Analysis of the polyphosphate-accumulating microflora in phosphorus-eliminating, anaerobic-aerobic activated sludge systems by using diaminopropane as a biomarker for rapid estimation of Acinetobacter spp

Characterization of a novel β-alanine biosynthetic pathway consisting of promiscuous metabolic enzymes

Bacteria adapt to utilize the nutrients available in their environment through a sophisticated metabolic system composed of highly specialized enzymes. Although these enzymes can metabolize molecules other than those for which they evolved, their efficiency toward promiscuous substrates is considered too low to be of physiological relevance. Herein, we investigated the possibility that these promiscuous enzymes are actually efficient enough at metabolizing secondary substrates to modify the phenotype of the cell. For example, in the bacterium Acinetobacter baylyi ADP1 (ADP1), panD (coding for l-aspartate decarboxylase) encodes the only protein known to catalyze the synthesis of β-alanine, an obligate intermediate in CoA synthesis. However, we show that the ADP1 ΔpanD mutant could also form this molecule through an unknown metabolic pathway arising from promiscuous enzymes and grow as efficiently as the wildtype strain. Using metabolomic analyses, we identified 1,3-diaminopropane and 3-aminopropanal as intermediates in this novel pathway. We also conducted activity screening and enzyme kinetics to elucidate candidate enzymes involved in this pathway, including 2,4-diaminobutyrate aminotransferase (Dat) and 2,4-diaminobutyrate decarboxylase (Ddc) and validated this pathway in vivo by analyzing the phenotype of mutant bacterial strains. Finally, we experimentally demonstrate that this novel metabolic route is not restricted to ADP1. We propose that the occurrence of conserved genes in hundreds of genomes across many phyla suggests that this previously undescribed pathway is widespread in prokaryotes.

The Acinetobacter baumannii disinfectant resistance protein, AmvA, is a spermidine and spermine efflux pump

Antimicrobial resistance genes, including multidrug efflux pumps, evolved long before the ubiquitous use of antimicrobials in medicine and infection control. Multidrug efflux pumps often transport metabolites, signals and host-derived molecules in addition to antibiotics or biocides. Understanding their ancestral physiological roles could inform the development of strategies to subvert their activity. In this study, we investigated the response of Acinetobacter baumannii to polyamines, a widespread, abundant class of amino acid-derived metabolites, which led us to identify long-chain polyamines as natural substrates of the disinfectant efflux pump AmvA. Loss of amvA dramatically reduced tolerance to long-chain polyamines, and these molecules induce expression of amvA through binding to its cognate regulator AmvR. A second clinically-important efflux pump, AdeABC, also contributed to polyamine tolerance. Our results suggest that the disinfectant resistance capability that allows A. baumannii to survive in hospitals may have evolutionary origins in the transport of polyamine metabolites.

Biodegradation of organophosphorus pesticides in moving bed biofilm reactors: Analysis of microbial community and biodegradation pathways

We investigated the performance of a lab-scale moving bed biofilm reactor (MBBR) with respect to general bioconversion processes and biotransformation of two commonly used organophosphorus pesticides, Chlorpyrifos (CHL) and Malathion (MAL). The reactor was operated for 300 days under different organic loads by changing hydraulic retention time (HRT). The decrease in organic load resulted in the formation of a thinner biofilm and the growth of more biomass in the bulk, which greatly shifted bioconversion processes. The low organic loading supported more nitrification in the reactor, but an opposite trend was observed for denitrification, which was enhanced at higher organic loading where the formation of anoxic zones in the thick biofilm was favored. 70% and 55% removal corresponding to 210 and 165 µg/m²/d occurred for MAL and CHL, respectively, at an HRT of 3 h and progressively increased with higher HRTs. Phylogenetic analysis revealed a shift in composition and abundance of taxa throughout the reactor operation where lower loading rate supported the growth of a more diverse and evenly distributed community. The analysis also highlighted the dominance of heterotrophic communities such as Flavobacterium and Acinetobacter johnsonii, which could be involved in the biotransformation of CHL and MAL through co-metabolism.

Comparison of two starch-based flocculants with polyacrylamide for the simultaneous removal of phosphorus and turbidity from simulated and actual wastewater samples in combination with FeCl3

Two laboratory-made cationic starch-based flocculants (St-CTA and St-AD) with different chain architectures were used to simultaneously remove phosphorus and turbidity from two simulated wastewaters and one actual wastewater with laboratory and pilot scales, respectively, in conjunction with FeCl₃. A commercial polyacrylamide (PAM) has been also tried and compared with aforementioned starch-based flocculants. The removal extents of phosphorus and turbidity increased, the required dosages of FeCl₃ decreased, and floc properties improved after dosing each polymeric flocculant after FeCl₃ in all tested wastewaters due to their synergistic effects. However, the three flocculants exhibited different improvement efficiencies on the treated wastewaters containing different forms of phosphorus and showed various synergistic mechanisms owing to their distinct structural features. In inorganic-phosphorus-simulated wastewater, the linear nonionic PAM with a high molecular weight had a more notable contribution than the two starch-based flocculants due to its efficient bridging flocculation effect. Given the branched-chain structure and high positive charge density of St-AD, it had a higher efficiency in treating real wastewater and organic-phosphorus-simulated wastewater than PAM and linear cationic St-CTA. These results may serve as references for the design and selection of a suitable flocculant in treating target wastewaters.

Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors

In light of the declining global malaria burden attained largely due to insecticides, a deeper understanding of the factors driving insecticide resistance is needed to mitigate its growing threat to malaria vector control programs. Following evidence of microbiota-mediated insecticide resistance in agricultural pests, we undertook a comparative study of the microbiota in mosquitoes of differing insecticide resistance status. The microbiota of wild-caught Anopheles albimanus, an important Latin American malaria vector, that were resistant (FEN_Res) or susceptible (FEN_Sus) to the organophosphate (OP) insecticide fenitrothion were characterized and compared using whole metagenome sequencing. Results showed differing composition of the microbiota and its functions between FEN_Res and FEN_Sus, with significant enrichment of OP-degrading bacteria and enzymes in FEN_Res compared to FEN_Sus. Lower bacterial diversity was observed in FEN_Res compared to FEN_Sus, suggesting the enrichment of bacterial taxa with a competitive advantage in response to insecticide selection pressure. We report and characterize for the first time whole metagenomes of An. albimanus, revealing associations between the microbiota and phenotypic resistance to the insecticide fenitrothion. This study lays the groundwork for further investigation of the role of the mosquito microbiota in insecticide resistance.

Microbial transcript and metabolome analysis uncover discrepant metabolic pathways in autotrophic and mixotrophic anammox consortia

The ability of anammox bacteria to utilize organic matter has drawn extensive attention. However, the metabolic discrepancies between autotrophic and mixotrophic anammox consortia need to be further explored. Here, microbial transcript and metabolomic analysis were conducted for the samples harvested in the reactors and batch assays to investigate the phenotype discrepancies and intrinsic causes in autotrophic and mixotrophic anammox consortia. Results showed that metabolically active community structures did not show significant difference between autotrophic and mixotrophic anammox consortia (C/N = 0.3). Changes in the metabolic state were the main cause for those discrepancies in virtue of the added acetate oxidized via the acetyl-CoA pathway by mixotrophic anammox bacteria. At C/N ratio of 0.3, anammox activity was obviously promoted compared to that in the autotrophic condition, due to higher levels of NADH and NAD⁺, as well as ATP consumption. Mixotrophic anammox consortia were found to yield more biomass, resulting from enhanced purine, pyrimidine, and putrescine synthetic pathways for regulating bacterial growth. Up-regulated amino sugar and nucleotide sugar metabolism pathways participating in regulating more extracellular polysaccharides secreted by mixotrophic anammox consortia. In adverse environment with higher COD concentration, more extracellular proteins were produced by anammox consortia to protect themselves and amino acids also accumulated in the cell. This study provides useful information to catch the optimal metabolism way of anammox consortia and accelerate anammox bacterial cultivation or reactor startup for wastewater treatment.

Phosphorus removal performance and biological dephosphorization process in treating reclaimed water by Integrated Vertical-flow Constructed Wetlands (IVCWs)

Phosphorous removal in adsorption had been extensively researched; however, the biological dephosphorization process and optimum operating parameters have not been discussed or quantified in Integrated Vertical-flow Constructed Wetlands (IVCWs). In this study, IVCWs planted with different plants were employed to evaluate total phosphorus (TP) treatment performance under different hydraulic retention times (HRTs), in summer and autumn. The results showed that the systems planted with Canna generalis showed the highest TP removal efficiency (77%) under a three-day HRT in autumn. The activities of exopolyphosphatase (PPX) and polyphosphate kinase (PPK) were determined, and it was found that PPK activity was seasonably variable and had been more active in autumn than that in summer (p<0.05). Highly significant correlation was revealed between PPK activity and TP removal efficiency (p<0.05). The 16S rDNA high-throughput sequencing results indicated that Pseudomonas genus might be the main participant in phosphorus aerobic biological adsorption in IVCWs.

Inorganic salts and intracellular polyphosphate inclusions play a role in the thermotolerance of the immunobiotic Lactobacillus rhamnosus CRL 1505

In this work, the thermotolerance of Lactobacillus rhamnosus CRL1505, an immunobiotic strain, was studied as a way to improve the tolerance of the strain to industrial processes involving heat stress. The strain displayed a high intrinsic thermotolerance (55°C, 20 min); however, after 5 min at 60°C in phosphate buffer a two log units decrease in cell viability was observed. Different heat shock media were tested to improve the cell survival. Best results were obtained in the mediumcontaining inorganic salts (KH₂PO₄, Na₂HPO₄, MnSO₄, and MgSO₄) likely as using 10% skim milk. Flow cytometry analysis evinced 25.0% live cells and a large number of injured cells (59.7%) in the inorganic salts medium after heat stress. The morphological changes caused by temperature were visualized by transmission electronic microscopy (TEM). In addition, TEM observations revealed the presence of polyphosphate (polyP) granules in the cells under no-stress conditions. A DAPI-based fluorescence technique, adjusted to Gram-positive bacteria for the first time, was used to determine intracellular polyP levels. Results obtained suggest that the high initial polyP content in L. rhamnosus CRL 1505 together with the presence of inorganic salts in the heat shock medium improve the tolerance of the cells to heat shock. To our knowledge, this is the first report giving evidence of the relationship between polyP and inorganic salts in thermotolerance of lactic acid bacteria.

Hyperconcentrated Sweet Whey, a New Culture Medium That Enhances Propionibacterium freudenreichii Stress Tolerance

Propionibacterium freudenreichii is used as a cheese-ripening starter and as a probiotic. Its reported physiological effects at the gut level, including modulation of bifidobacteria, colon epithelial cell proliferation and apoptosis, and intestinal inflammation, rely on active metabolism in situ Survival and activity are thus key factors determining its efficacy, creating stress adaptation and tolerance bottlenecks for probiotic applications. Growth media and growth conditions determine tolerance acquisition. We investigated the possibility of using sweet whey, a dairy by-product, to sustain P. freudenreichii growth. It was used at different concentrations (dry matter) as a culture medium. Using hyperconcentrated sweet whey led to enhanced multistress tolerance acquisition, overexpression of key stress proteins, and accumulation of intracellular storage molecules and compatible solutes, as well as enhanced survival upon spray drying. A simplified process from growth to spray drying of propionibacteria was developed using sweet whey as a 2-in-1 medium to both culture P. freudenreichii and protect it from heat and osmotic injury without harvesting and washing steps. As spray drying is far cheaper and more energy efficient than freeze-drying, this work opens new perspectives for the sustainable development of new starter and probiotic preparations with enhanced robustness.

IMPORTANCE

In this study, we demonstrate that sweet whey, a dairy industry by-product, not only allows the growth of probiotic dairy propionibacteria, but also triggers a multitolerance response through osmoadaptation and general stress response. We also show that propionibacteria accumulate compatible solutes under these culture conditions, which might account for the limited loss of viability after spray drying. This work opens new perspectives for more energy-efficient production of dairy starters and probiotics.

Accumulation of polyphosphate in Lactobacillus spp. and its involvement in stress resistance

Polyphosphate (poly-P) is a polymer of phosphate residues synthesized and in some cases accumulated by microorganisms, where it plays crucial physiological roles such as the participation in the response to nutritional stringencies and environmental stresses. Poly-P metabolism has received little attention in Lactobacillus, a genus of lactic acid bacteria of relevance for food production and health of humans and animals. We show that among 34 strains of Lactobacillus, 18 of them accumulated intracellular poly-P granules, as revealed by specific staining and electron microscopy. Poly-P accumulation was generally dependent on the presence of elevated phosphate concentrations in the culture medium, and it correlated with the presence of polyphosphate kinase (ppk) genes in the genomes. The ppk gene from Lactobacillus displayed a genetic arrangement in which it was flanked by two genes encoding exopolyphosphatases of the Ppx-GppA family. The ppk functionality was corroborated by its disruption (LCABL_27820 gene) in Lactobacillus casei BL23 strain. The constructed ppk mutant showed a lack of intracellular poly-P granules and a drastic reduction in poly-P synthesis. Resistance to several stresses was tested in the ppk-disrupted strain, showing that it presented a diminished growth under high-salt or low-pH conditions and an increased sensitivity to oxidative stress. These results show that poly-P accumulation is a characteristic of some strains of lactobacilli and may thus play important roles in the physiology of these microorganisms.

Structure and biosynthesis of fimsbactins A-F, siderophores from Acinetobacter baumannii and Acinetobacter baylyi

Novel chatechol/hydroxamate siderophores (named "fimsbactins") were identified in Acinetobacter baumannii ATCC 17978 and Acinetobacter baylyi ADP1. The major compound, fimsbactin A, was isolated from low-iron cultures of A. baylyi ADP1, and its chemical structure was elucidated by mass spectrometry, and detailed (1)H, (13)C and (15)N NMR spectroscopy. From inverse feeding experiments following HPLC-MS analysis, the structures of five additional derivatives were elucidated. The gene cluster encoding the fimsbactin synthetase (fbs) was identified in both genomes, and mutants in fbs genes in A. baylyi were analyzed, thus allowing prediction of the fimsbactin biosynthesis pathway.

Evolution of a novel lysine decarboxylase in siderophore biosynthesis

Structural backbones of iron-scavenging siderophore molecules include polyamines 1,3-diaminopropane and 1,5-diaminopentane (cadaverine). For the cadaverine-based desferroxiamine E siderophore in Streptomyces coelicolor, the corresponding biosynthetic gene cluster contains an ORF encoded by desA that was suspected of producing the cadaverine (decarboxylated lysine) backbone. However, desA encodes an l-2,4-diaminobutyrate decarboxylase (DABA DC) homologue and not any known form of lysine decarboxylase (LDC). The only known function of DABA DC is, together with l-2,4-aminobutyrate aminotransferase (DABA AT), to synthesize 1,3-diaminopropane. We show here that S. coelicolor desA encodes a novel LDC and we hypothesized that DABA DC homologues present in siderophore biosynthetic clusters in the absence of DABA AT ORFs would be novel LDCs. We confirmed this by correctly predicting the LDC activity of a DABA DC homologue from a Yersinia pestis siderophore biosynthetic pathway. The corollary was confirmed for a DABA DC homologue, adjacent to a DABA AT ORF in a siderophore pathway in the cyanobacterium Anabaena variabilis, which was shown to be a bona fide DABA DC. These findings enable prediction of whether a siderophore pathway will utilize 1,3-diaminopropane or cadaverine, and suggest that the majority of bacteria use DABA AT and DABA DC for siderophore, rather than norspermidine/polyamine biosynthesis.

Surface-associated motility, a common trait of clinical isolates of Acinetobacter baumannii, depends on 1,3-diaminopropane

While flagella-independent motility has long been described in representatives of the genus Acinetobacter, the mechanism of motility remains ambiguous. Acinetobacter baumannii, a nosocomial pathogen appearing increasingly multidrug-resistant, may profit from motility during infection or while persisting in the hospital environment. However, data on the frequency of motility skills among clinical A. baumannii isolates is scarce. We have screened a collection of 83 clinical A. baumannii isolates of different origin and found that, with the exception of one isolate, all were motile on wet surfaces albeit to varying degrees and exhibiting differing morphologies. Screening a collection of transposon mutants of strain ATCC 17978 for motility defects, we identified 2 akinetic mutants carrying transposon insertions in the dat and ddc gene, respectively. These neighbouring genes contribute to synthesis of 1,3-diaminopropane (DAP), a polyamine ubiquitously produced in Acinetobacter. Supplementing semi-solid media with DAP cured the motility defect of both mutants. HPLC analyses confirmed that DAP synthesis was abolished in ddc and dat mutants of different A. baumannii isolates and was re-established after genetic complementation. Both, the dat and ddc mutant of ATCC 17978 were attenuated in the Galleria mellonella caterpillar infection model. Taken together, surface-associated motility is a common trait of clinical A. baumannii isolates that requires DAP and may play a role in its virulence.

Acinetobacter indicus sp. nov., isolated from a hexachlorocyclohexane dump site

The taxonomic position of a Gram-negative, non-motile, oxidase negative and catalase positive strain, A648(T), isolated from a hexachlorocyclohexane (HCH) dump site located in Lucknow, India, was ascertained by using a polyphasic approach. A comparative analysis of a partial sequence of the rpoB gene and the 16S rRNA gene sequence revealed that strain A648(T) belonged to the genus Acinetobacter. DNA-DNA relatedness values between strain A648(T) and other closely related members (16S rRNA gene sequence similarity greater than 97%), namely Acinetobacter radioresistens DSM 6976(T), A. venetianus ATCC 31012(T), A. baumannii LMG 1041(T), A. parvus LMG 21765(T) A. junii LMG 998(T) and A. soli JCM 15062(T), were found to be less than 8%. The major cellular fatty acids of strain A648(T) were 18:1ω9c (19.6%), summed feature 3 (15.9%), 16:0 (10.6%) and 12:0 (6.4%). The DNA G+C content was 40.4 mol%. The polar lipid profile of strain A648(T) indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, followed by phosphatidylglycerol and phosphatidylcholine. The predominant polyamine of strain A648(T) was 1,3-diaminopropane and moderate amounts of putrescine, spermidine and spermine were also detected. The respiratory quinone consisted of ubiquinone with nine isoprene units (Q-9). On the basis of DNA-DNA hybridization, phenotypic characteristics and chemotaxonomic and phylogenetic comparisons with other members of the genus Acinetobacter, strain A648(T) is found to be a novel species of the genus Acinetobacter, for which the name Acinetobacter indicus sp. nov. is proposed. The type strain is A648(T) ( = DSM 25388(T) = CCM 7832(T)).

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.

Molecular analyses of the microbial community composition of an anoxic basin of a municipal wastewater treatment plant reveal a novel lineage of proteobacteria

A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples. The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total bacterial population rRNA within the anoxic basin.

Requirement of Acinetobacter junii for magnesium, calcium and potassium ions

The goal of this study was to determine the concentrations of Mg, Ca and K ions required for the formation of metabolically active population of phosphate (P)-accumulating bacterium Acinetobacter junii. The availability of Mg, Ca and K originating from natural minerals in the conditions of severe shortage of these cations was tested. In the case of shortage of Mg, Ca and K ions in wastewater the P removal was absent due to the decay of A. junii. In the cases of Mg or K shortage in wastewater the P removal was negligible due to the decay of A. junii, while Ca was not essential for the examined bacterium. The minimal required concentrations of Mg and K in synthetic wastewater were 0.64 mg Mg/mg P and 0.50 mg K/mg P. The natural zeolitized tuffs and bentonite, either in Mg, Ca or K form, successfully replaced the lack of Mg, Ca, K and trace metals in wastewater. The requirement of A. junii for examined cations was in the order: Mg>K>Ca.

Flow-FISH analysis and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target

By using hydrogenase gene-targeted polymerase chain reaction (PCR) and reverse transcriptase PCR (RT-PCR), the predominant clostridial hydrogenase that may have contributed to biohydrogen production in an anaerobic semi-solid fermentation system has been monitored. The results revealed that a Clostridium pasteurianum-like hydrogenase gene sequence can be detected by both PCR and RT-PCR and suggested that the bacterial strain possessing this specific hydrogenase gene was dominant in hydrogenase activity and population. Whereas another Clostridium saccharobutylicum-like hydrogenase gene can be detected only by RT-PCR and suggest that the bacterial strain possessing this specific hydrogenase gene may be less dominant in population. In this study, hydrogenase gene-targeted fluorescence in situ hybridization (FISH) and flow cytometry analysis confirmed that only 6.6% of the total eubacterial cells in a hydrogen-producing culture were detected to express the C. saccharobutylicum-like hydrogenase, whereas the eubacteria that expressed the C. pasteurianum-like hydrogenase was 25.6%. A clostridial strain M1 possessing the identical nucleotide sequences of the C. saccharobutylicum-like hydrogenase gene was then isolated and identified as Clostridium butyricum based on 16S rRNA sequence. Comparing to the original inoculum with mixed microflora, either using C. butyricum M1 as the only inoculum or co-culturing with a Bacillus thermoamylovorans isolate will guarantee an effective and even better production of hydrogen from brewery yeast waste.

Molecular detection of the clostridia in an anaerobic biohydrogen fermentation system by hydrogenase mRNA-targeted reverse transcription-PCR

Molecular biological approaches were developed to monitor the potential biohydrogen-producing clostridia in an anaerobic semisolid fermentation system that used brewery yeast waste as the fermentation substrate. The denaturing gradient gel electrophoresis with 16S rDNA gene-targeted polymerase chain reaction (PCR) analysis was employed to confirm the existence of clostridia in the system. Remarkably, reproducible nucleotide sequences of clostridia were obtained from different hydrogen production stages by using hydrogenase gene-targeted reverse transcription (RT)-PCR. These RNA-based information suggested that the predominant hydrogen-producing strains possess either a specific Clostridium pasteurianum-like or a specific Clostridium saccharobutylicum-like hydrogenase sequence. Comparison of the hydrogenase gene-targeted sequence profiles between PCR and RT-PCR revealed that the specific C. pasteurianum-like hydrogenase harboring bacterial strains were dominant in both mRNA and bacterial population level. On the other hand, the specific C. saccharobutylicum-like hydrogenase harboring strains expressed high level of hydrogenase mRNA but may not be dominant in population. Furthermore, quantitative real-time RT-PCR analysis showed the expression pattern of the clostridial hydrogenase mRNA and may serve as an activity index for the system.

Microbial communities in activated sludge performing enhanced biological phosphorus removal in a sequencing batch reactor

Microbial communities of activated sludge in an anaerobic/aerobic sequencing batch reactor (SBR) supplied with acetate as sole carbon source were analyzed to identify the microorganisms responsible for enhanced biological phosphorus removal. Various analytical methods were used such as electron microscopy, quinone, slot hybridization, and 16S rRNA gene sequencing analyses. Electron photomicrographs showed that coccus-shaped microorganisms of about 1 microm diameter dominated the microbial communities of the activated sludge in the SBR, which had been operated for more than 18 months. These microorganisms contained polyphosphate granules and glycogen inclusions, which suggests that they are a type of phosphorus-accumulating organism. Quinones, slot hybridization, and 16S rRNA sequencing analyses showed that the members of the Proteobacteria beta subclass were the most abundant species and were affiliated with the Rhodocyclus-like group. Phylogenetic analysis revealed that the two dominating clones of the beta subclass were closely related to the Rhodocyclus-like group. It was concluded that the coccus-shaped organisms related to the Rhodocyclus-like group within the Proteobacteria beta subclass were the most dominant species believed responsible for biological phosphorus removal in SBR operation with acetate.

The microbiology of biological phosphorus removal in activated sludge systems

Activated sludge systems are designed and operated globally to remove phosphorus microbiologically, a process called enhanced biological phosphorus removal (EBPR). Yet little is still known about the ecology of EBPR processes, the microbes involved, their functions there and the possible reasons why they often perform unreliably. The application of rRNA-based methods to analyze EBPR community structure has changed dramatically our understanding of the microbial populations responsible for EBPR, but many substantial gaps in our knowledge of the population dynamics of EBPR and its underlying mechanisms remain. This review critically examines what we once thought we knew about the microbial ecology of EBPR, what we think we now know, and what still needs to be elucidated before these processes can be operated and controlled more reliably than is currently possible. It looks at the history of EBPR, the currently available biochemical models, the structure of the microbial communities found in EBPR systems, possible identities of the bacteria responsible, and the evidence why these systems might operate suboptimally. The review stresses the need to extend what have been predominantly laboratory-based studies to full-scale operating plants. It aims to encourage microbiologists and process engineers to collaborate more closely and to bring an interdisciplinary approach to bear on this complex ecosystem.

Involvement of Rhodocyclus-related organisms in phosphorus removal in full-scale wastewater treatment plants

The participation of organisms related to Rhodocyclus in full-scale enhanced biological phosphorus removal (EBPR) was investigated. By using fluorescent in situ hybridization techniques, the communities of Rhodocyclus-related organisms in two full-scale wastewater treatment plants were estimated to represent between 13 and 18% of the total bacterial population. However, the fractions of these communities that participated in polyphosphate accumulation depended on the type of treatment process evaluated. In a University of Cape Town EBPR process, the percentage of Rhodocyclus-related cells that contained polyphosphate was about 20% of the total bacterial population, but these cells represented as much as 73% of the polyphosphate-accumulating organisms (PAOs). In an aerated-anoxic EBPR process, Rhodocyclus-related PAOs were less numerous, accounting for 6% of the total bacterial population and 26% of the total PAO population. In addition, 16S ribosomal DNA sequences 99.9% similar to the sequences of Rhodocyclus-related organisms enriched in acetate-fed bench-scale EBPR reactors were recovered from both full-scale plants. These results confirmed the involvement of Rhodocyclus-related organisms in EBPR and demonstrated their importance in full-scale processes. In addition, the results revealed a significant correlation between the type of EBPR process and the PAO community.

Psychrobacter faecalis sp. nov., a new species from a bioaerosol originating from pigeon faeces

The taxonomy of strain Iso-46T isolated from a bioaerosol generated by cleaning of a pigeon faeces contaminated room was investigated in a polyphasic approach. The beige pigmented Gram-negative, oxidase-negative organism contained a quinone system with mainly ubiquinone Q-8, and the polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, beside some hitherto uncharacterized phospholipids. Major polyamines were spermidine and putrescine and also small amounts of cadaverine. The analysis of the fatty acids revealed 3-OH 12:0 and 3-OH 14:0 (within summed feature 3) as hydroxylated fatty acids. These chemotaxonomic characteristics suggest that the strain belongs to the gamma-subclass of the Proteobacteria namely into the genus Psychrobacter. Analysis of the 16S rRNA gene supported the allocation into the genus Psychrobacter, but showing similarities to all described species of this genus lower than 97%. Iso-46T was able to grow on MacConkey agar and other high nutrient containing media within a temperature range of 4 degrees C to 36 degrees C. On the basis of nutritional and further physiological features, a clear differentiation from all other Psychrobacter species was possible. For these reasons it is proposed to create a new species with the name Psychrobacter faecalis sp. nov.

Yeast spores seem to be involved in biological phosphate removal: a microscopic in situ case study

The principal polyphosphate-accumulating organism (PAO) in a biological-phosphate-removal activated-sludge process was assessed microscopically. The organism was recognized by its distinct morphotype most easily after polyphosphate staining. The PAO occurred in large, homogeneous clusters. The cells of the PAO were the biggest cells abounding in the sludge--clearly bigger than average sludge bacteria. Typical of the principal PAO was a variation of cell size, even in fresh sludge. In acetate minimal medium containing ampicillin, the original principal PAO clusters were converted to clusters of clearly larger, polyphosphate-containing, vegetative yeast-like cells. Cycloheximide addition inhibited this and caused flock disintegration, disappearance of the principal PAO clusters and growth of free bacteria. The cell wall of the principal PAO was not of the usual bacterial character. It showed anomalous Gram staining, stained for chitin (not found in bacteria) and bound concanavalin A, like cell walls of many yeasts. In addition, the PAO cell wall was resistant to lysozyme, but sensitive to an enzyme mixture that lyses yeast cell walls. It was concluded that the principal PAO cells in the studied sludge were clustered spores of a yeast.

Inhibition of anaerobic phosphate release by nitric oxide in activated sludge

Activated sludge not containing significant numbers of denitrifying, polyphosphate [poly(P)]-accumulating bacteria was grown in a fill-and-draw system and exposed to alternating anaerobic and aerobic periods. During the aerobic period, poly(P) accumulated up to 100 mg of P x g of (dry) weight. When portions of the sludge were incubated anaerobically in the presence of acetate, 80 to 90% of the intracellular poly(P) was degraded and released as orthophosphate. Degradation of poly(P) was mainly catalyzed by the concerted action of polyphosphate:AMP phosphotransferase and adenylate kinase, resulting in ATP formation. In the presence of 0.3 mM nitric oxide (NO) in the liquid-phase release of phosphate, uptake of acetate, formation of poly-beta-hydroxybutyrate, utilization of glycogen, and formation of ATP were severely inhibited or completely abolished. In cell extracts of the sludge, adenylate kinase activity was completely inhibited by 0.15 mM NO. The nature of this inhibition was probably noncompetitive, similar to that with hog adenylate kinase. Activated sludge polyphosphate glucokinase was also completely inhibited by 0.15 mM NO. It is concluded that the inhibitory effect of NO on acetate-mediated phosphate release by the sludge used in this study is due to the inhibition of adenylate kinase in the phosphate-releasing organisms. The inhibitory effect of nitrate and nitrite on phosphate release is probably due to their conversion to NO. The lack of any inhibitory effect of NO on adenylate kinase of the poly(P)-accumulating Acinetobacter johnsonii 210A suggests that this type of organism is not involved in the enhanced biological phosphate removal by the sludges used.

Quinone Profiling of Bacterial Communities in Natural and Synthetic Sewage Activated Sludge for Enhanced Phosphate Removal

Respiratory quinones were used as biomarkers to study bacterial community structures in activated sludge reactors used for enhanced biological phosphate removal (EBPR). We compared the quinone profiles of EBPR sludges and standard sludges, of natural sewage and synthetic sewage, and of plant scale and laboratory scale systems. Ubiquinone (Q) and menaquinone (MK) components were detected in all sludges tested at molar MK/Q ratios of 0.455 to 0.981. The differences in MK/Q ratios were much larger when we compared different wastewater sludges (i.e., raw sewage and synthetic sewage) than when we compared sludges from the EBPR and standard processes or plant scale and laboratory scale systems. In all sludges tested a Q with eight isoprene units (Q-8) was the most abundant quinone. In the MK fraction, either tetrahydrogenated MK-8 or MK-7 was the predominant type, and there was also a significant proportion of MK-6 to MK-8 in most cases. A numerical cluster analysis of the profiles showed that the sludges tested fell into two major clusters; one included all raw sewage sludges, and the other consisted of all synthetic sewage sludges, independent of the operational mode and scale of the reactors and the phosphate accumulation. These data suggested that Q-8-containing species belonging to the class Proteobacteria (i.e., species belonging to the beta subclass) were the major constituents of the bacterial populations in the EBPR sludge, as well as in standard activated sludge. Members of the class Actinobacteria (gram-positive bacteria with high DNA G+C contents) were the second most abundant group in both types of sludge. The bacterial community structures in activated sludge processes may be affected more by the nature of the influent wastewater than by the introduction of an anaerobic stage into the process or by the scale of the reactors.

Phylogenetic analysis and in situ identification of bacteria in activated sludge

The bacterial community structure of activated sludge of a large municipal wastewater treatment plant was investigated by use of the rRNA approach. Almost-full-length genes coding for the small-subunit rRNA (rDNA) were amplified by PCR and subsequently cloned into the pGEM-T vector. Clones were screened by dot blot hybridization with group-specific oligonucleotide probes. The phylogenetic affiliations of clones were compared with the results obtained with the original sample by in situ hybridization with fluorescently labeled, rRNA-targeted oligonucleotide probes and found to be in general agreement. Twenty-five 16S rDNA clones were fully sequenced, 11 were almost fully (> 80%) sequenced, and 27 were partially sequenced. By comparative sequence analyses, the majority of the examined clones (35 of 67) could be affiliated with the beta subclass of the class Proteobacteria. The gamma and alpha subclasses of Proteobacteria were represented by 13 and 4 clones, respectively. Eight clones grouped with the epsilon group of Proteobacteria, and five clones grouped with gram-positive bacteria with a low DNA G+C content. The 16S rDNA of two clones showed similarity with 16S rDNA genes of members of the phyla Chlamydiae and Planctomyces. 16S rRNA-targeted oligonucleotide probes were designed and used for the enumeration of the respective bacteria. Interestingly, potentially pathogenic representatives of the genus Arcobacter were present in significant numbers (4%) in the activated sludge sample examined. Pairs of probes targeted to the 5' and 3' regions were used for detection of chimeric sequences by in situ hybridization. Two clones could be identified as chimera by applying such a pair of probes.

Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics

Most of the bacterial species are still unknown. Consequently, our knowledge about bacterial ecology is poor and expectations about specialized species with novel enzymatic functions or new products are high. Thus, bacterial identification is a growing field of interest within microbiology. In this review, suitability of developments for identification based on miniaturized biochemical and physiological investigations of bacteria are evaluated. Special emphasis is given to chemotaxonomic methods such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, peptidoglycan diaminoacids, as well as analytical fingerprinting methods and cellular protein patterning. 16S rDNA sequencing introduced to investigate the phylogenetic relationships of bacteria, nucleic acids hybridization techniques and G + C content determination are discussed as well as restriction fragment length polymorphism (RFLP), macrorestriction analysis and random amplified polymorphic DNA (RAPD). The importance of the different approaches in classification and identification of bacteria according to phylogenetic relationships are demonstrated on selected examples.

Characterization of Acinetobacter type strains and isolates obtained from wastewater treatment plants by PCR fingerprinting

Acinetobacter type strains and isolates from wastewater treatment plants were differentiated by PCR fingerprinting. On the first level, PCR fingerprinting with two tRNA-gene specific primers (T5B and T3A) was used for the identification of species (genospecies 1 to 17). On the second level, a single arbitrary primer (DAF 4) was employed for strain differentiation. Upon comparison of Acinetobacter type strains with 28 sewage sludge isolates, 2 could be classified as belonging to A. johnsonii, 8 isolates could be classified as A. lwoffii, 8 could be classified as A. baumannii, and 9 isolates were very closely related to the Acinetobacter species A. junii; only 1 isolate could not be classified as one of the Acinetobacter type strains. The PCR fingerprinting method was found to be a reproducible and fast method for differentiation and identification of Acinetobacter isolates. Because of some resulting discrepancies compared with previously described identification schemes, e.g., DNA-DNA hybridization methods, the original identification experiments should be repeated and the results should be reassessed.

Biology of polyphosphate-accumulating bacteria involved in enhanced biological phosphorus removal

Recent research on the process of biological phosphorus removal in lab-scale treatment systems has indicated that: (i) the development of an actively polyP-accumulating bacterial community after the introduction of an anaerobic period may take at least 4 months; (ii) up to 80% of all aerobic bacteria isolated from these communities are able to accumulate polyP; (iii) polyP synthesized by the bacterial communities of lab-scale treatment systems is probably mainly low polymeric, not exceeding 20 P-residues, and this polyP is rapidly degraded during the anaerobic period; (iv) the enzymatic hydrolysis of polyP under anaerobic conditions is accompanied by PHB formation from exogenous acetate, reducing equivalents are provided by the degradation of carbohydrates; and (v) nitric oxide inhibits the release of phosphate under anaerobic conditions in Renpho and F&D sludges. Bacteria belonging to the genus Acinetobacter occur in a wide variety of activated sludges in which enhanced biological phosphate removal is observed. A. johnsonii 210A was studied in detail with respect to the elemental composition of polyP granules, the enzymatic synthesis and degradation of polyP, the regulation of polyP metabolism, and the transport of phosphate. A. johnsonii 210A reflects activated sludge in a number of ways as far as polyP metabolism is concerned but its polyP is highly polymeric and the phosphate efflux rate under anaerobic conditions is relatively low and not increased by exogenous acetate. In addition to Acinetobacter, other polyP-accumulating microorganisms may be involved in biological phosphorus removal. The isolation of polyP-accumulating denitrifying bacteria may well have interesting implications for a new process design in wastewater treatment systems. Further studies on the enzymes involved in polyP biosynthesis and on the uptake and efflux systems of phosphate, potassium, magnesium and lower fatty acids in pure cultures will enlarge our insight in the energetics of the metabolism of polyP. In addition, the regulation of the metabolism of polyP-accumulating organisms needs to be studied in more detail.

Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge

Enhanced biological phosphate removal in an anaerobic-aerobic activated sludge system has generally been ascribed to members of the genus Acinetobacter. A genus-specific 16S rRNA-targeted oligonucleotide probe was developed to investigate the role of Acinetobacter spp. in situ. Nonisotopic dot blot hybridization to 66 reference strains, including the seven described Acinetobacter spp., demonstrated the expected probe specificity. Fluorescent derivatives were used for in situ monitoring of Acinetobacter spp. in the anaerobic and aerobic compartments of a sewage treatment plant with enhanced biological phosphate removal. Microbial community structures were further analyzed with oligonucleotide probes specific for the alpha, beta, or gamma subclasses of the class Proteobacteria, for the Cytophaga-Flavobacterium cluster, for gram-positive bacteria with a high G + C DNA content, and for all bacteria. Total cell counts were determined by 4',6-diamidino-2-phenylindole staining. In both the anaerobic and the aerobic basins, the activated sludge samples were dominated by members of the class Proteobacteria belonging to the beta subclass and by gram-positive bacteria with a high G + C DNA content. Acinetobacter spp. constituted less than 10% of all bacteria. For both basins, the microbial community structures determined with molecular techniques were compared with the compositions of the heterotrophic saprophytic microbiota determined with agar plating techniques. Isolates on nutrient-rich medium were classified by whole-cell hybridization with rRNA-targeted probes and fatty acid analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Polyphosphate-dependent enzymes in some coryneform bacteria isolated from sewage sludge

Eleven isolates obtained from a laboratory sewage treatment plant, most of them presumptively assigned to the coryneform genera Curtobacterium and Aureobacterium were studied for the presence of intracellular polyphosphates and polyphosphate dependent enzymes. All isolates stored polyphosphates and showed adenylate kinase activities ranging from 64 to 815 mU mg-1. Polyphosphate:AMP phosphotransferase could only be detected in one isolate. Three isolates showed a polyphosphate kinase activity also in minor amounts from 15 to 17 mU mg-1. A polyphosphate dependent NAD or 3-phosphoglycerate kinase could not be detected. Polyphosphate glucokinase activity was measured in cell-free extracts of nine isolates ranging from 2 to 376 mU mg-1. Three isolates showed in addition to the polyphosphate glucokinase, a glucose-6-phosphate-dependent NAD kinase. For the regeneration of NADP from NAD and polyphosphate, this enzyme system may give the isolates a distinct competitive advantage, especially for anabolic processes. The polyphosphate-dependent enzymes reported here may play an additional role in the complex process of 'biological' phosphate removal from wastewater.