Identity and potential functions of heterotrophic bacterial isolates from a continuous-upflow fixed-bed reactor for denitrification of drinking water with bacterial polyester as source of carbon and electron donor

16S and 18S rDNA Amplicon Sequencing Analysis of Aesthetically Problematic Microbial Mats on the Walls of the Petralona Cave: The Use of Essential Oils as a Cleaning Method

The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation of toxic compounds and damage the cave walls. Essential oils (EOs) have shown promising results in disrupting the cell membrane of bacteria and affecting their membrane permeability. In this study, we identified the microorganisms forming unwanted microbial communities on the walls and speleothems of Petralona Cave using 16S and 18S rDNA amplicon sequencing approaches and evaluated the efficacy of EOs in reducing the ATP levels of these ecosystems. The samples exhibited a variety of both prokaryotic and eukaryotic microorganisms, including Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, the SAR supergroup, Opisthokonta, Excavata, Archaeplastida, and Amoebozoa. These phyla are often found in various habitats, including caves, and contribute to the ecological intricacy of cave ecosystems. In terms of the order and genus taxonomy, the identified biota showed abundances that varied significantly among the samples. Functional predictions were also conducted to estimate the differences in expressed genes among the samples. Oregano EO was found to reduce ATP levels by 87% and 46% for black and green spots, respectively. Consecutive spraying with cinnamon EO further reduced ATP levels, with reductions of 89% for black and 88% for green spots. The application of a mixture solution caused a significant reduction up to 96% in ATP levels of both areas. Our results indicate that EOs could be a promising solution for the treatment of microbial communities on cave walls and speleothems.

High-rate iron sulfide and sulfur-coupled autotrophic denitrification system: Nutrients removal performance and microbial characterization

Iron sulfides-based autotrophic denitrification (IAD) is a promising technology for nitrate and phosphate removal from low C:N ratio wastewater due to its cost-effectiveness and low sludge production. However, the slow kinetics of IAD, compared to other sulfur-based autotrophic denitrification (SAD) processes, limits its engineering application. This study constructed a co-electron-donor (FeS and S⁰ with a volume ratio of 2:1) iron sulfur autotrophic denitrification (ISAD) biofilter and operated at as short as 1 hr hydraulic retention time (HRT). Long-term operation results showed that the superior total nitrogen and phosphate removals of the ISAD biofilter were 90-100% at 1-12 h HRT, with the highest denitrification rate up to 960 mg/L/d. Considering low sulfate production, HRT of 3 h could be the optimal condition. Such superior performance in the ISAD biofilter was achieved due to the interactions between FeS and S⁰, which accelerated the denitrification process and maintained the acidity-alkalinity balance. Metagenomic analysis found that the enriched nitrate-dependent iron-oxidizing (NDFO) bacteria (Acinetobacter and Acidovorax), sulfur-oxidizing bacteria (SOB), and dissimilatory nitrate reduction to ammonia (DNRA) bacteria likely supported stable nitrate reduction. The metabolic pathway analysis showed that completely denitrification and DNRA, coupled with sulfur oxidation, disproportionation, iron oxidation and phosphate precipitation with FeS and S⁰ as co-electron donors, were responsible for the high-rate nitrate and phosphate removal. This study provides the potential of ISAD as a highly efficient post-denitrification technology and sheds light on the balanced microbial S-N-Fe transformation.

Comparative investigation on heterotrophic denitrification driven by different biodegradable polymers for nitrate removal in mariculture wastewater: Organic carbon release, denitrification performance, and microbial community

Heterotrophic denitrification is widely studied to purify freshwater wastewater, but its application to seawater wastewater is rarely reported. In this study, two types of agricultural wastes and two types of synthetic polymers were selected as solid carbon sources in denitrification process to explore their effects on the purification capacity of low-C/N marine recirculating aquaculture wastewater (NO3 --N 30 mg/L, salinity 32‰). The surface properties of reed straw (RS), corn cob (CC), polycaprolactone (PCL) and poly3-hydroxybutyrate-hydroxypropionate (PHBV) were evaluated by Brunauer-Emmett-Teller, Scanning electron microscope and Fourier-transform infrared spectroscopy. Short-chain fatty acids, dissolved organic carbon (DOC), and chemical oxygen demand (COD) equivalents were used to analyze the carbon release capacity. Results showed that agricultural waste had higher carbon release capacity than PCL and PHBV. The cumulative DOC and COD of agricultural waste were 0.56-12.65 and 1.15-18.75 mg/g, respectively, while those for synthetic polymers were 0.07-1.473 and 0.045-1.425 mg/g, respectively. The removal efficiency of nitrate nitrogen (NO3 --N) was CC 70.80%, PCL 53.64%, RS 42.51%, and PHBV 41.35%. Microbial community analysis showed that Proteobacteria and Firmicutes were the most abundant phyla in agricultural wastes and biodegradable natural or synthetic polymers. Quantitative real-time PCR indicated the conversion from nitrate to nitrogen was achieved in all four carbon source systems, and all six genes had the highest copy number in CC. The contents of medium nitrate reductase, nitrite reductase and nitrous oxide reductase genes in agricultural wastes were higher than those in synthetic polymers. In summary, CC is an ideal carbon source for denitrification technology to purify low C/N recirculating mariculture wastewater.

Improved Denitrification Performance of Polybutylene Succinate/Corncob Composite Carbon Source by Proper Pretreatment: Performance, Functional Genes and Microbial Community Structure

Blending biodegradable polymers with plant materials is an effective method to improve the biodegradability of solid carbon sources and save denitrification costs, but the recalcitrant lignin in plant materials hinders the microbial decomposition of available carbon sources. In the present study, corncob pretreated by different methods was used to prepare polybutylene succinate/corncob (PBS/corncob) composites for biological denitrification. The PBS/corncob composite with alkaline pretreatment achieved the optimal NO₃^--N removal rate (0.13 kg NO₃^--N m^-3 day^-1) with less adverse effects. The pretreatment degree, temperature, and their interaction distinctly impacted the nitrogen removal performance and dissolved organic carbon (DOC) release, while the N₂O emission was mainly affected by the temperature and the interaction of temperature and pretreatment degree. Microbial community analysis showed that the bacterial community was responsible for both denitrification and lignocellulose degradation, while the fungal community was primarily in charge of lignocellulose degradation. The outcomes of this study provide an effective strategy for improving the denitrification performance of composite carbon sources.

Nitrate Removal from Groundwater by Heterotrophic and Electro-Autotrophic Denitrification

A heterotrophic and autotrophic denitrification (HAD) system shows satisfactory performance for groundwater with nitrate contamination. In this study, an HAD system combining solid-phase heterotrophic denitrification and electrochemical hydrogen autotrophic denitrification (SHD-EHD) was developed for the treatment of nitrate-contaminated groundwater, in which polycaprolactone (PCL) was used as the carbon source to enhance the nitrate removal performance and prevent secondary pollution of the electrochemical hydrogen autotrophic denitrification (EHD) system. The denitrification performance, microbial community structure and nitrogen metabolism were investigated. The results showed that a high nitrate removal rate of 99.04% was achieved with an influent nitrate concentration of 40 mg/L, a current of 40 mA and a hydraulic retention time (HRT) of 4 h. By comparing the performance with the EHD system, it was found that the HAD system with PCL promoted the complete denitrification and reduced the accumulation of NO2−-N. Analysis of the microbial community structure identified the key denitrifying bacteria: Dechloromonas, Thauera and Hydrogenophaga. A comparison of microbial communities from SHD-EHD and solid-phase heterotrophic denitrification (SHD) demonstrated that electrical stimulation promoted the abundance of the dominant denitrifying bacteria and the electroactive bacteria. Analysis of the nitrogen metabolic pathway revealed that the conversion of NO to N2O was the rate-limiting step in the overall denitrification pathway. The SHD-EHD developed in this study showed great potential for groundwater nitrate removal.

Cold temperature mediated nitrate removal pathways in electrolysis-assisted constructed wetland systems under different influent C/N ratios and anode materials

Electrolysis had proven to be useful for the enhanced performance in constructed wetlands (CWs). While at cold temperature, the nitrate removal pathways, plant physiological characteristics and microbial community structure in electrolysis-assisted CWs were unclear. Therefore, the purification performance of three electrolysis-assisted horizontal subsurface-flow constructed wetlands (E-HSCWs) with different anodes and a control system in cold seasons were evaluated in this study. E-HSCWs showed a 2.02-83.21% increase of total nitrogen (TN) removal when compared to control, and the gaps were enlarged with increasing C/N (chemical oxygen demand/total nitrogen, COD/TN) ratios. Nitrite accumulation in E-HSCWs presented a first increase then went down trend with increasing C/N ratios, compared to a steady increase in control system. The optimum C/N ratio was 8 in E-HSCWs for both TN and COD removal. Moreover, Ti|IrO₂-Ta₂O₅ (Ti) anode showed the highest potential for TN and COD removal. Less root weight, shorter root length and reduced TN and total phosphorus (TP) contents in roots were observed in wetland plants (Iris sibirica) of E-HSCWs. In E-HSCWs with Fe and C anodes, the nitrate removal was mainly accomplished by autotrophic denitrifier Hydrogenophaga. While in E-HSCWs with Ti anode, the synergistic effect of autotrophic denitrifier Hydrogenophaga and heterotrophic denitrifiers Acidovorax, Simplicispira, Zoogloea accounted for the nitrate removal. These results showed that E-HSCWs at proper C/N ratio of 8 would be promising for nitrate removal at cold temperature.

Denitrification performance and microbial community of bioreactor packed with PHBV/PLA/rice hulls composite

In this study, a novel biodegradable PHBV/PLA/rice hulls (PPRH) composite was applied and tested as biofilm attachment carrier and carbon source in two bioreactors for biological denitrification process. The denitrification performance, effect of operational conditions and microbial community structure of PPRH biofilm were evaluated. The batch experiment results showed that PPRH-packed bioreactor could completely remove 50 mg L^-1 of NO₃^--N at natural pH (ca. 7.5) and room temperature. The continuous flow experiments indicated that high NO₃^--N removal efficiency (77%-99%) was achieved with low nitrite (<0.48 mg L^-1) and ammonia (<0.81 mg L^-1) accumulation, when influent NO₃^--N concentration was 30 mg L^-1 and hydraulic retention time was 2-6 h. Furthermore, the microbial community analysis indicated that bacteria belonging to genus Diaphorobacter in phylum Proteobacteria were the most dominant and major denitrifiers in denitrification. In summary, PPRH composite was a promising carbon source for biological nitrate removal from water and wastewater.

Removal of Di-n-butyl phthalate from aged leachate under optimal hydraulic condition of leachate treatment process and in the presence of its dominant bacterial strains

The effects of hydraulic condition of reactor and the dominant degrading bacteria on the removal of di-n-butyl phthalate (DBP) from aged landfill leachate by anaerobic/anoxic/oxic (A/A/O) leachate treatment process were investigated. The optimal DBP removal (96.0%) was obtained from aged leachate when the hydraulic retention time (HRT) of the reactor was 3 d, internal reflux ratio of the reactor was 200%, and external reflux ratio of the reactor was 60%, respectively. The removal efficiency of DBP was significantly improved after the inoculation of the dominant DBP-degrading bacteria (Pseudomonas sp. W1) in the reactor. The mean removal efficiencies of DBP before and after inoculation were 94.1% and 97.7%, respectively. Furthermore, the inoculation of dominant DBP-degrading bacteria changed the original sludge structure and characteristics, which was more conducive to the removal of DBP. These results provide theoretical basis for the effective removal of DBP from aged leachate by the biological treatment process.

Influence mechanism of filling ratio on solid-phase denitrification with polycaprolactone as biofilm carrier

In this study, three up-flow fixed-bed bioreactors were constructed with three different filling ratios (filling volume/effective volume: 30%, 60% and 90%) of polycaprolactone (PCL). Above 98% of nitrate removal efficiency was achieved with low accumulations of nitrite and ammonium for each filling ratio. Low filling ratio of PCL had extensive folds and pores that favored the attachment and growth of microorganisms; however, excessive biomass restrained nitrate specific reduction rate (NaSRR). The most dominant genera were Comamonas (0.80-57.64%), Stenotrophomonas (2.59-54.39%), Acidovorax (7.32-23.55%), Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium (0.30-19.74%) and Thermomonas (0.12-14.58%). Nitrate reductase (EC 1.7.99.4), nitrite reductase (EC 1.7.2.1) and nitric oxide reductase (EC 1.7.2.5) predicted by PICRUSt2 were abundant in high influent nitrate load (NaL). According to the analysis of carbon balance model, the utilization rate (η) of PCL showed a highly positive correlation with influent NaL, indicating reducing filling ratio or HRT might be an effective measure to save cost for nitrate removal.

Nitrate removal performance and diversity of active denitrifying bacteria in denitrification reactors using poly(L-lactic acid) with enhanced chemical hydrolyzability

Poly(L-lactic acid) (PLLA) can be used as an external electron donor in denitrification reactors to treat drinking water, aquaculture water, and industrial wastewater with an imbalanced carbon/nitrogen ratio. However, for PLLA to function in these applications, its chemical hydrolyzability requires improvement. Although the adjustment of the crystallinity (X_c) is effective in improving the hydrolyzability of PLLA, the condition for the X_c of PLLA, in which a sufficient amount of lactic acid is released for denitrification, must be clarified. Therefore, this study investigated the effective X_c range and optimal PLLA content as an electron donor for continuous nitrate removal in denitrification reactors. This study also explored the abundance, succession, and diversity of active denitrifying bacteria in denitrification reactors. The nitrate removal activity of activated sludge using the highly crystalline PLLA (X_c = 39.4%) was 1.8 mg NO₃^- -N g MLSS^-1 h^-1, which is 2.4 times higher than that using the nearly amorphous PLLA (X_c = 0.9%). During the 57 days of operation, the denitrification reactor with 3% (w/v) highly crystalline PLLA continued to completely remove nitrate, with a maximum nitrate removal activity of 22.8 mg NO₃^- -N g MLSS^-1 h^-1. The 16S rRNA amplicon sequencing and clone library analyses are using transcripts of two nitrite reductase genes, encoding cytochrome cd₁ nitrite reductase, and copper-containing nitrite reductase revealed that bacteria belonging to the families Comamonadaceae, Rhodocyclaceae, and Alcaligenaceae were active denitrifying bacteria in the denitrification reactor using PLLA.

Simultaneous nitrification and denitrification (SND) bioaugmentation with Pseudomonas sp. HJ3 inoculated for enhancing phenol and nitrogen removal in coal gasification wastewater

A simultaneous nitrification and denitrification (SND) bioaugmention system with Pseudomonas sp. HJ3 inoculated was established to explore the potential of simultaneous phenol and nitrogen removal in coal gasification wastewater (CGW). When the concentration of influent chemical oxygen demand (COD) and total phenols (TPh) was 1,765.94 ± 27.43 mg/L and 289.55 ± 10.32 mg/L, the average removal efficiency of COD and TPh at the stable operating stage reached 64.07% ± 0.76% and 74.91% ± 0.33%, respectively. Meanwhile, the average removal efficiency of NH₄ ⁺-N and total nitrogen (TN) reached 67.96% ± 0.17% and 57.95% ± 0.12%, respectively. The maximum SND efficiency reached 83.51%. Furthermore, SND bioaugmentation performed with good nitrification tolerance of phenol shock load and significantly reduced toxic inhibition of organisms. Additionally, the microbial community analysis indicated that Pseudomonas sp. HJ3 was the predominant bacterium in the SND bioaugmentation system. Moreover, the indigenous nitrogen removal bacteria such as Thauera, Acidovorax and Stenotrophomonas were enriched, which further enhanced the nitrogen removal in the SND bioaugmentation system. The results demonstrated the promising application of SND bioaugmentation for enhancing simultaneous phenol and nitrogen removal in CGW treatment.

Regeneration of Fe II /Fe III complex from NO chelating absorption by microbial fuel cell

Ferrous chelates (Fe^IIEDTA) can effectively absorb NO, but the regeneration of them usually consumes large amounts of organic matter or energy. In this study, a new approach to regenerate NO absorbed ferrous chelates with simultaneous electricity generation was investigated by a microbial fuel cell (MFC). The performance and mechanisms of Fe^IIEDTA regeneration were evaluated in the cathode of MFC reactor with and without the presence of microorganisms (referring to biocathode and abiotic cathode), respectively. It was found that Fe^IIEDTA-NO and Fe^IIIEDTA could be used as the cathode electron acceptors in MFC. Low pH (pH = 5) was beneficial to electricity generation and Fe^IIIEDTA/Fe^IIEDTA-NO reduction by the abiotic cathode. The biocathode performed better in electricity generation and Fe^IIEDTA regeneration, and achieved a Fe^IIIEDTA reducing rate of 0.34 h^-1 and a Fe^IIEDTA-NO reducing rate of 0.97 L mmol^-1 h^-1, which are much higher that than those for the abiotic cathode (0.23 h^-1 for Fe^IIIEDTA, 0.44 L mmol^-1 h^-1 for Fe^IIEDTA-NO). This was likely because the activation polarization loss and over cathode potential were reduced as a result of the catalytic activity of NO and iron reducing bacteria.

Microbial aerobic denitrification dominates nitrogen losses from reservoir ecosystem in the spring of Zhoucun reservoir

The mechanism and factors influencing nitrogen loss in the Zhoucun reservoir were explored during the spring. The results showed that the nitrate and total nitrogen concentration decreased from 1.84 ± 0.01 mg/L and 2.34 ± 0.06 mg/L to 0.06 ± 0.01 mg/L and 0.48 ± 0.09 mg/L, respectively. Meanwhile, the nitrate and total nitrogen removal rate reached 97.02% ± 0.25 and 79.38% ± 3.32, respectively. Moreover, the abundance of nirS gene and aerobic denitrification bacteria increased from 1.04-3.38 × 10³ copies/mL and 0.71 ± 0.22 × 10² cfu/mL to 5.36-5.81 × 10³ copies/mL and 8.64 ± 2.08 × 10³ cfu/mL, respectively. The low MW fractions of DOM (<5 kDa) increased from 0.94 ± 0.02 mg/L in February to 1.51 ± 0.09 mg/L in April. E3/E4 and absorption spectral slope ratio (S_R) showed that fulvic acid accounted for the main proportion with autochthonous characteristics. These findings were consistent with the fluorescence components and fluorescence characteristic indices based on EEM-PARAFAC. Meanwhile, the microbial metabolism activity increased significantly from February to April, which contributed to the cycle of nutrients within the reservoir water system. Moreover, the abundance of the bacterial species involved in denitrification (Exiguobacterium, Brevundimonas, Deinococcus, Paracoccus, and Pseudomonas) increased significantly. The relative abundance of KOs related to nitrogen metabolism, were initially increased and then decreased. Specifically, K02567 (napA) represented the main proportion of KOs related to denitrification. The abundance of napA-type denitrifying bacteria (Dechloromonas, Pseudomonas, Azospira, Rhodopseudomonas, Aeromonas, Zobellella, Sulfuritalea, Bradyrhizobium, Achromobacter, Enterobacter, Thauera, and Magnetospirillum) increased significantly during the period of nitrogen loss. Furthermore, the levels of nitrate, T, DO, and AWCD were the most important factors affecting the N-functional bacteria composition. The systematic investigation of the nitrogen loss would provide a theoretical foundation for the remediation of the water reservoir via aerobic denitrification in the future.

Bioaugmentation with Diaphorobacter polyhydroxybutyrativorans to enhance nitrate removal in a poly (3-hydroxybutyrate-co-3-hydroxyvalerate)-supported denitrification reactor

A newly isolated and identified Diaphorobacter polyhydroxybutyrativorans strain (SL-205) was employed to enhance the denitrification performance of a laboratory-scale solid-phase denitrification (SPD) reactor using poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) as a carbon source, and dynamic variations in microbial communities in the reactor were investigated. Results indicated that bioaugmentation with strain SL-205 enabled rapid reactor startup and improved denitrification performance relative to the reactor inoculated with activated sludge. Illumina sequencing revealed that bioaugmentation also significantly increased Proteobacteria abundance along with increased influent nitrate loading. Additionally, two genera of PHBV-degrading denitrifers, Diaphorobacter and Acidovorax, exhibited higher abundance, and elevated expression of denitrification-associated genes (narG, nirK, and nirS) was observed following bioaugmentation relative to the control at influent nitrate loading ranging from 1.28 g N/(L·d) to 1.6 g N/(L·d).

PHBV polymer supported denitrification system efficiently treated high nitrate concentration wastewater: Denitrification performance, microbial community structure evolution and key denitrifying bacteria

Biodegradable polymer supported denitrification (BPD) system shows good denitrification performance for the wastewater with low nitrate concentrations. In this study, a BPD system using Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) polymer as carbon source was developed to treat the wastewater with high nitrate concentrations. The denitrification performance, utilization ratio of PHBV polymers, and microbial community structure evolution and key denitrifying bacteria were comprehensively studied. Results indicated that an average nitrate removal efficiency of 99% could be achieved with an influent NO₃^--N concentration of 100 mg L^-1 and a hydraulic retention time (HRT) of 7.25 h. Mass balance model predicted that 80% of the PHBV polymers were consumed by denitrifying bacteria, close to 72% consumption in real condition, suggesting the model might be useful for PHBV polymers management in BPD system. Further, the bacterial community structures varied along the bioreactor profile, which closely linked to the concentration profiles of nitrate and ammonia. Metatranscriptomic analysis identified the key denitrifying bacteria as Comamonas, Acidovorax and Dechloromonas. The PHBV supported denitrification system developed in this study shows potential for removal of high concentration of nitrate from wastewater.

Slowly released carbon source from composite materials system for removing nitrate pollution in groundwater

Chemoheterotrophic denitrification technologies using biopolymers as a solid carbon source and biofilm carriers have been widely trialed to remove nitrate from groundwater.

Denitrification of groundwater using PHBV blends in packed bed reactors and the microbial diversity

In the present study, three kinds of biopolymers, PHBV, PHBV/starch and PHBV/bamboo powder (BP) blends were used as carbon source and biofilm carriers for denitrification in packed bed reactors to remove nitrate from groundwater. Results showed that a fast start-up was obtained in bioreactors filled with both PHBV/Starch and PHBV/BP blends without external inocula and it took more than 3 month for PHBV reactor to reach the same loading rate. The PHBV/BP packed reactor exhibited a better nitrate removal efficiency (87.4 ± 7.0%) and less adverse effects in nitrite accumulation and DOC release (below 0.5 mg NO2N L(-1) and 10.5 mg DOC L(-1) in the effluent) during stable operation. Pyrosequencing analysis demonstrated that bacteria belonging to genus Clostridium in phylum Firmicus, which play the primary role in degrading the biopolymers, are the most dominant (33-15% of the sequences). The predominant species in all samples is related to Clostridium crotonatovorans. All the identified 11 genera of denitrifying bacteria affiliated with phylum Proteobacteria and constituted 30-55% in the representative sequences. The PHBV/BP blend is economically attractive carbon source with good denitrification performance.

Effect of dissolved oxygen on heterotrophic denitrification using poly(butylene succinate) as the carbon source and biofilm carrier

The effect of dissolved oxygen (DO) on heterotrophic denitrification using poly(butylene succinate) as the carbon source and biofilm carrier was evaluated in a lab-scale experiment. Aerated, low-oxygen, and anoxic treatment groups were set up, which had average DO concentrations of 5.2±1.0, 1.4±1.2, and 0.5±0.3 mg L(-1), respectively. The NO3(-)-N and total nitrogen (TN) removal rates in the aerated group (37.44±0.24 and 36.24±0.48 g m(-3) d(-1), respectively) were higher than those in the other two groups. There was no significant difference between the low-oxygen and anoxic groups for the NO3(-)-N or TN removal rate. Accumulation of NO2(-)-N reached 5.0 mg L(-1) in the aerated group; no nitrite accumulation was found in the other two treatment groups. Bacterial communities of the low-oxygen and anoxic groups showed high similarity and were significantly different from those of the aerated group.

Characterization of pbt genes conferring increased Pb2+ and Cd2+ tolerance upon Achromobacter xylosoxidans A8

The cluster of pbtTFYRABC genes is carried by plasmid pA81. Its elimination from Achromobacter xylosoxidans A8 resulted in increased sensitivity towards Pb(2+) and Cd(2+). Predicted pbtTRABC products share strong similarities with Pb(2+) uptake transporter PbrT, transcriptional regulator PbrR, metal efflux P1-ATPases PbrA and CadA, undecaprenyl pyrophosphatase PbrB and its signal peptidase PbrC from Cupriavidus metallidurans CH34. Expression of pbtABC or pbtA in a metal-sensitive Escherichia coli GG48 rendered the strain Pb(2+)-, Cd(2+)- and Zn(2+)-tolerant and caused decreased accumulation of the metal ions. Accumulation of Pb(2+), but not of Cd(2+) or Zn(2+), was promoted in E. coli expressing pbtT. Additional genes of the pbt cluster are pbtF and pbtY, which encode the cation diffusion facilitator (CDF)-like transporter and a putative fatty acid hydroxylase of unknown function, respectively. Expression of pbtF did not confer increased metal tolerance upon E. coli GG48, although the protein showed measurable Pb(2+)-efflux activity. Unlike the pbtT promoter, promoters of pbtABC, pbtF and pbtY contain features characteristic of promoters controlled by metal-responsive transcriptional regulators of the MerR family. Upregulation of pbtABC, pbtF and pbtY upon Pb(2+), Cd(2+) and Zn(2+) exposure was confirmed in wild-type Achromobacter xylosoxidans A8. Gel shift assays proved binding of purified PbtR to the respective promoters.

Denitrification performance and biofilm characteristics using biodegradable polymers PCL as carriers and carbon source

In this study, a fixed bed bioreactor filled with biopolymer polycaprolactone (PCL) was developed to remove nitrate from groundwater through denitrification. PCL serves both as carbon source and biofilm carriers. During a long-term operation of 561 d, the performance of the reactor in nitrogen removal, characteristics of biofilm attached to biodegradable carriers, and the hydrolysis and utilization of solid carbon source were studied. With temperatures exceeding 24 °C, the average nitrate concentration in the effluent was lower than 3.7 mg NL(-1), and more than 95% of TN was removed at hydraulic retention time of 3-6h. Nitrite and ammonium remained at low levels (less than 0.32 and 0.78 mg NL(-1), respectively). The calculated PCL amount consumed ranged between 1.6 and 3.7 g PCL g(-1) NO₃-N. The FT-IR spectrum of the used PCL indicated the chain scission by hydrolytic degradation. A pyrosequencing analysis of the biofilm showed that genus Diaphorobacter belonging to family Comamonadaceae accounted for most of the sequences. Bacteria of genera Hydrogenophaga, Rhodocyclaceae uncultured and Desulfovibrio were highly enriched in the PCL biofilm. Microelectrode data indicated that the biofilm had an average thickness of around 800 μm and the intensive denitrification activities occurred in the area of 300-500 μm of biofilm with values up to 400 μmol cm(-3)h(-1).

Denitrification performance and microbial diversity in a packed-bed bioreactor using biodegradable polymer as carbon source and biofilm support

A novel kind of biodegradable polymer, i.e., starch/polycaprolactone (SPCL) was prepared and used as carbon source and biofilm support for biological denitrification in a packed-bed bioreactor. The denitrification performances and microbial diversity of biofilm under different operating conditions were investigated. The results showed that the average denitrification rate was 0.64 ± 0.06 kg N/(m(3)d), and NH3-N formation (below 1mg/L) was observed during denitrification. The nitrate removal efficiency at 15°C was only 55.06% of that at 25°C. An initial excess release of DOC could be caused by rapid biodegradation of starch in the surfaces of SPCL granules, then it decreased to 10.08 mg/L. The vast majority of species on SPCL biofilm sample (99.71%) belonged to six major phyla: Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Spirochaetes and Actinobacteria. Proteobacteria were the most abundant phylum (85.50%) and mainly consisted of β-proteobacteria (82.39%). Diaphorobacter and Acidovorax constituted 52.75% of the identified genera which were denitrifying bacteria.

Comparison of denitrification performance and microbial diversity using starch/polylactic acid blends and ethanol as electron donor for nitrate removal

Starch/polylactic acid (SPLA9) was prepared and used as electron donor for biological nitrate removal. The denitrification performance and microbial diversity were investigated and compared with that of ethanol supported denitrification system. The results showed that the SPLA9 system had richer microbial diversity by analyzing Shannon's diversity index, but the ethanol system showed higher denitrification rate. The formation of NH3-N was observed during denitrification for both systems, but its concentration in the SPLA9 system was lower than that in the ethanol system. The quick release and accumulation of dissolved organic carbon (DOC) were observed in SPLA9 system during the start-up period. Fortunately it decreased to about 5mg/L. Proteobacteria was the major phylum and Alicycliphilus and Thauera were the most abundant genera for both systems. Organisms from the genus Desulfovibrio were identified in both systems, which probably contributed to the dissimilatory nitrate reduction to ammonia (DNRA) reaction.

Triggers of aggregation and extracellular polysaccharide polymer production in Acidovorax temperans

Bacterial aggregation has important implications for the maintenance of bacteria in engineered environments. The triggers for aggregation, however, are poorly understood. A strain of Acidovorax temperans CB2Hn isolated from activated sludge was found to exhibit transient aggregation and was applied as a model to investigate factors that regulate biological aggregation. Growth kinetic studies indicate CB2Hn has exponential growth rates (μ(max)) ranging from 0.11 to 0.75 (log(CFU mL(-1))h(-1)) depending on nutrient conditions. CB2Hn exhibited variable aggregation in growth media that differed in the type of available carbon. Aggregation indices and extracellular polysaccharide polymer levels showed transient maxima which occurred at different points in the growth curve for each medium type. Maximum aggregation points were detected at the beginning of log phase in media containing complex carbon sources. In contrast, maximum values were detected in early log phase and mid-to-late log phase in media containing both simple and complex carbon sources. The results suggest that aggregation is regulated by nutritional cues and is possibly triggered by the switch to utilisation of complex carbon substrates.

Identification of nitrite-reducing bacteria using sequential mRNA fluorescence in situ hybridization and fluorescence-assisted cell sorting

Sequential mRNA fluorescence in situ hybridization (mRNA FISH) and fluorescence-assisted cell sorting (SmRFF) was used for the identification of nitrite-reducing bacteria in mixed microbial communities. An oligonucleotide probe labeled with horseradish peroxidase (HRP) was used to target mRNA of nirS, the gene that encodes nitrite reductase, the enzyme responsible for the dissimilatory reduction of nitrite to nitric oxide. Clones for nirS expression were constructed and used to provide proof of concept for the SmRFF method. In addition, cells from pure cultures of Pseudomonas stutzeri and denitrifying activated sludge were hybridized with the HRP probe, and tyramide signal amplification was performed, conferring a strongly fluorescent signal to cells containing nirS mRNA. Flow cytometry-assisted cell sorting was used to detect and physically separate two subgroups from a mixed microbial community: non-fluorescent cells and an enrichment of fluorescent, nitrite-reducing cells. Denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of 16S ribosomal RNA (rRNA) genes were used to compare the fragments amplified from the two sorted subgroups. Sequences from bands isolated from DGGE profiles suggested that the dominant, active nitrite reducers were closely related to Acidovorax BSB421. Furthermore, following mRNA FISH detection of nitrite-reducing bacteria, 16S rRNA FISH was used to detect ammonia-oxidizing and nitrite-oxidizing bacteria on the same activated sludge sample. We believe that the molecular approach described can be useful as a tool to help address the longstanding challenge of linking function to identity in natural and engineered habitats.

Metaproteogenomic analysis of a community of sponge symbionts

Sponges harbour complex communities of diverse microorganisms, which have been postulated to form intimate symbiotic relationships with their host. Here we unravel some of these interactions by characterising the functional features of the microbial community of the sponge Cymbastela concentrica through a combined metagenomic and metaproteomic approach. We discover the expression of specific transport functions for typical sponge metabolites (for example, halogenated aromatics, dipeptides), which indicates metabolic interactions between the community and the host. We also uncover the simultaneous performance of aerobic nitrification and anaerobic denitrification, which would aid to remove ammonium secreted by the sponge. Our analysis also highlights the requirement for the microbial community to respond to variable environmental conditions and hence express an array of stress protection proteins. Molecular interactions between symbionts and their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators. Finally, some sponge-associated bacteria (for example, a Phyllobacteriaceae phylotype) appear to undergo an evolutionary adaptation process to the sponge environment as evidenced by active mobile genetic elements. Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities.

Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity

The deterioration of the stone built and sculptural heritage has prompted the search and development of novel consolidation/protection treatments that can overcome the limitations of traditional ones. Attention has been drawn to bioconservation, particularly bacterial carbonatogenesis (i.e. bacterially induced calcium carbonate precipitation), as a new environmentally friendly effective conservation strategy, especially suitable for carbonate stones. Here, we study the effects of an in situ bacterial bioconsolidation treatment applied on porous limestone (calcarenite) in the sixteenth century San Jeronimo Monastery in Granada, Spain. The treatment consisted in the application of a nutritional solution (with and without Myxococcus xanthus inoculation) on decayed calcarenite stone blocks. The treatment promoted the development of heterotrophic bacteria able to induce carbonatogenesis. Both the consolidation effect of the treatment and the response of the culturable bacterial community present in the decayed stone were evaluated. A significant surface strengthening (consolidation) of the stone, without altering its surface appearance or inducing any detrimental side effect, was achieved upon application of the nutritional solution. The treatment efficacy was independent of the presence of M. xanthus (which is known as an effective carbonatogenic bacterium). The genetic diversity of 116 bacterial strains isolated from the stone, of which 113 strains showed carbonatogenic activity, was analysed by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) and 16S rRNA gene sequencing. The strains were distributed into 31 groups on the basis of their REP-PCR patterns, and a representative strain of each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that isolates belong to a wide variety of phylogenetic groups being closely related to species of 15 genera within the Proteobacteria, Firmicutes and the Actinobacteria. This study shows that the abundant carbonatogenic bacteria present in the decayed stone are able to effectively consolidate the degraded stone by producing new calcite (and vaterite) cement if an adequate nutritional solution is used. The implications of these results for the conservation of cultural heritage are discussed.

Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination

In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria), and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genus Rhodanobacter are a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis, Rhodanobacter species contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

Microbial community diversity in seafloor basalt from the Arctic spreading ridges

Microbial communities inhabiting recent (< or =1 million years old; Ma) seafloor basalts from the Arctic spreading ridges were analyzed using traditional enrichment culturing methods in combination with culture-independent molecular phylogenetic techniques. Fragments of 16S rDNA were amplified from the basalt samples by polymerase chain reaction, and fingerprints of the bacterial and archaeal communities were generated using denaturing gradient gel electrophoresis. This analysis indicates a substantial degree of complexity in the samples studied, showing 20-40 dominating bands per profile for the bacterial assemblages. For the archaeal assemblages, a much lower number of bands (6-12) were detected. The phylogenetic affiliations of the predominant electrophoretic bands were inferred by performing a comparative 16S rRNA gene sequence analysis. Sequences obtained from basalts affiliated with eight main phylogenetic groups of Bacteria, but were limited to only one group of the Archaea. The most frequently retrieved bacterial sequences affiliated with the gamma-proteobacteria, alpha-proteobacteria, Chloroflexi, Firmicutes, and Actinobacteria. The archaeal sequences were restricted to the marine Group 1: Crenarchaeota. Our results indicate that the basalt harbors a distinctive microbial community, as the majority of the sequences differed from those retrieved from the surrounding seawater as well as from sequences previously reported from seawater and deep-sea sediments. Most of the sequences did not match precisely any sequences in the database, indicating that the indigenous Arctic ridge basalt microbial community is yet uncharacterized. Results from enrichment cultures showed that autolithotrophic methanogens and iron reducing bacteria were present in the seafloor basalts. We suggest that microbial catalyzed cycling of iron may be important in low-temperature alteration of ocean crust basalt. The phylogenetic and physiological diversity of the seafloor basalt microorganisms differed from those previously reported from deep-sea hydrothermal systems.

Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov

Gram-negative bacteria were isolated from the rhizoplane of Brassica napus in France and from root nodules of Argyrolobium uniflorum, Astragalus algerianus and Lathyrus numidicus growing in the infra-arid zone of southern Tunisia. Based on phylogenetic analysis of the 16S rRNA gene sequences, the seven isolates belong to the Alphaproteobacteria and are related to Phyllobacterium myrsinacearum strains. The isolates formed three clusters; clusters A and C consist of Tunisian strains, whereas cluster B consists of two strains from Brassica napus from France. Phylogenetic reconstruction based on the atpD gene strongly supports their affiliation to the genus Phyllobacterium. DNA-DNA hybridizations revealed that (i) none of the isolates belong to the species P. myrsinacearum, (ii) clusters A and C represent two distinct genomospecies and (iii) the two strains of cluster B represent two separate genomospecies. Distinctive phenotypic features were deduced from numerical analysis of phenotypic data. Based on this polyphasic approach, four novel species are proposed: Phyllobacterium leguminum sp. nov. (type strain ORS 1419T = CFBP 6745T = LMG 22833T), Phyllobacterium ifriqiyense sp. nov. (type strain STM 370T = CFBP 6742T = LMG 22831T), Phyllobacterium brassicacearum sp. nov. (type strain STM 196T = CFBP 5551T = LMG 22836T) and Phyllobacterium bourgognense sp. nov. (type strain STM 201T = CFBP 5553T = LMG 22837T). The description of the genus Phyllobacterium is emended accordingly.

Biological denitrification in drinking water treatment using the seaweed Gracilaria verrucosa as carbon source and biofilm carrier

Chemical and microbiological aspects were investigated with regard to biological denitrification of drinking water using the seaweed Gracilaria verrucosa as the carbon and energy substrate and as physical support for the microbial flora in semibatch, fixed-bed reactors. Complete removal of nitrate (100 mg/L) was readily achieved without accumulation of nitrite. Microbiological analysis indicated that the effluent of the reactor contained high numbers of bacteria (>10(6)/mL total count). Among the 44 bacterial strains isolated directly from the samples or isolated after enrichment at 37 degrees C, 25 different fatty acid profiles were found, indicating a complex microflora, including potential pathogens.

Molecular detection and isolation from Antarctica of methylotrophic bacteria able to grow with methylated sulfur compounds

This study is the first demonstration that a diverse facultatively methylotrophic microbiota exists in some Antarctic locations. PCR amplification of genes diagnostic for methylotrophs was carried out with bacterial DNA isolated from 14 soil and sediment samples from ten locations on Signy Island, South Orkney Islands, Antarctica. Genes encoding the mxaF of methanol dehydrogenase, the fdxA for Afipia ferredoxin, the msmA of methanesulfonate monooxygenase, and the 16S rRNA gene of Methylobacterium were detected in all samples tested. The mxaF gene sequences corresponded to those of Hyphomicrobium, Methylobacterium, and Methylomonas. Over 30 pure cultures of methylotrophs were isolated on methanesulfonate, dimethylsulfone, or dimethylsulfide from ten Signy Island lakes. Some were identified from 16S rRNA gene sequences (and morphology) as Hyphomicrobium species, strains of Afipia felis, and a methylotrophic Flavobacterium strain. Antarctic environments thus contain diverse methylotrophic bacteria, growing on various C1-substrates, including C1-sulfur compounds.

Isolation and identification of bacteria from spent nuclear fuel pools

The aim of the present research was to isolate and identify bacteria from spent nuclear fuel pools of a Spanish nuclear power plant. Water samples were collected and inoculated onto different culture media to isolate the highest number of species. 16S rDNA fragments from colonies growing on solid media were amplified and analysed by denaturing gradient gel electrophoresis. Sequencing revealed the presence of 21 different bacteria belonging to several phylogenetic groups (alpha, beta, and gamma-Proteobacteria, Actinomycetales, Flavobacterium, and the Bacillus/Staphylococcus group). The isolation of these microorganisms in this particular environment (oligotrophic and radioactive) is highly interesting because of the possibility of their being used for the bioremediation of radionuclide-contaminated waters.

Isolation and properties of methanesulfonate-degrading Afipia felis from Antarctica and comparison with other strains of A. felis

Three novel strains of methylotrophic Afipia felis were isolated from several locations on Signy Island, Antarctica, and a fourth from estuary sediment from the River Douro, Portugal. They were identified as strains of the alpha-2 proteobacterium A. felis by 16S rRNA gene sequence analysis. Two strains tested were shown to contain the fdxA gene, diagnostic for A. felis. All strains grew with methanesulfonate (and two strains with dimethylsulfone) as sole carbon substrate. Growth on methanesulfonate required methanesulfonate monooxygenase (MSAMO), using NADH as the reductant and stimulated by reduced flavin nucleotides and Fe(II). Polymerase chain reaction amplification of DNA from an Antarctic strain showed a typical msmA gene for the alpha-hydroxylase of MSAMO, and both Antarctic and Portuguese strains contained mxaF, the methanol dehydrogenase large subunit gene. This is the first report of methanesulfonate-degrading bacteria from the Antarctic and of methylotrophy in Afipia, and the first description of any bacterium able to use both methanesulfonate and dimethylsulfone. In contrast, the type strain of A. felis DSM 7326(T) was not methylotrophic, but grew in defined mineral medium with a wide range of single simple organic substrates. Free-living Afipia strains occurring widely in the natural environment may be significant as methylotrophs, degrading C(1)-sulfur compounds, including the recalcitrant organosulfur compound methanesulfonate.

Brevundimonas mediterranea sp. nov., a non-stalked species from the Mediterranean Sea

Six strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from the Mediterranean Sea. 16S rRNA gene sequence analysis indicated that the strains were affiliated within the alphaproteobacterial genus Brevundimonas, with Brevundimonas intermedia (99.4 %) and Brevundimonas vesicularis (99.2 %) as their closest relatives. This affiliation was supported by chemotaxonomic data (major polar lipids: phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol; major fatty acids: C(18 : 1), C(16 : 0), C(16 : 1), C(15 : 0), C(17 : 1)omega8c, 11-Me-C(18 : 1)omega5t). The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the strains from all recognized Brevundimonas species. The strains therefore represent a novel species, for which the name Brevundimonas mediterranea sp. nov. is proposed, with the type strain V4.BO.10T)(=LMG 21911T=CIP 107934T).

Application of polyhydroxyalkanoates for denitrification in water and wastewater treatment

Application of polyhydroxyalkanoates (PHAs) and related biodegradable polymers has gained momentum in various areas of biotechnology. A promising application that started appearing in the past decade is the use of PHAs as the solid substrate for denitrification of water and wastewater. This type of denitrification, termed here "solid-phase denitrification", has several advantages over the conventional system supplemented with liquid organic substrate. PHAs serve not only as constant sources of reducing power for denitrification but also as solid matrices favorable for development of microbial films. In addition, in contrast to conventional processes, the use of PHAs has no potential risk of release of dissolved organic carbon with the resultant deterioration of effluent water quality. If the production cost of PHAs can be brought down, its application to the denitrification process will become economically more promising. A number of PHA-degrading denitrifying bacteria have been isolated and characterized from activated sludge and continuous flow-bed reactors for denitrification with PHAs. Most of these isolates have been assigned phylogenetically to members of beta-Proteobacteria, especially those of the family Comamonadaceae. The metabolic and regulatory relationships between PHA degradation and denitrification, and the interactive relationship between PHA-degrading cells and the solid surface structure are important subjects awaiting future studies, which would provide a new insight into our comprehensive understanding of the solid-phase denitrification process.

Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes

Microbial mats, growing in Antarctic lakes constitute unique and very diverse habitats. In these mats microorganisms are confronted with extreme life conditions. We isolated 746 bacterial strains from mats collected from ten lakes in the Dry Valleys (lakes Hoare and Fryxell), the Vestfold Hills (lakes Ace, Druzhby, Grace, Highway, Pendant, Organic and Watts) and the Larsemann Hills (lake Reid), using heterotrophic growth conditions. These strains were investigated by fatty acid analysis, and by numerical analysis, 41 clusters, containing 2 to 77 strains, could be delineated, whereas 31 strains formed single branches. Several fatty acid groups consisted of strains from different lakes from the same region, or from different regions. The 16S rRNA genes from 40 strains, representing 35 different fatty acid groups were sequenced. The strains belonged to the alpha, beta and gamma subclasses of the Proteobacteria, the high and low percent G+C Gram-positives, and to the Cytophaga-Flavobacterium-Bacteroides branch. For strains representing 16 fatty acid clusters, validly named nearest phylogenetic neighbours showed pairwise sequence similarities of less than 97%. This indicates that the clusters they represent, belong to taxa that have not been sequenced yet or as yet unnamed new taxa, related to Alteromonas, Bacillus, Clavibacter, Cyclobacterium, Flavobacterium, Marinobacter, Mesorhizobium, Microbacterium, Pseudomonas, Saligentibacter, Sphingomonas and Sulfitobacter.