its relationship with VB rinds for the first time, elucidating that the processing environment and the cheese microbiota should be considered as microbiologically linked ecosystems with the goal of better defining the events that take place during cheese maturation.

Nachweis von Weissella spp. in Viertelgemelksproben von zwei Milchkühen mit klinischer Mastitis

Dieser Fallbericht beschreibt die Isolierung und Differenzierung von Weissella (W.) spp. aus der Milch zweier Kühe mit klinischer Mastitis (Milchveränderung, Euterschwellung und Zellzahlerhöhung). Viertelgemelksproben von zwei Milchkühen (A und B) aus unterschiedlichen Betrieben wurden an das Milchlabor der Universitätsklinik für Wiederkäuer in Wien zur bakteriologischen Untersuchung eingesendet. Es wurden α-hämolysierende, Katalase-negative, grampositive Kokken in Reinkultur auf Columbia-Blut-Agar isoliert, die sich keiner Lancefield-Gruppe zuordnen ließen. Die biochemische Charakterisierung der Isolate (API® 20 Strep, bioMérieux) ergab Leuconostoc spp. Eine Kontrolluntersuchung des Tieres B innerhalb von 7 Wochen bestätigte diese Ergebnisse. Mittels 16S-rDNA-Sequenzierung wurden die drei Isolate als W. paramesenteroides (Tier A) bzw. W. cibaria (Tier B) identifiziert. Die Analyse durch die Pulsfeldgelelektrophorese (PFGE) ergab ein identisches Smal/Apal-Profil für beide W.-cibaria-Isolate (Kuh B), das sich vom W.-paramesenteroides-Fingerprint der Kuh A unterschied (67% Ähnlichkeit). Diese Untersuchung verweist auf einen möglichen Zusammenhang zwischen dem Nachweis von Weissella spp. und dem Auftreten von Euterentzündungen beim Rind.

A glucanolytic Pseudomonas sp. associated with Smilax bona-nox L. displays strong activity against Phytophthora parasitica

Biological control is an eco-friendly strategy for mitigating and controlling plant diseases with negligible effects on human health and environment. Biocontrol agents are mostly isolated from field crops, and microbiomes associated with wild native plants is underexplored. The main objective of this study was to characterize the bacterial isolates associated with Smilax bona-nox L, a successful wild plant with invasive growth habits. Forty morphologically distinct bacterial isolates were recovered from S. bona-nox. Based on 16S rRNA gene sequencing, these isolates belonged to 12 different genera namely Burkholderia, Pseudomonas, Xenophilus, Stenotrophomonas, Pantoea, Enterobactriaceae, Kosakonia, Microbacterium, Curtobacterium, Caulobacter, Lysinibacillus and Bacillus. Among them, Pseudomonas sp. EA6 and Pseudomonas sp. EA14 displayed the highest potential for inhibition of Phytophthora. Based on sequence analysis of rpoD gene, these isolates revealed a 97% identity with a Pseudomonas fluorescence strain. Bioactivity-driven assays for finding bioactive compounds revealed that crude proteins of Pseudomonas sp. EA6 inhibited mycelial growth of P. parasitica, whereas crude proteins of Pseudomonas sp. EA14 displayed negligible activity. Fractionation and enzymatic analyses revealed that the bioactivity of Pseudomonas sp. EA6 was mostly due to glucanolytic enzymes. Comparison of chromatographic profile and bioactivity assays indicated that the secreted glucanolytic enzymes consisted of β-1,3 and β-1,4 glucanases, which acted together in hydrolyzing Phytophthora cell walls. Since the biological activity of the crude glucanolytic extract was >60-fold higher than the purified β-1,3 glucanase, the glucanolytic enzyme system of Pseudomonas sp. EA6 likely acts synergistically in cell wall hydrolysis of P. parasitica.

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage

Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 10⁴ – 4.9 × 10⁷ archaeal amoA copies ∗ μg DNA^-1, 1.5 × 10³ – 5.3 × 10⁵ AOB 16S rRNA copies ∗ μg DNA^-1, and 1.3 × 10⁶ – 7.7 × 10⁷Nitrospira nxrB copies ∗ μg DNA^-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but were correlated to the relative abundances of several individual OTUs. These findings extend our understanding of the distribution of nitrifying microbes in AMD-impacted systems and provide a platform for further research.

The effects of climate, catchment land use and local factors on the abundance and community structure of sediment ammonia-oxidizing microorganisms in Yangtze lakes

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in regulating the nitrification process in lake ecosystems. However, the relative effects of climate, catchment land use and local conditions on the sediment ammonia-oxidizing communities in lakes remain unclear. In this study, the diversity and abundance of AOA and AOB communities were investigated in ten Yangtze lakes by polymerase chain reaction (PCR), clone library and quantitative PCR techniques. The results showed that the abundances of both AOA and AOB in bare sediments were considerably but not significantly higher than those in vegetated sediments. Interestingly, AOB communities were more sensitive to changes in local environmental factors and vegetation characteristics than were AOA communities. Amongst climate and land use variables, mean annual precipitation, percentage of agriculture and percentage of vegetation were the key determinants of AOB abundance and diversity. Additionally, total organic carbon and chlorophyll-a concentrations in lake water were significantly related to AOB abundance and diversity. The results of the ordination analysis indicated that 81.2 and 84.3% of the cumulative variance for the species composition of AOA and AOB communities could be explained by the climate, land use and local factors. The climate and local environments played important roles in shaping AOA communities, whereas catchment agriculture and water chlorophyll-a concentration were key influencing factors of AOB communities. Our findings suggest that the composition and structure of sediment ammonia-oxidizing communities in Yangtze lakes are strongly influenced by different spatial scale factors.

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium "Candidatus Nitrospira nitrosa"

Nitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as “Candidatus Nitrospira nitrosa,” and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in “Ca. Nitrospira nitrosa” mainly attributed to each strain’s niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of “Ca. Nitrospira nitrosa” and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus.

IMPORTANCENitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

Author Video: An author video summary of this article is available.

AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome

BACKGROUND

Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited.

METHODS

Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons.

RESULTS

We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype.

CONCLUSION

Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.

Visualizing the dental biofilm matrix by means of fluorescence lectin-binding analysis

The extracellular matrix is a poorly studied, yet important component of dental biofilms. Fluorescence lectin-binding analysis (FLBA) is a powerful tool to characterize glycoconjugates in the biofilm matrix. This study aimed to systematically investigate the ability of 75 fluorescently labeled lectins to visualize and quantify extracellular glycoconjugates in dental biofilms. Lectin binding was screened on pooled supragingival biofilm samples collected from 76 subjects using confocal microscopy. FLBA was then performed with 10 selected lectins on biofilms grown in situ for 48 h in the absence of sucrose. For five lectins that proved particularly suitable, stained biovolumes were quantified and correlated to the bacterial composition of the biofilms. Additionally, combinations of up to three differently labeled lectins were tested. Of the 10 lectins, five bound particularly well in 48-h-biofilms: Aleuria aurantia (AAL), Calystega sepiem (Calsepa), Lycopersicon esculentum (LEA), Morniga-G (MNA-G) and Helix pomatia (HPA). No significant correlation between the binding of specific lectins and bacterial composition was found. Fluorescently labeled lectins enable the visualization of glycoconjugates in the dental biofilm matrix. The characterization and quantification of glycoconjugates in dental biofilms require a combination of several lectins. For 48-h-biofilms grown in absence of sucrose, AAL, Calsepa, HPA, LEA, and MNA-G are recommendable.

Reduction of greenhouse gases emissions during anoxic wastewater treatment by strengthening nitrite-dependent anaerobic methane oxidation process

Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered process performed by NC10 phylum, which plays an important role in greenhouse gases (GHG) reduction. In this study, co-existence of n-damo bacteria and methanogens was successfully achieved by using upflow anaerobic sludge blanket (UASB) reactor. Reactor with inorganic carbon source (CO₂/H₂) showed the highest abundance of n-damo bacteria and the highest n-damo potential activity, resulted in its highest nitrogen removal rate. Significant reduction in GHG was obtained after introduction of n-damo process, especially for N₂O. Furthermore, GHG emissions decreased with the increase of n-damo bacteria abundance. Community structure analysis found carbon source could influence the diversity of n-damo bacteria indirectly. And phylogenetic analysis showed that all the obtained sequences were assigned to group B, mainly due to in situ production and consumption of CH₄.