An outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process

High-rate partial nitritation as a pretreatment of anammox process

In this study, a laboratory-scale partial nitrification reactor (PN reactor) was used to treat high-ammonia-nitrogen wastewater, by changing the influent NH4+-N conversion rate as the main operating strategy, to investigate the upper limit of its NH4+-N conversion rate (ACR) and explore its feasibility as an anammox pre-process. During the experiment, PN reactor was successfully activated in only 10 days. The PN reactor reached the highest ACR value of approximately 10.24 kg N/(m3 · day) when the influent ACR was 16.57 kg N/(m3 · day), and the ammonia conversion efficiency (ACE) was 61.78% at this time. The ratio of [NO2--N]Eff/[NH4+-N]Eff was approximately 1.37 which was close to the theoretical ratio of 1.32. And feasibility exploration experiment proved that it was feasible to use this PN reactor as a pre-process of anammox. The PCR-DGGE results showed that the dominant phylum and genus in the reactor during the ACR experiment were Proteobacteria and Nitrosomonas, respectively. With the increase in the ACR, the relative concentration of Nitrosomonas sp. G1 increased from 15 to 40%. This indicates that its abundance is directly correlated with the increase in the ACR. High-throughput sequencing showed that increasing the ACR of the PN reactor greatly reduced the diversity and abundance of the system microbial community structure and changed the dominant phylum and genus; however, the stability of the system was not disrupted. High-throughput sequencing experiments showed that the abundance value of nitrosation enzymes accounted for 91.62%, which was positively correlated with the expression of nitrification genes in the genus Nitrosomonas.

Characterization and Biodegradation of Phenol by Pseudomonas aeruginosa and Klebsiella variicola Strains Isolated from Sewage Sludge and Their Effect on Soybean Seeds Germination

Phenols are very soluble in water; as a result, they can pollute a massive volume of fresh water, wastewater, groundwater, oceans, and soil, negatively affecting plant germination and animal and human health. For the detoxification and bioremediation of phenol in wastewater, phenol biodegradation using novel bacteria isolated from sewage sludge was investigated. Twenty samples from sewage sludge (SS) were collected, and bacteria in SS contents were cultured in the mineral salt agar (MSA) containing phenol (500 mg/L). Twenty colonies (S1 up to S20) were recovered from all the tested SS samples. The characteristics of three bacterial properties, 16S rDNA sequencing, similarities, GenBank accession number, and phylogenetic analysis showed that strains S3, S10, and S18 were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Klebsiella variicola, respectively. P. aeruginosa, K. pneumoniae, and K. variicola were able to degrade 1000 mg/L phenol in the mineral salt medium. The bacterial strains from sewage sludge were efficient in removing 71.70 and 74.67% of phenol at 1000 mg/L within three days and could tolerate high phenol concentrations (2000 mg/L). The findings showed that P. aeruginosa, K. pneumoniae, and K. variicola could potentially treat phenolic water. All soybean and faba bean seeds were germinated after being treated with 250, 500, 750, and 1000 mg/L phenol in a mineral salt medium inoculated with these strains. The highest maximum phenol removal and detoxification rates were P. aeruginosa and K. variicola. These strains may help decompose and detoxify phenol from industrial wastewater with high phenol levels and bioremediating phenol-contaminated soils.

Quantitative and Qualitative Changes in the Genetic Diversity of Bacterial Communities in Anaerobic Bioreactors with the Diatomaceous Earth/Peat Cell Carrier

This paper analyses the impact of the diatomaceous earth/peat (DEP; 3:1) microbial carrier on changes in the bacterial microbiome and the development of biofilm in the anaerobic digestion (AD) of confectionery waste, combined with digested sewage sludge as inoculum. The physicochemical properties of the carrier material are presented, with particular focus on its morphological and dispersion characteristics, as well as adsorption and thermal properties. In this respect, the DEP system was found to be a suitable carrier for both mesophilic and thermophilic AD. The evaluation of quantitative and qualitative changes in the genetic diversity of bacterial communities, carried out using next-generation sequencing (NGS), showed that the material has a modifying effect on the bacterial microbiome. While Actinobacteria was the most abundant cluster in the WF-control sample (WF—waste wafers), Firmicutes was the dominant cluster in the digested samples without the carrier (WF-dig.; dig.—digested) and with the carrier (WF + DEP). The same was true for the count of Proteobacteria, which decreased twofold during biodegradation in favor of Synergistetes. The Syntrophomonas cluster was identified as the most abundant genus in the two samples, particularly in WF + DEP. This information was supplemented by observations of morphological features of microorganisms carried out using fluorescence microscopy. The biodegradation process itself had a significant impact on changes in the microbiome of samples taken from anaerobic bioreactors, reducing its biodiversity. As demonstrated by the results of this innovative method, namely the BioFlux microfluidic flow system, the decrease in the number of taxa in the digested samples and the addition of DEP contributed to the microbial adhesion in the microfluidic system and the formation of a stable biofilm.

Silica/Lignin Carrier as a Factor Increasing the Process Performance and Genetic Diversity of Microbial Communities in Laboratory-Scale Anaerobic Digesters

The article aims to present results of research on anaerobic digestion (AD) of waste wafers (WF-control) and co-substrate system–waste wafers and cheese (WFC-control), combined with digested sewage sludge, as inoculum. The purpose of this paper is to confirm the outcome of adding silica/lignin (S/L; 4:1) material, as a microbial carrier, on the process performance and genetic diversity of microbial communities. The experiment was conducted in a laboratory under mesophilic conditions, in a periodical operation mode of bioreactors. Selected physicochemical parameters of the tested carrier, along with the microstructure and thermal stability, were determined. Substrates, batches and fermenting slurries were subjected to standard parameter analysis. As part of the conducted analysis, samples of fermented food were also tested for total bacterial count, dehydrogenase activity. Additionally, DNA extraction and next-generation sequencing (NGS) were carried out. As a result of the conducted study, an increase in the volume of produced biogas was recorded for samples fermented with S/L carrier: in the case of WF + S/L by 18.18% to a cumulative biogas yield of 833.35 m3 Mg−1 VS, and in the case of WFC + S/L by 17.49% to a yield of 950.64 m3 Mg−1 VS. The largest total bacterial count, during the process of dehydrogenase activity, was maintained in the WFC + S/L system. The largest bacterial biodiversity was recorded in samples fermented with the addition of cheese, both in the case of the control variant and in the variant when the carrier was used. In contrast, three phyla of bacteria Firmicutes, Proteobacteria and Actinobacteria predominated in all experimental facilities.

Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin

A novel actinobacterium, designated strain NEAU-HG-1^T, was isolated from soil collected from Harbin, Heilongjiang Province, Northeast China and characterised using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-HG-1^T belonged to the genus Micromonospora, and shared high sequence similarities with Micromonospora auratinigra DSM 44815^T (98.9%) and Micromonospora coerulea DSM 43143^T (98.7%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Micromonospora. Cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The polar lipid contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipid and phosphatidylinositol. The predominant menaquinones were MK-10(H₂), MK-10(H₄) and MK-10(H₆). The major fatty acids were C_17:0 cycle, iso-C_15:0, and iso-C_16:0. Furthermore, strain NEAU-HG-1^T displayed a DNA-DNA relatedness of 33.8 ± 2.2% with M. coerulea DSM 43143^T. The level of digital DNA-DNA hybridization between strain NEAU-HG-1^T and M. auratinigra DSM 44815^T was 27.2% (24.8-29.7%). The value was well below the criteria for species delineation of 70% for dDDH. Whole-genome average nucleotide identity analyses result also indicated that the isolate should be assigned to a new species under the genus Micromonospora. Therefore, it is concluded that strain NEAU-HG-1^T represents a novel species of the genus Micromonospora, for which the name Micromonospora rubida sp. nov. is proposed, with NEAU-HG-1^T (= CGMCC 4.7479^T = JCM 32386^T) as the type strain.

Adding an anaerobic step can rapidly inhibit sludge bulking in SBR reactor

Activated sludge from wastewater treatment plants was seeded into a sequencing batch reactor (SBR) in which synthetic wastewater was used as the influent. The sludge was bulked by decreasing the concentration of dissolved oxygen (DO). By adding a 30 min step of anaerobic stirring after the water inflow, the sludge bulking was rapidly inhibited after 10 running cycles, and the sludge volume index (SVI) decreased from 222 to 74 mL·g^-1. The results of high-throughput sequencing showed that the relative abundance of bacteria Thiothrix, bacteria norank_o_Sphingobacteriales and fungi Trichosporon was increased by 6.3, 4.3 and 81.2%, after initial SBR stages, but these bacteria were inhibited by the addition of an anaerobic step, as their relative abundances decreased by 0.7, 0.8 and 14.7%, respectively. The proliferation of Thiothrix, norank_o_Sphingobacteriales and Trichosporon was the primary reason for the observed sludge bulking in the reactor. After the anaerobic step was added, the sludge extracellular polymeric substances (EPS) concentration was increased from 84.4 to 104.0 mg·(gMLSS)^-1 (grams of mixed liquor suspended solids). Thus, the addition of an anaerobic step can inhibit the growth of filamentous bacteria, increasing the sludge EPS concentration and promoting the precipitation of activated sludge.

16S rRNA-Based metagenomic analysis of microbial communities associated with wild Labroides dimidiatus from Karah Island, Terengganu, Malaysia

This study was designed to evaluate the bacterial composition of the Labroides dimidiatus and its surrounding water. Fish and carriage water samples were obtained from corals of the Karah Island in Terengganu Malaysia. DNA was extracted and the bacteria communities on the skin mucus and stomach as well as water sample were classified (to family level) using the 16S rRNA-based metagenomics analysis. 1,426,740 amplicon sequence reads corresponding to 508 total operational taxonomic units were obtained from the three metagenomics libraries in this study. The Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria were the most dominant bacterial phyla in all samples. A total of 36 different classes and 132 families were identified, many of which had shared presence in all samples while others were exclusive to different sample. Thirty-three of these were identified as pathogenic zoonotic bacterial. The results obtained indicate a strong influence of host environment on the composition of its microbiota. Knowing the composition of the microbiota is the first step toward exploring proper management of this ornamental fish in captivity.

Performance and microbial community dynamics in bioaugmented aerated filter reactor treating with coking wastewater

In this study, zeolite-biological aerated filters (Z-BAFs) bioaugmented by free and magnetically immobilized cells of Arthrobacter sp. W1 were designed to treat coking wastewater containing high concentrations of phenol and naphthalene along with carbazole (CA), dibenzofuran (DBF), and dibenzothiophene (DBT). All treatments were carried out for a period of 100days and the data indicated that bioaugmented Z-BAFs with magnetically immobilized cells was most efficient for treating coking wastewaters. Illumina high-throughput sequencing was used to reveal the microbial community structures of Z-BAFs. Both bioaugmentation treatments could accelerate the shift of the bacterial community structures. The introduced strain W1 remained dominant in the bioaugmented Z-BAFs with magnetically immobilized cells, indicating both strain W1 and the indigenous degrading bacteria played the most significant role in the treatment. Overall, bioaugmented Z-BAF with magnetically immobilized cells can be used to efficiently degrade phenol, naphthalene, CA, DBF, and DBT in coking wastewater.

Relationship between phenol degradation efficiency and microbial community structure in an anaerobic SBR

Phenol is a common wastewater contaminant from various industrial processes, including petrochemical refineries and chemical compounds production. Due to its toxicity to microbial activity, it can affect the efficiency of biological wastewater treatment processes. In this study, the efficiency of an Anaerobic Sequencing Batch Reactor (ASBR) fed with increasing phenol concentrations (from 120 to 1200 mg L(-1)) was assessed and the relationship between phenol degradation capacity and the microbial community structure was evaluated. Up to a feeding concentration of 800 mg L(-1), the initial degradation rate steadily increased with phenol concentration (up to 180 mg L(-1) d(-1)) and the elimination capacity remained relatively constant around 27 mg phenol removed∙gVSS(-1) d(-1). Operation at higher concentrations (1200 mg L(-1)) resulted in a still efficient but slower process: the elimination capacity and the initial degradation rate decreased to, respectively, 11 mg phenol removed∙gVSS(-1) d(-1) and 154 mg L(-1) d(-1). As revealed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, the increase of phenol concentration induced level-dependent structural modifications of the community composition which suggest an adaptation process. The increase of phenol concentration from 120 to 800 mg L(-1) had little effect on the community structure, while it involved drastic structural changes when increasing from 800 to 1200 mg L(-1), including a strong community structure shift, suggesting the specialization of the community through the emergence and selection of most adapted phylotypes. The thresholds of structural and functional disturbances were similar, suggesting the correlation of degradation performance and community structure. The Canonical Correspondence Analysis (CCA) confirmed that the ASBR functional performance was essentially driven by specific community traits. Under the highest feeding concentration, the most abundant ribotype probably involved in successful phenol degradation at 1200 mg L(-1) was affiliated to the Anaerolineaceae family.

Phylogenetic diversity of bacteria associated with the marine sponge Gelliodes carnosa collected from the Hainan Island coastal waters of the South China Sea

Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria and contributes to the growing database of the bacterial communities within sponges.

Repetitive extragenic palindromic PCR (REP-PCR) as a method used for bulking process detection in activated sludge

Bulking of activated sludge is a world-widely prevalent problem and can lead to loss of bio-oxidation, further deterioration of effluent quality, and even to a complete breakdown of the entire treatment process. Most common reasons of bulking are bacterial community changes, especially excessive growth of filamentous bacteria or excess of biopolymers on surface of non-filamentous microbes. Because of complex nature of the bulking phenomenon, the successful bulking control strategy finding is still a very important need awaiting new options and advices. The repetitive extragenic palindromic PCR (REP-PCR) fingerprinting method has been applied to distinguish bacterial community in non-bulking and bulking activated sludge. The characteristic REP-PCR fingerprinting patterns, using the Ward's clustering method, have been analyzed to determine homology/similarity relation between particular non-bulking and bulking sludge sampling. The received clustering results were in high concordance with activated sludge typing done based on physicochemical sludge analysis. The choice and application of molecular typing method in sludge analysis will depend upon the needs, skill level, and resources of the laboratory. The proposed REP-PCR method and statistical analysis of fingerprinting patterns seems to be simple, rapid, and effective methods to show differences between population in non-bulking and bulking activated sludge. It is easy to implement, and it may be useful for routinely activated sludge monitoring as well as may be helpful in early detection of bulking process.

Biofilm coupled with UV irradiation for phenol degradation and change of its community structure

The extensive use of phenol compounds and the inability to remove these compounds during wastewater treatment have resulted in the widespread occurrence of phenols in the natural environment. Phenols have been linked to serious risks to human and environmental health. Hence, the need to develop technologies that can effectively remove phenols from wastewater and source waters is a pressing challenge. In this study, light ceramic particles were immersed in activated sludge acclimated to degrade phenol, and microorganisms were allowed to attach to the particles surface to form biofilm. Then the ceramic particles with biofilm were moved into the photolytic circulating-bed biofilm reactor made of quartz glass, which was used for the degradation of phenol by three protocols: photolysis with UV light alone (P), biodegradation alone (B), and the two mechanisms operating simultaneously (photobiodegradation, P&B). The experimental results indicated that phenol removal rate was quickest by B experiment. However, P&B experiment gave more complete mineralization of phenol than that by other protocols. During P&B experiment, the microorganisms grown on porous ceramic carrier still kept the bioactivity degrading phenol, even under UV light irradiation. However, the dominant members of the bacterial community changed dramatically after the intimately coupled photobiodegradation, according to molecular biological analysis to the biofilm. Whereas Beijerinckia sp. was the dominant strain in the inoculum, it was replaced by Thauera sp. MZ1T that played a main role on degrading phenol during P&B experiment.

Identification of wastewater bacteria involved in the degradation of triclocarban and its non-chlorinated congener

Triclocarban (TCC) is an antimicrobial additive of personal care products that is only partially degraded during wastewater treatment. Bacteria responsible for its transformation are unknown. We obtained wastewater bacteria capable of using as the sole carbon source TCC or its non-chlorinated analog, carbanilide (NCC). Enrichments established using activated sludge amended with TCC and NCC, respectively, were maintained for 1 year through successive transfers. Enrichments displayed exponential growth after 2 weeks, reaching stationary phase after 1 month. The NCC enrichment was shown to accumulate aniline. Denaturing gradient gel electrophoresis of amplified 16S rRNA genes indicated markedly reduced community richness compared to the inoculum and a single, prominent taxonomic unit emerged in both chlorinated and non-chlorinated carbanilide enrichment cultures. Cloned 16S rRNA genes showed both enrichments were dominated by a single genotype related to uncharacterized organisms within the Alcaligenaceae. Of ∼30 sequences from each enrichment, no other organisms were detected in the TCC enrichment while, a small, flanking community of alpha proteobacteria was detected in the NCC enrichment. Study results demonstrate that growth of wastewater bacteria on TCC and its lower chlorinated analog can be linked to bacteria within the family Alcaligenaceae. These organisms are promising agents for the bioremediation of hazardous phenylurea pollutants.

Maintenance of phenol hydroxylase genotypes at high diversity in bioreactors exposed to step increases in phenol loading

To better understand how the composition of bacterial communities changes in response to different environmental conditions, we examined the influence of increasing phenol load on the distribution of the protein-coding functional gene of the largest subunit of phenol hydroxylase (LmPH) and of the 16S rRNA gene in lab-scale activated sludge reactors. LmPH diversity was assessed initially from a total of 124 clone sequences retrieved from two reactors exposed to a low (0.25 g L(-1)) and a high (2.5 g L(-1)) phenol concentration. The quantitative changes in the concentration of the eight detected genotypes accompanied changes in the phenol degradation rates, indicating a community structure-function relationship. Nonmetric dimensional analysis showed that LmPH genotypes and the denaturing gradient gel electrophoresis banding patterns clustered together by phenol concentration, rather than by reactor identity. Seven isolates, representing cultivated strains of each of the observed LmPH genotypes, exhibited a rather narrow range of physiological diversity, in terms of the growth rate and the kinetic parameters of the phenol-degrading activity. We suggest that lab-scale reactors support many ecological niches, which allow the maintenance of a high diversity of ecotypes through varying concentrations of phenol, but the ability of particular strains to become dominant members of the community under the different environmental conditions cannot be predicted easily solely from their phenol-degrading properties.

A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans

AIMS

To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans.

METHODS AND RESULTS

An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore.

CONCLUSIONS

Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology.

SIGNIFICANCE AND IMPACT OF THE STUDY

These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.

Treatment of phenolics containing synthetic wastewater in an internal loop airlift bioreactor (ILALR) using indigenous mixed strain of Pseudomonas sp. under continuous mode of operation

The scope of this study is to evaluate the performance of internal loop airlift bioreactor (ILALR) in treating synthetic wastewater containing phenol and m-cresol, in single and multi component systems. The microbe utilized in the process was an indigenous mixed strain of Pseudomonas sp. isolated from a wastewater treatment plant. The reactor was operated at both lower and higher hydraulic retention times (HRTs) i.e., 4.1 and 8.3 h, respectively, by providing an inlet feed flow rate of 5 and 10 mL/min. Shock loading experiments were also performed up to a maximum concentration of 800 mg/L for phenol at 8.3 h HRT and 500 mg/L for m-cresol at 4.1 h HRT. The study showed complete degradation of both phenol and m-cresol, when they were degraded individually at a HRT of 8.3 h. Experiments with both phenol and m-cresol present as mixtures were performed based on the 2(2) full factorial design of experiments.

Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China

The diversity of bacterial communities at three sites impacted by acid mine drainage (AMD) from the Yinshan Mine in China was studied using comparative sequence analysis of two molecular markers, the 16S rRNA and gyrB genes. The phylogenetic analyses retrieved sequences from six classes of bacteria, Nitrospira, Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Acidobacteria, and Actinobacteria, as well as sequences related to the plastid of the cyanobacterium Cyanidium acidocaldarium and also some unknown bacteria. The results of phylogenetic analyses based on gyrB and 16S rRNA were compared. This confirmed that gyrB gene analysis may be a useful tool, in addition to the comparative sequence analysis of the 16S rRNA gene, for the analysis of microbial community compositions. Moreover, the Mantel test showed that the geochemical characteristics, especially the pH value and the concentration of iron, strongly influenced the composition of the microbial communities.

Molecular diversity of 16S rRNA and gyrB genes in copper mines

The molecular diversities of the microbial communities from four sites impacted by acid mine drainage (AMD) at Dexing Copper Mine in Jiangxi province of China were studied using 16S rRNA sequences and gyrB sequences. Of the four sampled sites, each habitat exhibited distinct geochemical characteristics and the sites were linked geographically allowing us to correlate microbial community structure to geochemical characteristics. In the present study, we examined the molecular diversity of 16S rRNA and gyrB genes from water at these sites using a PCR-based cloning approach. We found that the microbial community appears to be composed primarily of Proteobacteria, Acidobacteria, Actinobacteria, Nitrospira, Firmicutes, Chlorella and unknown phylotypes. Of clones affiliated with Nitrospira, Leptospirillum ferrooxidans, Leptospirillum ferriphilum and Leptospirillum group III were all detected. Principal-component analysis (PCA) revealed that the distribution of the microbial communities was influenced greatly by geochemical characteristics. The overall PCA profiles showed that the sites with similar geochemical characteristics had more similar microbial community structures. Moreover, our results also indicated that gyrB sequence analysis may be very useful for differentiating very closely related species in the study of microbial communities.

Profiling mechanisms of alkane hydroxylase activity in vivo using the diagnostic substrate norcarane

Mechanistically informative chemical probes are used to characterize the activity of functional alkane hydroxylases in whole cells. Norcarane is a substrate used to reveal the lifetime of radical intermediates formed during alkane oxidation. Results from oxidations of this probe with organisms that contain the two most prevalent medium-chain-length alkane-oxidizing metalloenzymes, alkane omega-monooxygenase (AlkB) and cytochrome P450 (CYP), are reported. The results--radical lifetimes of 1-7 ns for AlkB and less than 100 ps for CYP--indicate that these two classes of enzymes are mechanistically distinguishable and that whole-cell mechanistic assays can identify the active hydroxylase. The oxidation of norcarane by several recently isolated strains (Hydrocarboniphaga effusa AP103, rJ4, and rJ5, whose alkane-oxidizing enzymes have not yet been identified) is also reported. Radical lifetimes of 1-3 ns are observed, consistent with these organisms containing an AlkB-like enzyme and inconsistent with their employing a CYP-like enzyme for growth on hydrocarbons.

Granulicoccus phenolivorans gen. nov., sp. nov., a Gram-positive, phenol-degrading coccus isolated from phenol-degrading aerobic granules

A Gram-positive bacterium, designated strain PG-02T, was isolated by serial dilution from aerobic granules obtained from a laboratory-scale sequencing batch reactor for bioremediation of phenolic wastewater. Strain PG-02T grew axenically as cocci and is an oxidase-negative and catalase-positive, non-motile facultative anaerobe. It does not reduce nitrate and grows between 15 and 37 °C, with an optimum temperature of 30 °C. The pH range for growth is between 5.0 and 8.5, with an optimum pH of 7.0. Strain PG-02T contains type A3γ peptidoglycan (ll-A2pm←Gly with alanine at position 1 of the peptide subunit). The G+C content of the DNA is 69 mol%. Menaquinone MK-9(H4) was the major isoprenoid quinone. The polar lipids included diphosphatidylglycerol and phosphatidylglycerol, while 13-methyltetradecanoic acid (i-C15 : 0) and 1,1-dimethoxy-iso-pentadecane (i-C15 : 0 DMA) were the major components in whole-cell methanolysates. PG-02T stained positively for intracellular polyphosphate granules but not poly-β-hydroxyalkanoates. It produces capsular material and possesses an autoaggregation capability. Phenotypic and 16S rRNA gene sequence analyses showed that PG-02T differed from its closest phylogenetic relatives, namely members of the suborder Propionibacterineae, which includes the genera Tessaracoccus, Microlunatus, Luteococcus, Micropruina, Propionibacterium, Propioniferax, Nocardioides, Friedmanniella and Aeromicrobium, and that it should be placed in a new genus and species as Granulicoccus phenolivorans gen. nov., sp. nov. The type strain of Granulicoccus phenolivorans is PG-02T (=ATCC BAA-1292T=DSM 17626T).

Influence of sustainability and immigration in assembling bacterial populations of known size and function

The rational assembly of microbial communities to perform desired functions would be of great practical benefit to society. Broadly speaking, there are two major theoretical foundations for microbial community assembly: one based on island biogeography theory and another based on niche theory. In this study, we compared a parameter from each theory (immigration rate and sustainability, respectively) to ascertain which was more influential in establishing a functional bacterial population in phenol degrading activated sludge over a 30-day period. Two bacterial strains originally isolated from activated sludge, but differing in their ability to sustain a population in this environment, were repeatedly added to activated sludge reactors at different doses. The resulting size of each population was monitored by competitive polymerase chain reaction. Large, unexpected, yet reproducible fluctuations in population sizes were observed. Irrespective of this, difference in the ability to sustain a population in this environment, overshadowed the influence of 100-fold differences in immigration rate.

Modeling of local dynamic behavior of phenol degradation in an internal loop airlift bioreactor by yeastCandida tropicalis

A coupled computational fluid dynamic (CFD) model, combining hydrodynamics with biochemical reactions, was developed to simulate the local transient flow patterns and the dynamic behaviors of cell growth and phenol biodegradation by yeast Candida tropicalis in an internal loop airlift reactor (ILALR). To validate this proposed model effectively, the simulated local hydrodynamic characteristics of the gas-mineral salt medium solution (gas-liquid) two-phase system, at a phenol concentration of 1,200 mg L(-1) and no presence of cells, was experimentally investigated in the ILALR using laser Doppler anemometer (LDA) measurements and conductivity probe. Furthermore, the validation of the simulated phenol biodegradation behavior by C. tropicalis at different initial concentrations of phenol and cell was also carried out in the ILALR. The time-averaged and transient results of the model simulations illustrated a satisfactory agreement with the experimental data. Finally, the local instantaneous flow and phenol biodegradation features, including gas holdup, gas velocity, liquid velocity, cell concentration, and phenol concentration inside the ILALR were successfully predicted by the proposed model.

Degradation of phenol by aerobic granules and isolated yeastCandida tropicalis

Aerobic granules effectively degrade phenol at high concentrations. This work cultivated aerobic granules that can degrade phenol at a constant rate of 49 mg-phenol/g x VSS/h up to 1,000 mg/L of phenol. Fluorescent staining and confocal laser scanning microscopy (CLSM) tests demonstrated that an active biomass was accumulated at the granule outer layer. A strain with maximum ability to degrade phenol and a high tolerance to phenol toxicity isolated from the granules was identified as Candida tropicalis via 18S rRNA sequencing. This strain degrades phenol at a maximum rate of 390 mg-phenol/g x VSS/h at pH 6 and 30 degrees C, whereas inhibitory effects existed at concentrations >1,000 mg/L. The Haldane kinetic model elucidates the growth and phenol biodegradation kinetics of the C. tropicalis. The fluorescence in situ hybridization (FISH) and CLSM test suggested that the Candida strain was primarily distributed throughout the surface layer of granule; hence, achieving a near constant reaction rate over a wide range of phenol concentration. The mass transfer barrier provided by granule matrix did not determine the reaction rates for the present phenol-degrading granule.

Mechanism for sludge acidification in aerobic treatment of coking wastewater

This work was undertaken to investigate the cause of sludge acidification that led to disruption of the activated sludge process treating coking wastewater from a steel-making plant in Taiwan. An activated sludge reactor (ASR) with a working volume of 80 L was used as a model system to simulate the behavior of the real wastewater treatment process. Parameters that may cause acidification or inactivation of the sludge (NH(3), SCN(-), S(2)O(3)(2-) and CN(-)) were studied individually to examine for their effects on the performance of the ASR. The results show that high loading of NH(3), SCN(-) and CN(-) did not lead to pH decrease, while the ASR attained 85% COD removal and nearly 100% SCN degradation. In contrast, when the wastewater was supplemented with ca. 1,000 mg/L of S(2)O(3)(2-), the pH dropped to nearly 4.0 in 2 days and the COD and SCN removal yields were significantly lower (at 50 and 0-20%, respectively). Thus, overloading of S(2)O(3)(2-) was apparently a key factor causing sludge acidification. The results suggest that to ensure a normal functioning of the activated sludge, the influent S(2)O(3)(2-) concentration should be closely monitored and that the pH control of the ASR is indispensable when the S(2)O(3)(2-) loading is in excess.

First record of Leptospira borgpetersenii isolation in the Amami Islands, Japan

In 2003, a Leptospira survey was performed on Yoroshima Island of the Amami Islands located in the southwestern part of Japan. Seven Leptospira strains were isolated from the field rat Rattus rattus, which were identified as L. borgpetersenii by flaB sequencing, 16S rDNA sequencing and gyrB sequencing, and serovar Javanica was determined by a microscopic agglutination test. NotI-long restriction fragment analysis indicated that these isolates were genetically indistinguishable from an isolate from the Okinawa Islands. The present results suggest that L. borgpetersenii is migrating into the Amami Islands in Japan.

Physiological traits of bacterial strains isolated from phenol-degrading aerobic granules

The physiological characteristics of ten bacterial strains isolated from phenol-degrading aerobic granules were evaluated in order to identify competitive traits for dominant growth in aerobic granules. The ten strains showed a wide diversity in specific growth rates and oxygen utilization kinetics, and could be divided into four catabolic types of phenol degradation. While some strains degraded phenol mainly via the meta pathway or the ortho pathway, other strains degraded phenol via both these pathways. The ten strains also exhibited high levels of autoaggregation and coaggregation activity. Within the collection of ten strains, 36.7% of all possible strain pairings displayed a measurable degree of coaggregation. Strain PG-08 possessed the strongest autoaggregation activity and showed significant coaggregation (coaggregation indices of 67% to 74%) with PG-02. The three strains PG-01, PG-02 and PG-08 belonging to dominant groups in the granules possessed different competitive characteristics. Microcosm experiments showed the three strains could not coexist at the high phenol concentration of 250 mg L(-1), but could coexist at lower phenol concentrations in a spatially heterogeneous environment. This study illustrated that the spatial heterogeneity provided by the aerobic granules led to niche differentiation and increased physiological diversity in the resident microbial community.

RNA-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline-contaminated groundwater

Stable isotope probing (SIP) of benzene-degrading bacteria in gasoline-contaminated groundwater was coupled to denaturing gradient gel electrophoresis (DGGE) of DNA fragments amplified by reverse transcription-PCR from community 16S rRNA molecules. Supplementation of the groundwater with [(13)C(6)]benzene together with an electron acceptor (nitrate, sulfate, or oxygen) showed that a phylotype affiliated with the genus Azoarcus specifically appeared in the (13)C-RNA fraction only when nitrate was supplemented. This phylotype was also observed as the major band in DGGE analysis of bacterial 16S rRNA gene fragments amplified by PCR from the gasoline-contaminated groundwater. In order to isolate the Azoarcus strains, the groundwater sample was streaked on agar plates containing nonselective diluted CGY medium, and the DGGE analysis was used to screen colonies formed on the plates. This procedure identified five bacterial isolates (from 60 colonies) that corresponded to the SIP-identified Azoarcus phylotype, among which two strains (designated DN11 and AN9) degraded benzene under denitrifying conditions. Incubation of these strains with [(14)C]benzene showed that the labeled carbon was mostly incorporated into (14)CO(2) within 14 days. These results indicate that the Azoarcus population was involved in benzene degradation in the gasoline-contaminated groundwater under denitrifying conditions. We suggest that RNA-based SIP identification coupled to phylogenetic screening of nonselective isolates facilitates the isolation of enrichment/isolation-resistant microorganisms with a specific function.

Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany

The phylogenetic diversity and seasonal dynamics of freshwater Actinobacteria populations in four limnologically different lakes of the Mecklenburg-Brandenburg Lake District (northeastern Germany) were investigated. Fluorescence in situ hybridization was used to determine the seasonal abundances and dynamics of total Actinobacteria (probe HGC69a) and the three actinobacterial subclusters acI, acI-A, and acI-B (probes AcI-852, AcI-840-1, and AcI-840-2). Seasonal means of total Actinobacteria abundances in the epilimnia of the lakes varied from 13 to 36%, with maximum values of 30 to 58%, of all DAPI (4',6'-diamidino-2-phenylindole)-stained cells. Around 80% of total Actinobacteria belonged to the acI cluster. The two subclusters acI-A and acI-B accounted for 60 to 91% of the acI cluster and showed seasonal means of 49% (acI-B) and 23% (acI-A) in relation to the acI cluster. Total Actinobacteria and members of the clusters acI and acI-B showed distinct seasonal changes in their absolute abundances, with maxima in late spring and fall/winter. In eight clone libraries constructed from the lakes, a total of 76 actinobacterial 16S rRNA gene sequences were identified from a total of 177 clones. The majority of the Actinobacteria sequences belonged to the acI and acIV cluster. Several new clusters and subclusters were found (acSTL, scB1-4, and acIVA-D). The majority of all obtained 16S rRNA gene sequences are distinct from those of already-cultured freshwater Actinobacteria.

Analysis of community composition of biofilms in a submerged filter system for the removal of ammonia and phenol from industrial wastewater

The bacterial diversity of a submerged filter, used for the removal of ammonia and phenol from an industrial wastewater with high salinity, was studied by a cultivation-independent approach based on PCR/TGGE (temperature-gradient gel electrophoresis). The wastewater treatment plant (laboratory scale) combined the nitrification and denitrification processes and consisted of two separated columns (one anoxic and one aerated) connected through a valve. The spatial diversity of bacterial communities in the plant biofilms was analysed by taking samples at four different heights in the system. TGGE profiles of PCR-amplified sequences of the 16 S rRNA gene (V3-hypervariable region) showed significant variations of the bacterial diversity, mainly depending on the concentration of O2 along the system. Several bands separated by TGGE were reamplified and sequenced, in order to explore the composition of the microbial communities in the biofilms. Most of the sequenced bands (10 out of 13) were closely related to the 16 S rRNA gene of marine α-proteobacteria, mainly grouping in the periphery of the genus Roseobacter. Other sequences were related to those of γ-proteobacteria, the nitrite oxidizer Nitrospira marina and anaerobic phenol-degrading bacteria of the Desulfobacteraceae.

An oil-absorber-bioscrubber system to stabilize biotreatment of pollutants present in waste gas. Fluctuating loads of 1,2-dichloroethane

Biotreatment technologies offer a cost-effective and efficient method for dealing with point-source releases of solvents. However, a major problem hampering these technologies is the fluctuating pollutant loads, which is especially critical for inhibitory pollutants. Provision of biotreatment systems able to cope with this problem is a significant technological and environmental challenge. This study investigates the potential for an absorber to act as buffer for shock loadings of inhibitory pollutants in waste-gas streams undergoing biological treatment. 1,2-Dichloroethane (DCE) was used as an example of a toxic and inhibitory organic pollutant. The stability of a combined oil-absorber-bioscrubber (OAB) system was compared to that of a bioscrubber only (BO) system when each was subjected to shock loads of DCE. The BO system was inoculated with Xanthobacter autotrophicus strain GJ10 and was submitted to sharp, sequential pulses in DCE inlet load, which caused system instability. Complete inhibition of the BO process occurred for a 3 h DCE pulse, leading to 9125 g of DCE m(-3)bioscrubber total organic discharged (TODDCE). Following the pulse, fluorescence in situ hybridization (FISH) showed that the active strain GJ10 was effectively washed-out. In contrast, the performance of the OAB system was stable during DCE shock loads. The carbon dioxide production remained stable, and low levels of effluent DCE and total organic carbon concentrations were found. For the 3 h pulse TODDCE was only 173 g of DCE m(-3)bioscrubber, and FISH indicated that the GJ10 strain remained active. We conclude that the OAB system offers an effective solution to the biological treatment of waste-gas containing fluctuating pollutant concentrations.

TGGE analysis of the diversity of ammonia-oxidizing and denitrifying bacteria in submerged filter biofilms for the treatment of urban wastewater

The spatial and temporal diversity of the bacterial community-forming biofilms in a pilot-scale submerged biofilter used for the treatment of urban wastewater was analyzed by a temperature-gradient gel electrophoresis (TGGE) approach. TGGE profiles based on partial sequence of the 16S rRNA gene showed that the community composition of the biofilms remained fairly stable along the column system and during the whole time of operation of the biofilter (more than 1 year). Community-profiling based on the amplification and separation of partial ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes demonstrated that ammonia-oxidizing and denitrifying bacteria coexisted in both the anoxic and the aerated parts of the system. Several amoA and nosZ bands separated by TGGE were reamplified and sequenced, in order to further analyze the composition of these microbial communities in the biofilm. Phylogeny inferred from amoA/AmoA revealed the prevalence of Nitrosomonas species with five sequences affiliated to Nitrosomonas oligotropha, six sequences affiliated to Nitrosomonas europaea, and three sequences that showed only 75.7-76.1% identity of the DNA sequence with the closest described species (Nitrosomonas nitrosa). According to literature, this low identity value is indicative of previously undiscovered species. Eighteen new partial nosZ sequences were obtained which were mostly related to nosZ of gamma-proteobacteria (Pseudomonas) or clustered in the periphery of previously known denitrifying alpha-proteobacteria (Bradyrhizobium and Azospirillum).

Isolation and characterization of a phenol-degrading bacterium from an industrial activated sludge

This paper reports the successful isolation and characterization of a new phenol-degrading bacterium, strain EDP3, from activated sludge. Strain EDP3 is a nonmotile, strictly aerobic, Gram-negative, and short-rod or coccobacillary bacterium, which occurs singly, in pairs, or in clusters. 16S rRNA gene sequence analysis revealed that strain EDP3 belonged to the gamma group of Proteobacteria, with a 97.0% identity to 16S rRNA gene sequences of Acinetobacter calcoaceticus. Strain EDP3 could aerobically grow on a number of aromatic compounds, such as phenol, sodium benzoate, p-hydroxybenzoate, phenylacetate, benzene, ethylbenzene, benzylalcohol, and so on. In particular, it could mineralize up to 1,000 mg l(-1) phenol at room temperature (25 degrees C). The growth kinetics of strain EDP3 on phenol as a sole carbon and energy source at 25 degrees C can be described using the Haldane equation. It has a maximal specific growth rate (mu(max)) of 0.28 h(-1), a half-saturation constant (K(S)) of 1,167.1 mg l(-1), and a substrate inhibition constant (Ki) of 58.5 mg l(-1). Values of yield coefficient (Y(X/S)) are between 0.4 and 0.6 mg dry cell (mg phenol)(-1). Strain EDP3 has high tolerance to the toxicity of phenol (up to 1,000 mg l(-1)). It therefore could be an excellent candidate for the biotreatment of high-strength phenol-containing industrial wastewaters and for the in situ bioremediation of phenol-contaminated soils.