Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov

Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns

The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.

Systematic evaluation of the impact of standard storage conditions on plasmid conjugation behavior in wastewater samples

Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, -20 °C, -80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at -80 °C maintained conjugation activities in activated sludge more effectively compared to -20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and -20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and -20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants

The development of industrial parks has become an important global trend contributing significantly to economic and industrial growth. However, this growth comes at a cost, as the treatment of multisource industrial wastewater generated in these parks can be difficult owing to its complex composition. Microorganisms play a critical role in pollutant removal during industrial park wastewater treatment. Therefore, our study focused on the microbial communities in five full-scale industrial park wastewater treatment plants (WWTPs) with similar treatment processes and capacities. The results showed that denitrifying bacteria were dominant in almost every process section of all the plants, with heterotrophic denitrification being the main pathway. Moreover, autotrophic sulfur denitrification and methane oxidation denitrification may contribute to total nitrogen (TN) removal. In plants where the influent had low levels of COD and TN, dominant bacteria included oligotrophic microorganisms like Prosthecobacter (2.88 % ~ 10.02 %) and hgcI_clade (2.05 % ~ 9.49 %). Heavy metal metabolizing microorganisms, such as Norank_f__PHOS-HE36 (3.96 % ~ 5.36 %) and Sediminibacterium (1.86 % ~ 5.34 %), were prevalent in oxidation ditch and secondary settling tanks in certain plants. Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed that microbial communities in the regulation and hydrolysis tanks exhibited higher potential activity in the nitrogen (N) and sulfur (S) cycles than those in the oxidation ditch. Sulfate/sulfite reduction was common in most plants, whereas the potential occurrence of sulfide compounds and thiosulfate oxidation tended to be higher in plants with a relatively high sulfate concentration and low COD content in their influent. Our study provides a new understanding of the microbial community in full-scale industrial park WWTPs and highlights the critical role of microorganisms in the treatment of industrial wastewater.

Characterization of microbial communities in seven wetlands with different anthropogenic burden using Next Generation Sequencing in Bogotá, Colombia

Wetlands represent key ecosystems due to their remarkable biodiversity, ecological functions and multiple ecosystem services provided. In Colombia, there are 31,702 wetlands, 13 of which are in Bogotá, capital of the country. Despite the fundamental socioecological support of these aquatic ecosystems, a tremendous loss and degradation of these ecosystems has been observed due to anthropogenic perturbations. Therefore, the aim of this study was to describe the status of seven Bogotá wetlands with variable anthropogenic interventions by measuring organoleptic, physicochemical, and microbiological parameters, using commercial kits, highly sensitive equipment, and next-generation sequencing of the 16S- and 18S-rRNA genes. Our findings describe the status of seven wetlands with different anthropogenic burden in Bogotá-Colombia where physicochemical and microbiology signals of contamination were observed. Additionally, some profiles in the composition of the microbial communities, together with certain physicochemical characteristics, may represent an insight into the environmental dynamics, where Beta Proteobacteria such as Malikia represent a potential keystone in aquatic ecosystems impacted by wastewater effluent discharges; the presence of nitrates and phosphates explain the abundance of bacteria capable of oxidizing these compounds, such as Polynucleobacter. Moreover, the presence of specific prokaryotic and eukaryotic organisms, such as Clostridium, Cryptococcus, Candida, and Naegleria, reported in one or more of the wetlands assessed here, could represent a possible pathogenic risk for human and animal health. This study performed a complete evaluation of seven Bogotá wetlands with different anthropogenic impacts for the first time, and our findings emphasize the importance of maintaining continuous monitoring of these water bodies given their remarkable ecological importance and potential spill-over of several pathogens to humans and animals.

Macromonas nakdongensis sp. nov., Isolated from Freshwater and Characterization of Bacteriophage BK-30P-The First Phage That Infects Genus Macromonas

A Gram-stain-negative, non-motile, non-pigmented, rod-shaped bacterium was isolated from a freshwater sample of Nakdong River in South Korea and designated as strain BK-30T. An analysis of the 16S rRNA gene sequence of strain BK-30T revealed its closest phylogenetic neighbors were members of the genus Macromonas. Specifically, the strain formed a robust clade with Macromonas bipunctata DSM 12705T, sharing 98.4% similarity in their 16S rRNA gene sequences. The average nucleotide identity value between strain BK-30T and M. bipunctata DSM 12705T was 79.8%, and the genome-to-genome distance averaged 21.3%, indicating the representation of a novel genomic species. Strain BK-30T exhibited optimum growth at 30 °C and pH 7.0, in the absence of NaCl. The major respiratory isoprenoid quinone identified was ubiquinone-8 (Q-8). The principal fatty acids detected were C16:1ω7c and/or C16:1ω6c (49.6%), C16:0 (27.5%), and C18:1ω7c and/or C18:1 ω6c (9.2%). The DNA G+C content of the strain was determined to be 67.3 mol%. Based on these data, we propose a novel species within the genus Macromonas, named Macromonas nakdongensis sp. nov., to accommodate the bacterial isolate. Strain BK-30T is designated as the type strain (=KCTC 52161T = JCM 31376T = FBCC-B1). Additionally, we present the isolation and complete genome sequence of a lytic phage infecting strain BK-30T, named BK-30P. This bacteriophage is the first reported to infect Macromonas, leading us to propose the name "Macromonasphage".

Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments

In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams.

The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow

Microbial communities in wastewater treatment plants (WWTPs) play a key role in water purification. Microbial communities of activated sludge (AS) vary extensively based on plant operating technology, influent characteristics and WWTP capacity. In this study we performed 16S rRNA gene profiling of AS at nine large-scale WWTPs responsible for the treatment of municipal sewage from the city of Moscow, Russia. Two plants employed conventional aerobic process, one plant—nitrification/denitrification technology, and six plants were operated with the University of Cape Town (UCT) anaerobic/anoxic/oxic process. Microbial communities were impacted by the technology and dominated by the Proteobacteria, Bacteroidota and Actinobacteriota. WWTPs employing the UCT process enabled efficient removal of not only organic matter, but also nitrogen and phosphorus, consistently with the high content of ammonia-oxidizing Nitrosomonas sp. and phosphate-accumulating bacteria. The latter group was represented by Candidatus Accumulibacter, Tetrasphaera sp. and denitrifiers. Co-occurrence network analysis provided information on key hub microorganisms in AS, which may be targeted for manipulating the AS stability and performance. Comparison of AS communities from WWTPs in Moscow and worldwide revealed that Moscow samples clustered together indicating that influent characteristics, related to social, cultural and environmental factors, could be more important than a plant operating technology.

Long-term effects of three compound probiotics on water quality, growth performances, microbiota distributions and resistance to Aeromonas veronii in crucian carp Carassius auratus gibelio

Probiotics could promote the healthy growth of aquatic animals and have been widely used in aquaculture. However, the influence of high concentration compound probiotics on the aquatic animals has not been reported. In the present study, a compound probiotics was used in high-density culture of crucian carps under the condition of micro-water exchange. During nearly 7-weeks feeding experiment, the aquaculture water quality, growth performances, disease resistance and microbiota distributions of crucian carps were tested. Under the high concentrations of compound probiotics, the content of total ammonia nitrogen and nitrite were finally in a state of dynamic equilibrium. The body length and weight of crucian carps in the experimental group (E) was significantly higher than that in the recirculating group (R). The antioxidant enzymes in the intestines and gills of the E group including SOD, CAT, GSH and MDA, were significantly higher than those in R group. The mortality of crucian carps in E group was significantly lower after the immersion infection of Aeromonas veronii. The addition of compound probiotics significantly increased the number of microorganisms detected in the intestines and gills of crucian carps in E group. The bacteria including Firmicutes, Planctomycetes, Verrucomicrobiota at the phylum level in E group were higher than those in R group. At the genus level, these bacteria (Pirellula, Roseimicrobium, Malikia) were not only higher in E group water, but also significantly higher in the intestines and gills than R group. The results of present study systematically analyzed the impact of high-concentration probiotics on crucian carps breeding, and speculated genus Pirellula, Roseimicrobium, Malikia may be used as aquatic probiotics. The present study will provide a new idea for the green and sustainable development of aquaculture.

Bacterial Diversity of Water and Sediment Samples from Gull Point State Park (West Okoboji, Iowa) Determined Using 16S rRNA Gene Amplicon Sequencing

Gull Point State Park is located on a peninsula on the west shore of West Okoboji Lake (Iowa, USA). It is the primary state park in the Iowa Great Lakes region. Sediment and water samples from three locations at the Gull Point pond were analyzed for their microbial composition.

Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs

Three highly alkaliphilic bacterial strains designated as A1T, H1T and B1T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1T, H1T and B1T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1T, H1T and B1T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1-96.4 %), Macromonas (93.0-93.6 %) and Hydrogenophaga (93.0-96.6 %) in the family Comamonadaceae. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1T, H1T and B1T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA-DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1T=NBRC 111848T=DSM 103917T), Serpentinimonas barnesii sp. nov. (type strain H1T= NBRC 111849T=DSM 103920T) and Serpentinimonas maccroryi sp. nov. (type strain B1T=NBRC 111850T=DSM 103919T) belonging to the family Comamonadaceae. We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.

Wastewater effluents cause microbial community shifts and change trophic status

Widespread wastewater pollution is one of the greatest challenges threatening the sustainable management of rivers globally. Understanding microbial responses to gradients in environmental stressors, such as wastewater pollution, is crucial to identify thresholds of community change and to develop management strategies that protect ecosystem integrity. This study used multiple lines of empirical evidence, including a novel combination of microbial ecotoxicology methods in the laboratory and field to link pressure-stressor-response relationships. Specifically, community-based whole effluent toxicity (WET) testing and environmental genomics were integrated to determine real-world community interactions, shifts and functional change in response to wastewater pollution. Here we show that wastewater effluents above moderate (>10%) concentrations caused consistent significant shifts in bacterial community structure and function. These thresholds of community shifts were also linked to changes in the trophic state of receiving waters in terms of nutrient concentrations. Differences in the community responses along the effluent concentration gradient were primarily driven by two globally relevant bacterial indicator taxa, namely Malikia spp. (Burkholderiales) and hgcI_clade (Frankiales). Species replacement occurred above moderate effluent concentrations with abundances of Malikia spp. increasing, while abundances of hgcI_clade decreased. The responses of Malikia spp. and hgcI_clade matched gene patterns associated with globally important nitrogen cycling pathways, such as denitrification and nitrogen fixation, which linked the core individual taxa to putative function and ecosystem processes, rarely achieved in previous studies. This study has identified potential indicators of change in trophic status and the functional consequences of wastewater pollution. These findings have immediate implications for both the management of environmental stressors and protection of aquatic ecosystems.

Limited carbon sources prevent sulfate remediation in circumneutral abandoned mine drainage

Passive remediation systems (PRS) use both biotic and abiotic processes to precipitate contaminants from abandoned mine drainage (AMD) so that the contaminants do not spread into local watersheds. PRS are efficient at removing heavy metals but sulfate remediation frequently does not occur. To understand the reasons for the lack of sulfate remediation, we studied four PRS that treat circumneutral AMD and one raw mine drainage discharge. Using 16S sequencing analysis, microbial community composition revealed a high relative abundance of bacterial families with sulfur cycling genera. Anaerobic abiotic studies showed that sulfide was quickly geochemically oxidized in the presence of iron hydroxides, leading to a buildup of sulfur intermediates. Supplementation of laboratory grown microbes from the PRS with lactate demonstrated the ability of actively growing microbes to overcome this abiotic sulfide oxidation by increasing the rate of sulfate reduction. Thus, the lack of carbon sources in the PRS contributes to the lack of sulfate remediation. Bacterial community analysis of 16S rRNA gene revealed that while the microbial communities in different parts of the PRS were phylogenetically distinct, the contaminated environments selected for communities that shared similar metabolic capabilities.

Combined impact of organic matter, phosphorus, nitrate, and ammonia nitrogen on the process of blackwater

Blackwater events are frequently reported over the world and become a serious environmental problem. However, the mechanisms of blackwater occurrence are not fully understood yet. This study simulated the process of blackwater with the combined pollution in an orthogonal experiment, which had 4 factors (TOC, TP, NH4+-N, and NO3--N) and 4 levels (None, Low, Middle, and High). Results showed that the process of water condition changes was divided into two parts, which were "exogenous" and "algae-derived" blackwater, and the influence of four different pollutants on the occurrence of the blackwater was ranked as follows: TOC > TP > NO3--N > NH4+-N. With the increase of organic matter addition, the anaerobic condition in water was prolonged and the concentration of Fe2+ had a significant increase. In addition, under the None phosphorus condition, the descent rates of DO and COD in the water were reduced, and the algae bloom was obviously deferred. Moreover, the addition of organic matter or phosphorus changed the microbial community structure and led to different water processes. Particularly, only on the condition of the high content of TOC and phosphorus, the diversity of sulfate-reducing bacteria (e.g., Pseudomonas, Paludibacter, and Bacteroides) increased significantly, which accounted for 51.4%, causing the significant production of S2- in the water. Water's lack of phosphorus showed a low rate of decomposition of organic matter, which might be the result of a considerable increase in the abundance of aerobic Trichococcus and Malikia. This study shows that organic matter and phosphorus have synergistic effect on blackwater occurrence. In the treatment of blackwater, the exogenous pollutant control should reduce the discharge of organic pollutants, and endogenous control should focus on phosphorus abatement and reduce nitrogen control.

Metabarcoding profiling of microbial diversity associated with trout fish farming

Earthy and musty off-flavors are routinely observed in farmed trout worldwide. The microbial association to the production of those off-flavors was previously reported. The current manuscript aimed to catalog the microbial enrichment (eukaryotes and prokaryotes) in semi-intensive aquaculture freshwater sources that might influence the trout aquaculture quality production. The 16S rRNA and ITS metabarcoding analyses were applied on the inflow- and pond-water samples from trout farms previously recorded a malodor fish products and located alongside Moosach and Sempt Rivers in Bavaria province, Germany. The results showed that more than 99% of the detected prokaryotic OTUs (Operational Taxonomic Unit identification) were bacteria as of ~ 75.57% were Proteobacteria, and ~ 14.4% were Bacteroidetes. Meanwhile, 118 out of 233 of the eukaryotic OTUs were known species. Of these, ~ 45% were plant pathogens, and ~ 28% were mushroom/yeasts. Based on the comparative analysis between inflow- and pond-water samples, several pro- and eukaryotic microorganisms that affect the trout aquaculture water quality and industry have been detected, including the malodor-producing microorganisms, e.g., Cyanobacteria and Actinobacteria, along with fish infectious microorganisms, e.g., Chilodonella cyprinid, Metschnikowia bicuspidate. Additionally, the effect of the human- and industrial-related activities around the sampling area on the microbiota of the investigated farms were highlighted.

Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis

The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.

Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter

Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent

To enhance nitrogen removal efficiency, a new electrolysis augmented constructed wetland (E-CW) was applied for nitrogen removal from waste water treatment plant (WWTP) effluent. This work demonstrated that E-CW could remove NO₃^- efficiently (45.5%-83.4%) under low C_COD/N ratio (average 2.29 ± 0.45) with little amount of NH₄⁺ and NO₂^- generation. High throughput 16S rRNA sequence analysis revealed that Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Verrucomicrobia were the dominant phyla in the E-CW. However, abundance of denitrifiers and denitrification genes decreased along with the operation of E-CW. Four functional gene pairs of anammox-amoA, (narG + napA)-(nirK + nirS), (narG + napA)-nosZ and qnorB-nosZ showed positive correlations with each other. Co-occurrence network analysis results indicated that functional guilds of FeOB and FeRB coupled with denitrifiers and contributed to the process of nitrogen removal in the E-CW. Overall, this work illustrated E-CW was a feasible and effective technology for enhancing nitrogen removal, and provided a theoretical basis for better design and operation of E-CW.

Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species

Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.

Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces

The Feast-Famine (FF) process has been frequently used to select polyhydroxyalkanoate (PHA)-accumulating mixed cultures (MCs), but there has been little insight into the ecophysiology of the microbial community during the selection process. In three FF systems with well-defined conditions, synchronized variations in higher-order properties of MCs and complicate microbial community succession mainly including enrichment and elimination of non-top competitors and unexpected turnover of top competitors, were observed. Quantification of PHA-accumulating function genes (phaC) revealed that the top competitors maintained the PHA synthesis by playing consecutive roles when the highly dynamic turnover occurred. Due to its specific physiological characteristics during the PHA-accumulating process, Thauera strain OTU 7 was found to be responsible for the fluctuating SVI, which threatened the robustness of the FF system. This trait was also responsible for its later competitive exclusion by the other PHA-producer, Paracoccus strain OTU 1. Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase. However, neutral processes, likely caused by predation from bacterial phages, also occurred, which led to the unpredictable temporal dynamics of the top competitors.

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams

Through a combined approach using analytical chemistry, real-time quantitative polymerase chain reaction (qPCR), and targeted amplicon sequencing, we studied the impact of wastewater treatment plant effluent sources at six sites on two sampling dates on the chemical and microbial population regimes within the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, Pennsylvania, USA. These water bodies contribute flow to the Schuylkill River, one of the major drinking water sources for Philadelphia, Pennsylvania. Effluent was observed to be a significant source of nutrients, human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources, which we hypothesize is controlled by distance from effluent source. Antecedent moisture conditions were observed to impact overall microbial community diversity, with higher diversity occurring after rainfall. Finally, the efficacy of using a subset of the microbial community including the orders of Bifidobacteriales, Bacteroidales, and Clostridiales to estimate the degree of influence due to sewage and fecal sources was explored and verified.

Correlative Cryogenic Spectromicroscopy to Investigate Selenium Bioreduction Products

Accurate mapping of the composition and structure of minerals and associated biological materials is critical in geomicrobiology and environmental research. Here, we have developed an apparatus that allows the correlation of cryogenic transmission electron microscopy (cryo-TEM) and synchrotron hard X-ray microprobe (SHXM) data sets to precisely determine the distribution, valence state, and structure of selenium in biofilms sampled from a contaminated aquifer near Rifle, CO. Results were replicated in the laboratory via anaerobic selenate-reducing enrichment cultures. 16S rRNA analyses of field-derived biofilm indicated the dominance of Betaproteobacteria from the Comamonadaceae family and uncultivated members of the Simplicispira genus. The major product in field and culture-derived biofilms is ∼25-300 nm red amorphous Se⁰ aggregates of colloidal nanoparticles. Correlative analyses of the cultures provided direct evidence for the microbial dissimilatory reduction of Se(VI) to Se(IV) to Se⁰. Extended X-ray absorption fine-structure spectroscopy showed red amorphous Se⁰ with a first shell Se-Se interatomic distance of 2.339 ± 0.003 Å. Complementary scanning transmission X-ray microscopy revealed that these aggregates are strongly associated with a protein-rich biofilm matrix. These findings have important implications for predicting the stability and mobility of Se bioremediation products and understanding of Se biogeochemical cycling. The approach, involving the correlation of cryo-SHXM and cryo-TEM data sets from the same specimen area, is broadly applicable to biological and environmental samples.

Bio-prospecting Bacterial Diversity of Hot Springs in Northern Himalayan Region of India for Laccases

Bacterial diversity of hot springs of northern Himalayan region of India was studied and explored for laccases, the multicopper enzymes applicable in a large number of industries due to their ability to utilize a wide range of substrates. 220 operational taxonomic units (OTUs) out of 5551 sequence reads for bacterial diversity and 3 OTUs out of 19 sequence reads for Laccase like multicopper oxidases (LMCOs) diversity were generated. Bacteroidetes (74.28%) was the most abundant phylum including genus Paludibacter (66.96%), followed by phylum Proteobacteria (24.53%) including genera Chitinilyticum (7.55%) and Cellvibrio (6.14%). In case of laccase diversity, three LMCO sequences showed affiliation with proteobacteria and one with two domain laccase from uncultivable bacteroidetes. LMCO sequences belonged to H and N families.

Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring

Two closely related thermophilic bacterial strains, designated YIM 73013T and YIM 73008, were isolated from a sediment sample collected from a hot spring in Tibet, western Tibet province, China. The taxonomic positions of the two isolates were investigated using a polyphasic approach. The novel isolates were Gram-stain-negative, aerobic, short-rod-shaped and motile by means of a polar flagellum. They were oxidase- and catalase-positive and were able to grow at 30-55 °C (optimum, 37-45 °C), at pH 6.0-8.0 (optimum, pH 7.0) and with NaCl tolerance up to 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 73013T and YIM 73008 formed a distinct lineage with respect to closely related genera in the family Comamonadaceae and shared highest 16S rRNA gene sequences similarities with Acidovorax caeni R-24608T (96.3 and 96.4 %, respectively). The respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids observed were C17 : 1ω6c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The genomic DNA G+C contents of strains YIM 73013T and YIM 73008 were 68.7 and 68.3 mol%, respectively. Based on the morphological, phylogenetic and chemotaxonomic results, the two isolates represent a novel species in a new genus, for which the name Tibeticola sediminis gen. nov., sp. nov. is proposed. The type strain of Tibeticola sediminis is YIM 73013T (=DSM 101684T=KCTC 42873T).

A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems

Understanding the microbiology of phosphorus (P) removal is considered essential to knowledge-based optimization of enhanced biological P removal (EBPR) systems. Biological P removal is achieved in these systems by promoting the growth of organisms collectively known as the polyphosphate accumulating organisms (PAOs). Also considered important to EBPR are the glycogen accumulating organisms (GAOs), which are theorized to compete with the PAOs for resources at the expense of P removal efficiency. Numerous studies have sought to identify the PAOs and their GAOs competitors, with several candidates proposed for each over the last few decades. The current study collectively assessed the abundance and diversity of all proposed PAOs and GAOs in 18 Danish full-scale wastewater treatment plants with well-working biological nutrient removal over a period of 9 years using 16S rRNA gene amplicon sequencing. The microbial community structure in all plants was relatively stable over time. Evidence for the role of the proposed PAOs and GAOs in EBPR varies and is critically assessed, in light of their calculated amplicon abundances, to indicate which of these are important in full-scale systems. Bacteria from the genus Tetrasphaera were the most abundant of the PAOs. The “Candidatus Accumulibacter” PAOs were in much lower abundance and appear to be biased by the amplicon-based method applied. The genera Dechloromonas, Microlunatus, and Tessaracoccus were identified as abundant putative PAO that require further research attention. Interestingly, the actinobacterial Micropruina and sbr-gs28 phylotypes were among the most abundant of the putative GAOs. Members of the genera Defluviicoccus, Propionivibrio, the family Competibacteraceae, and the spb280 group were also relatively abundant in some plants. Despite observed high abundances of GAOs (periodically exceeding 20% of the amplicon reads), P removal performance was maintained, indicating that these organisms were not outcompeting the PAOs in these EBPR systems. Phylogenetic diversity within each of the PAOs and GAOs genera was observed, which is consistent with reported metabolic diversity for these. Whether or not key traits can be assigned to sub-genus level clades requires further investigation.

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.

Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality

The aim of this study was to determine the impacts of anthropogenic disturbances on bacterial community composition in an urban river (Mooi River). Physico-chemical analysis, bacterial enumeration and 454-pyrosequencing were conducted on the Mooi River system upstream and downstream of an urban settlement in the North West Province, South Africa. Pyrosequencing and multivariate analysis showed that nutrient inputs and faecal pollution strongly impacted the physico-chemical and microbiological quality at the downstream sites. Also, bacterial communities showed higher richness and evenness at the downstream sites. Multivariate analysis suggested that the abundances of Betaproteobacteria, Epsilonproteobacteria, Acidobacteria, Bacteroidetes and Verrucomicrobia are related to temperature, pH, dissolved oxygen (DO), sulphate and chlorophyll-a levels. These results suggest that urbanisation caused the overall water quality of this river to deteriorate, which in turn affected the bacterial community composition. In addition, our work identified potential indicator groups that may be used to track faecal and organic pollution in freshwater systems.

Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using ¹⁵N-based stable isotope probing (SIP) and enrichment with ^14∕15N-ammonium or ^14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. ¹⁵N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used ¹⁵N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.

Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison

Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to natural and human-induced fluctuations in flow-status and permanence.

Biological phosphorus removal from abattoir wastewater at very short sludge ages mediated by novel PAO clade Comamonadaceae

Recent increases in global phosphorus costs, together with the need to remove phosphorus from wastewater to comply with water discharge regulations, make phosphorus recovery from wastewater economically and environmentally attractive. Biological phosphorus (Bio-P) removal process can effectively capture the phosphorus from wastewater and concentrate it in a form that is easily amendable for recovery in contrast to traditional (chemical) phosphorus removal processes. However, Bio-P removal processes have historically been operated at medium to long solids retention times (SRTs, 10-20 days typically), which inherently increases the energy consumption while reducing the recoverable carbon fraction and hence makes it incompatible with the drive towards energy self-sufficient wastewater treatment plants. In this study, a novel high-rate Bio-P removal process has been developed as an energy efficient alternative for phosphorus removal from wastewater through operation at an SRT of less than 4 days. The process was most effective at an SRT of 2-2.5 days, achieving >90% phosphate removal. Further reducing the SRT to 1.7 days resulted in a loss of Bio-P activity. 16S pyrotag sequencing showed the community changed considerably with changes in the SRT, but that Comamonadaceae was consistently abundant when the Bio-P activity was evident. FISH analysis combined with DAPI staining confirmed that bacterial cells of Comamonadaceae arranged in tetrads contained polyphosphate, identifying them as the key polyphosphate accumulating organisms at these low SRT conditions. Overall, this paper demonstrates a novel, high-rate phosphorus removal process that can be effectively integrated with short SRT, energy-efficient carbon removal and recovery processes.

Human serum transferrin fibrils: nanomineralisation in bacteria and destruction of red blood cells

Fibrils formed by human serum transferrin [(1-3 μM) apo-Tf, partially iron-saturated (Fe0.6 -Tf) and holo-Tf (Fe2 -Tf) forms], from dilute bicarbonate solutions, were deposited on formvar surfaces and studied by electron microscopy. We observed that possible bacterial contamination appears to give rise to long, pea-pod-like (PPL) structures for Fe2 -Tf, attributable to the formation of polyhydroxybutyrate (PHB) storage granules, under the nutrient-limiting conditions used. These PPL structures contained periodic nanomineralisation sites susceptible to uranyl stain. Extended incubation of transferrin solutions (about four days) gave rise to extensive transferrin fibril structures. Optical microscopy and AFM studies showed that red blood cells (RBCs) readily adhere to these fibrils. Moreover, the fibrils appear to penetrate RBC membranes and to induce rapid cell destruction (within about 5 h). It is speculated that in situations in vivo where transferrin fibrils can form, such interactions might have adverse physiological consequences, and further studies could aid the understanding of related pathological events.

Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site

Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here we describe physiological and genomic features of three related Betaproteobacterial strains isolated from highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California. All three strains are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic growth with hydrogen, calcium carbonate and oxygen. The three strains exhibit differences, however, regarding the utilization of organic carbon and electron acceptors. Their global distribution and physiological, genomic and transcriptomic characteristics indicate that the strains are adapted to the alkaline and calcium-rich environments represented by the terrestrial serpentinizing ecosystems. We propose placing these strains in a new genus ‘Serpentinomonas’.

Microbes can dwell in highly alkaline environments in the absence of obvious food sources. Here, the authors describe physiological and genomic features of a group of bacteria that live on hydrogen, calcium carbonate and oxygen at a very high pH.

Seasonal variations and resilience of bacterial communities in a sewage polluted urban river

The Zenne River in Brussels (Belgium) and effluents of the two wastewater treatment plants (WWTPs) of Brussels were chosen to assess the impact of disturbance on bacterial community composition (BCC) of an urban river. Organic matters, nutrients load and oxygen concentration fluctuated highly along the river and over time because of WWTPs discharge. Tag pyrosequencing of bacterial 16S rRNA genes revealed the significant effect of seasonality on the richness, the bacterial diversity (Shannon index) and BCC. The major grouping: -winter/fall samples versus spring/summer samples- could be associated with fluctuations of in situ bacterial activities (dissolved and particulate organic carbon biodegradation associated with oxygen consumption and N transformation). BCC of the samples collected upstream from the WWTPs discharge were significantly different from BCC of downstream samples and WWTPs effluents, while no significant difference was found between BCC of WWTPs effluents and the downstream samples as revealed by ANOSIM. Analysis per season showed that allochthonous bacteria brought by WWTPs effluents triggered the changes in community composition, eventually followed by rapid post-disturbance return to the original composition as observed in April (resilience), whereas community composition remained altered after the perturbation by WWTPs effluents in the other seasons.

Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae

An alkalitolerant, thermotolerant, strictly aerobic and Gram-staining negative bacterial strain, designated YIM 78140(T), was isolated from a water sample in Hehua hot spring, Tengchong, Yunnan province, south-west China. The colonies were light brown, convex and circular. Phylogenetic analysis of the 16S rRNA gene sequence of strain YIM 78140(T) indicated that it was clustered with members of β-Proteobacteria (with the similarity from 96.9 to 93.6 %). Good growth occurred at 40-50 °C, pH 8.0-9.0 and in the presence of 0-3 % (w/v) NaCl. The predominant ubiquinones were Q-8 and Q-9. The major fatty acids were C16:0, C17:0 cyclo, C18:1 ω7c and summed feature 3. The G+C content of genomic DNA was 70.8 mol%. The results of physiological and biochemical characteristics, phylogenetic analysis allowed the phenotypic and genotypic differentiation of strain YIM 78140(T) from its closest phylogenetic neighbours. Therefore, the strain YIM 78140(T) represents a novel genus of the family Comamonadaceae, for which the name Zhizhongheella caldifontis gen. nov., sp. nov. is proposed. The type strain is YIM 78140(T) (= BCRC 80649(T) = KCTC 32557(T)).

Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs

Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats.

Metabolic characteristics of the species Variovorax paradoxus

This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3'-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations.

Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae

A novel strain, named S4(T), was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China. Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum. Normal cells were 0.8-0.9 × 1.3-1.9 µm and the cells elongated to 10-25 µm when cultivated at high temperatures. Strain S4(T) grew at 15-50 °C (optimum at 48 °C), pH 5.5-8.5 (optimum 7.0-7.5) and 0-2% (optimum 0.5%) (w/v) NaCl. Ubiquinone-8 was the predominant respiratory quinone. C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and C17:0 cyclo were the major cellular fatty acids. The major 3-OH fatty acid was C10:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid. The genomic DNA G+C content was 68.8 mol%. Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera Comamonas (94.6-95.6% similarities), Giesbergeria (94.9-95.6%), Acidovorax (94.8-95.4%), Brachymonas (94.1-95.2%) and Macromonas (95.1%). Phylogenetic analysis showed the closest relatives of strain S4(T) were members of the genus Macromonas. Based on phenotypic and phylogenetic characteristics, we suggest that strain S4(T) represents a novel species of a new genus of the family Comamonadaceae, for which the name Extensimonas vulgaris gen. nov., sp. nov. is proposed. The type strain of Extensimonas vulgaris is S4(T) (=CGMCC 1.10977(T)=JCM 17803(T)).

Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei Oilfield, China

The distribution of microbial communities in the Menggulin (MGL) and Ba19 blocks in the Huabei Oilfield, China, were studied based on 16S rRNA gene analysis. The dominant microbes showed obvious block-specific characteristics, and the two blocks had substantially different bacterial and archaeal communities. In the moderate-temperature MGL block, the bacteria were mainly Epsilonproteobacteria and Alphaproteobacteria, and the archaea were methanogens belonging to Methanolinea, Methanothermobacter, Methanosaeta, and Methanocella. However, in the high-temperature Ba19 block, the predominant bacteria were Gammaproteobacteria, and the predominant archaea were Methanothermobacter and Methanosaeta. In spite of shared taxa in the blocks, differences among wells in the same block were obvious, especially for bacterial communities in the MGL block. Compared to the bacterial communities, the archaeal communities were much more conserved within blocks and were not affected by the variation in the bacterial communities.

Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment

Wastewater treatment often suffers from instabilities and the failure of specific functions such as biological phosphorus removal by polyphosphate accumulating organisms. Since most of the microorganisms involved in water clarification are unknown it is challenging to operate the process accounting for the permanent varying abiotic parameters and the complex composition and unrevealed metabolic capacity of a wastewater microbial community. Fulfilling the demands for water quality irrespective of substrate inflow conditions may emit severe problems if the limited management resources of municipal wastewater treatment plants are regarded. We used flow cytometric analyses of cellular DNA and polyphosphate to create patterns mirroring dynamics in community structure. These patterns were resolved in up to 15 subclusters, the presence and abundances of which correlated with abiotic data. The study used biostatistics to determine the kind and strength of the correlation. Samples investigated were obtained from a primary clarifier and two activated sludge basins. The stability of microbial community structure was found to be high in the basins and low in the primary clarifier. Despite major abiotic changes certain subcommunities were dominantly present (up to 80% stability), whereas others emerged only sporadically (down to 3% stability, both according to equivalence testing). Additionally, subcommunities of diagnostic value were detected showing positive correlation with substrate influxes. For instance blackwater (r(s) = 0.5) and brewery inflow (both r(s) = 0.6) were mirrored by increases in cell abundances in subclusters 1 and 6 as well as 4 and 8, respectively. Phosphate accumulation was obviously positively correlated with nitrate (r(s) = 0.4) and the presence of denitrifying organisms (Rhodacyclaceae). Various other correlations between community structure and abiotic parameters were apparent. The bacterial composition of certain subcommunities was determined by cell sorting and phylogenetic tools like T-RFLP. In essence, we developed a monitoring tool which is quick, cheap and causal in its interpretation. It will make laborious PCR based technique less obligatory as it allows reliable process monitoring and control in wastewater treatment plants.

Research advances and challenges in the microbiology of enhanced biological phosphorus removal--a critical review

Enhanced biological phosphorus removal (EBPR) is a well-established technology for removing phosphorus from wastewater. However, the process remains operationally unstable in many systems, primarily because there is a lack of understanding regarding the microbiology of EBPR. This paper presents a review of advances made in the study of EBPR microbiology and focuses on the identification, enrichment, classification, morphology, and metabolic capacity of polyphosphate- and glycogen-accumulating organisms. The paper also highlights knowledge gaps and research challenges in the field of EBPR microbiology. Based on the review, the following recommendations regarding the future direction of EBPR microbial research were developed: (1) shifting from a reductionist approach to a more holistic system-based approach, (2) using a combination of culture-dependent and culture-independent techniques in characterizing microbial composition, (3) integrating ecological principles into system design to enhance stability, and (4) reexamining current theoretical explanations of why and how EBPR occurs.