Bacterial community structure and physiological state within an industrial phenol bioremediation system

Debromination of decabromodiphenyl ether (BDE-209) and bacterial community responses in aerobic and anaerobic soil microcosms

Polybrominated diphenyl ethers (PBDEs) are a class of persistent organic pollutants that may pose risks to human health and environmental biota, including soil microbial communities. These risks are further affected by a multitude of factors, including environmental conditions encountered in real-world settings. A comprehensive understanding of how PBDEs transform and microbial communities respond to the exposure under varying environmental conditions is paramount for assessing the ecological risks or identifying potential degraders. In this study, soil microcosms spiked with or without 10 mg kg-1 decabromodiphenyl ether (BDE-209) were established and incubated under either aerobic or anaerobic conditions for a duration of up to 180 days. The results demonstrated mono- to nine-brominated PBDE congeners accounted for approximately 4.03 % and 6.18 % of the initial concentration of BDE-209 added to the soil in both aerobic and anaerobic conditions, respectively. Anaerobic microcosms demonstrated faster and deeper debromination compared to the aerobic microcosms. Bacterial communities were monitored during the incubation to evaluate the community succession under the PBDE stress. Oxygen significantly shaped the richness, diversity, composition, and network complexity of soil bacterial community. BDE-209 had profound impacts on the network structure of bacterial communities. Random Forest model identified Desulfosporosinus and Polaromonas that might be related to BDE-209 debromination under anaerobic conditions. Overall, our findings shed light on the bacterial community effects of BDE-209 in aerobic or anaerobic soils, thus providing a theoretical basis for remediation of soil contaminated by PBDEs.

Phenol biodegradation using bio-filter tower packed column with immobilized bacterial consortium: a batch test study

The effluents from pulp and paper manufacturing industries contain high concentrations of phenol, which when discharged directly into surface water streams, increases the biological oxygen demand (BOD) and chemical oxygen demand (COD). In this study, two dominant bacteria SP-4 and SP-8 were isolated from the effluent emanating with a pulp and paper industry. The selected phenol-degrading isolates were identified as Staphylococcus sp. and Staphylococcus sciuri respectively by using nucleotide sequence alignment and phylogenetic analysis of 16 S rRNA regions of the genome. The two isolates used for the biodegradation process effectively degraded phenol concentration of pulp and paper industry effluent upto 1600 and 1800 mg/L resepctively. The individual isolates and consortium were immobilized using activated carbon, wood dust, and coal ash. Additionally, the effluent was treated using a bio-filter tower packed column immobilized with bacterial cells at a constant flow rate of 5 mL/min. The present study showed that the developed immobilized microbial consortium can effectively degrade 99% of the phenol present in pulp and paper industry effluents, resulting in a significant reduction in BOD and COD of the system. This study can be well implemented on real-scale systems as the bio-filter towers packed with immobilized bacterial consortium can effectively treat phenol concentrations up to 1800 mg/L. The study can be implemented for bioremediation processes in phenolic wastewater-contaminated sites.

Coupling between 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) debromination and methanogenesis in anaerobic soil microcosms

Polybrominated diphenyl ethers (PBDEs) are persistent pollutants that may undergo microbial-mediated debromination in anoxic environments, where diverse anaerobic microbes such as methanogenic archaea co-exist. However, current understanding of the relations between PBDE pollution and methanogenic process is far from complete. To address this knowledge gap, a series of anaerobic soil microcosms were established. BDE-47 (2, 2', 4, 4'-tetrabromodiphenyl ether) was selected as a model pollutant, and electron donors were supplied to stimulate the activity of anaerobes. Debromination and methane production were monitored during the 12 weeks incubation, while obligate organohalide-respiring bacteria (OHRBs), methanogenic, and the total bacterial communities were examined at week 7 and 12. The results demonstrated slow debromination of BDE-47 in all microcosms, with considerable growth of Dehalococcoides and Dehalogenimonas over the incubation observed in most BDE-47 spiked treatments. In addition, the accumulation of intermediate metabolites positively correlated with the abundance of Dehalogenimonas at week 7, suggesting potential role of these OHRBs in debromination. Methanosarcinaceae were identified as the primary methanogenic archaea, and their abundance were correlated with the production of debrominated metabolites at week 7. Furthermore, it was observed for the first time that BDE-47 considerably enhanced methane production and increased the abundance of mcrA genes, highlighting the potential effects of PBDE pollution on climate change. This might be related to the inhibition of reductive N- and S-transforming microbes, as revealed by the quantitative microbial element cycling (QMEC) analysis. Overall, our findings shed light on the intricate interactions between PBDE and methanogenic processes, and contribute to a better understanding of the environmental fate and ecological implication of PBDE under anaerobic settings.

Impact of lignin constituents on the bacterial community and polycyclic aromatic hydrocarbon co-metabolism in an agricultural soil

Lignin is a complex biopolymer comprising phenolic monomers with different degrees of methoxylation and may potentially enhance the degradation of soil pollutants such as polycyclic aromatic hydrocarbons (PAHs) through co-metabolism. However, the contribution of lignin constituents, including phenolic and methoxy subunits, to PAH biodegradation remains unclear. Here, p-hydroxybenzoate (pHBA), vanillate and methanol were selected to simulate phenolic units and methoxy groups of lignin. Soil microcosms receiving these compounds were established to evaluate their regulation on the bacterial community and PAH co-metabolism. There were different effects of different components on the biodegradation of a four-ring PAH, benzo(a)anthracene (BaA), as characterized using an isotopic tracer. Only vanillate significantly stimulated BaA mineralization to CO2, with pHBA and methanol leading to no appreciable change in the allocation of BaA in soil compartments. The lignin constituents had differential impacts on the soil bacterial community, with substantial enrichment of methylotrophs occurring in methanol-supplemented microcosms. Both vanillate and pHBA selected several aromatic degraders. Vanillate caused additional enrichment of methylotrophs, suggesting structure-dependent stimulation of bacterial functional guilds by lignin monomers. Compared with its constituents, lignin produced more extensive responses in terms of bacterial diversity and composition and the fate of BaA. However, it was difficult to link BaA co-metabolism to any specific bacterial taxa in the presence of lignin or its subunits. The results indicate that the co-metabolism effects of lignin may not be directly associated with phenolic or methoxy metabolism but with its regulation of the soil microbiome.

Contrasting responses of bacterial community to 4,4'-dibromodiphenyl ether (BDE-15) contamination in soil microcosms at different temperatures

Polybrominated diphenyl ethers (PBDEs) are biodegradable organic pollutants and pose potential risks to microorganisms exposed to the contamination, which are also affected by a variety of factors, such as temperature, in real environmental settings. A better understanding of the microbial community responses to PBDEs at different temperatures has practical significance for assessing ecological risks or possible degraders of these widely used flame retardants. In this study, soil microcosms spiked with or without 100 mg kg^-1 4,4'-dibromodiphenyl ether (BDE-15) were established and incubated at four different temperatures (4 °C, 20 °C, 37 °C, and varying ambient temperature) for up to 180 days. Concentration and carbon isotope analyses were used to verify the transformation of BDE-15. Bacterial communities were monitored during the incubation to evaluate the community succession under the PBDE stress. The results showed the majority of added BDE-15 remained after the incubation period, with limited degradation occurred at all four temperatures. Temperature significantly shaped the richness, diversity, composition and co-occurrence network of soil bacterial community, while the impacts of PBDE on soil bacteria were temperature dependent. When incubated at 4 °C, BDE-15 substantially reduced the network complexity and changed the ratio of negative to positive interactions between taxa (nodes), highlighting the PBDE-associated risks at low temperature. At higher temperatures, BDE-15 had negligible influence on the community characteristics and network. Random forest model identified distinct taxa that might be related to PBDE degradation at different incubation temperatures. These findings demonstrate contrasting bacterial community effects of PBDE at different temperatures, thus attention should be paid to the ecological impacts of soil pollution under real environmental conditions.

The Geochemical Drivers of Bacterial Community Diversity in the Watershed Sediments of the Heihe River (Northern China)

The city of Zhangye (Gansu Region, China) has been subjected to several changes related to the development of new profitable human activities. Unfortunately, this growth has led to a general decrease in water quality due to the release of several toxic wastes and pollutants (e.g., heavy metals) into the Heihe River. In order to assess the environmental exposure and the potential threat to human health, microbiological diversity for the monitoring of water pollution by biotic and abiotic impact factors was investigated. In particular, we analysed samples collected on different sites using 454 pyrotag sequencing of the 16S ribosomal genes. Then, we focused on alpha-diversity indices to test the hypothesis that communities featuring lower diversity show higher resistance to the disturbance events. The findings report that a wide range of environmental factors such as pH, nutrients and chemicals (heavy metals (HMs)), affected microbial diversity by stimulating mutualistic relationships among bacteria. Furthermore, a selection in bacterial taxa related to the different concentrations of polluting compounds was highlighted. Supporting the hypothesis, our investigation highlights the importance of microbial communities as sentinels for ecological status diagnosis.

Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil

Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO₂, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.

Desulfovulcanus ferrireducens gen. nov., sp. nov., a thermophilic autotrophic iron and sulfate-reducing bacterium from subseafloor basalt that grows on akaganéite and lepidocrocite minerals

A deep-sea thermophilic bacterium, strain Ax17T, was isolated from 25 °C hydrothermal fluid at Axial Seamount. It was obligately anaerobic and autotrophic, oxidized molecular hydrogen and formate, and reduced synthetic nanophase Fe(III) (oxyhydr)oxide minerals, sulfate, sulfite, thiosulfate, and elemental sulfur for growth. It produced up to 20 mM Fe2+ when grown on ferrihydrite but < 5 mM Fe2+ when grown on akaganéite, lepidocrocite, hematite, and goethite. It was a straight to curved rod that grew at temperatures ranging from 35 to 70 °C (optimum 65 °C) and a minimum doubling time of 7.1 h, in the presence of 1.5-6% NaCl (optimum 3%) and pH 5-9 (optimum 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was 90-92% identical to other genera of the family Desulfonauticaceae in the phylum Pseudomonadota. The genome of Ax17T was sequenced, which yielded 2,585,834 bp and contained 2407 protein-coding sequences. Based on overall genome relatedness index analyses and its unique phenotypic characteristics, strain Ax17T is suggested to represent a novel genus and species, for which the name Desulfovulcanus ferrireducens is proposed. The type strain is Ax17T (= DSM 111878T = ATCC TSD-233T).

Sulphate-reducing bacterial community structure from produced water of the Periquito and Galo de Campina onshore oilfields in Brazil

Sulphate-reducing bacteria (SRB) cause fouling, souring, corrosion and produce H2S during oil and gas production. Produced water obtained from Periquito (PQO) and Galo de Campina (GC) onshore oilfields in Brazil was investigated for SRB. Produced water with Postgate B, Postgate C and Baars media was incubated anaerobically for 20 days. DNA was extracted, 16S rDNA PCR amplified and fragments were sequenced using Illumina TruSeq. 4.2 million sequence reads were analysed and deposited at NCBI SAR accession number SRP149784. No significant differences in microbial community composition could be attributed to the different media but significant differences in the SRB were observed between the two oil fields. The dominant bacterial orders detected from both oilfields were Desulfovibrionales, Pseudomonadales and Enterobacteriales. The genus Pseudomonas was found predominantly in the GC oilfield and Pleomorphominas and Shewanella were features of the PQO oilfield. 11% and 7.6% of the sequences at GC and PQO were not classified at the genus level but could be partially identified at the order level. Relative abundances changed for Desulfovibrio from 29.8% at PQO to 16.1% at GC. Clostridium varied from 2.8% at PQO and 2.4% at GC. These data provide the first description of SRB from onshore produced water in Brazil and reinforce the importance of Desulfovibrionales, Pseudomonadales, and Enterobacteriales in produced water globally. Identifying potentially harmful microbes is an important first step in developing microbial solutions that prevent their proliferation.

Characterization of arsenic oxidation and uranium bioremediation potential of arsenic resistant bacteria isolated from uranium ore

Arsenic (As) is often found naturally as the co-contaminant in the uranium (U)-contaminated area, obstructing the bioremediation process. Although the U-contaminated environment harbors microorganisms capable of interacting with U which could be exploited in bioremediation. However, they might be unable to perform with their full potential due to As toxicity. Therefore, potential in arsenic resistance and oxidation is greatly desired among the microorganisms for a continued bioremediation process. In this study, arsenic-resistant bacteria were isolated from U ore collected from Bundugurang U mine, characterized and their As oxidation and U removal potentials were determined. 16S rRNA gene sequencing and phylogenetic analysis showed the affiliation of isolated bacteria with Microbacterium, Micrococcus, Shinella, and Bacillus. Except Bacillus sp. EIKU7, Microbacterium sp. EIKU5, Shinella sp. EIKU6, and Micrococcus sp. EIKU8 were found to resist more than 400 mM As(V); however, all the isolates could survive in 8 mM As(III). The isolates were found to readily oxidize As under different culture conditions and are also resistant towards Cd, Cr, Co, Ni, and Zn. All the isolates could remove more than 350 mg U/g dry cells within 48 h which were found to be highly dependent upon the concentration of U, biomass added initially, and on the time of exposure. Ability of the isolates to grow in nitrogen-free medium indicated that they can flourish in the nutrition deprived environment. Therefore, the recovery of isolates with the potent ability to resist and oxidize As from U ore might play an important role in toxic metal bioremediation including U.

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes. While CBM is an established framework for studying the metabolism of single species with linear stoichiometric models, CBM of communities with balanced growth is more complicated, not only due to the larger size of the multi-species metabolic network but also because of the bilinear nature of the resulting community models. Moreover, the solution space of these community models often contains biologically unrealistic solutions, which, even with model linearization and under application of certain objective functions, cannot easily be excluded. Here we present RedCom, a new approach to build reduced community models in which the metabolisms of the participating organisms are represented by net conversions computed from the respective single-species networks. By discarding (single-species) net conversions that violate a minimality criterion in the exchange fluxes, it is ensured that unrealistic solutions in the community model are excluded where a species altruistically synthesizes large amounts of byproducts (instead of biomass) to fulfill the requirements of other species. We employed the RedCom approach for modeling communities of up to nine organisms involved in typical degradation steps of anaerobic digestion in biogas plants. Compared to full (bilinear and linearized) community models, we found that the reduced community models obtained with RedCom are not only much smaller but allow, also in the largest model with nine species, extensive calculations required to fully characterize the solution space and to reveal key properties of communities with maximum methane yield and production rates. Furthermore, the predictive power of the reduced community models is significantly larger because they predict much smaller ranges of feasible community compositions and exchange fluxes still being consistent with measurements obtained from enrichment cultures. For an enrichment culture for growth on ethanol, we also used metaproteomic data to further constrain the solution space of the community models. Both model and proteomic data indicated a dominance of acetoclastic methanogens (Methanosarcinales) and Desulfovibrionales being the least abundant group in this microbial community.

Microbial communities are involved in many fundamental processes in nature, health and biotechnology. The elucidation of interdependencies between the involved players of microbial communities and how the interactions shape the composition, behavior and characteristic features of the consortium has become an important branch of microbiology research. Many communities are based on the exchange of metabolites between the species and constraint-based metabolic modeling has become an important approach for a formal description and quantitative analysis of these metabolic dependencies. However, the complexity of the models rises quickly with a growing number of organisms and the space of predicted feasible behaviors often includes unrealistic solutions. Here we present RedCom, a new approach to build reduced stoichiometric models of balanced microbial communities based on net conversions of the single-species models. We demonstrate the applicability of our RedCom approach by modeling communities of up to nine organisms involved in degradation steps of anaerobic digestion in biogas plants. As one of the first studies in this field, we compare simulation results from the community models with experimental data of laboratory-scale biogas reactors for growth on ethanol and glucose-cellulose media. The results also demonstrate a higher predictive power of the RedCom vs. the full models.

Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox)

The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems

The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.

Detection of Androgenic-Mutagenic Compounds and Potential Autochthonous Bacterial Communities during In Situ Bioremediation of Post-methanated Distillery Sludge

Sugarcane-molasses-based post-methanated distillery waste is well known for its toxicity, causing adverse effects on aquatic flora and fauna. Here, it has been demonstrated that there is an abundant mixture of androgenic and mutagenic compounds both in distillery sludge and leachate. Gas chromatography-mass spectrometry (GC-MS) analysis showed dodecanoic acid, octadecanoic acid, n-pentadecanoic acid, hexadecanoic acid, β-sitosterol, stigmasterol, β-sitosterol trimethyl ether, heptacosane, dotriacontane, lanosta-8, 24-dien-3-one, 1-methylene-3-methyl butanol, 1-phenyl-1-propanol, 5-methyl-2-(1-methylethyl) cyclohexanol, and 2-ethylthio-10-hydroxy-9-methoxy-1,4 anthraquinone as major organic pollutants along with heavy metals (all mg kg^-1): Fe (2403), Zn (210.15), Mn (126.30, Cu (73.62), Cr (21.825), Pb (16.33) and Ni (13.425). In a simultaneous analysis of bacterial communities using the restriction fragment length polymorphism (RFLP) method the dominance of Bacillus sp. followed by Enterococcus sp. as autochthonous bacterial communities growing in this extremely toxic environment was shown, indicating a primary community for bioremediation. A toxicity evaluation showed a reduction of toxicity in degraded samples of sludge and leachate, confirming the role of autochthonous bacterial communities in the bioremediation of distillery waste in situ.

The biological effect of metal ions on the granulation of aerobic granular activated sludge

As a special biofilm structure, microbial attachment is believed to play an important role in the granulation of aerobic granular activated sludge (AGAS). This experiment was to investigate the biological effect of Ca(2+), Mg(2+), Cu(2+), Fe(2+), Zn(2+), and K(+) which are the most common ions present in biological wastewater treatment systems, on the microbial attachment of AGAS and flocculent activated sludge (FAS), from which AGAS is always derived, in order to provide a new strategy for the rapid cultivation and stability control of AGAS. The result showed that attachment biomass of AGAS was about 300% higher than that of FAS without the addition of metal ions. Different metal ions had different effects on the process of microbial attachment. FAS and AGAS reacted differently to the metal ions as well, and in fact, AGAS was more sensitive to the metal ions. Specifically, Ca(2+), Mg(2+), and K(+) could increase the microbial attachment ability of both AGAS and FAS under appropriate concentrations, Cu(2+), Fe(2+), and Zn(2+) were also beneficial to the microbial attachment of FAS at low concentrations, but Cu(2+), Fe(2+), and Zn(2+) greatly inhibited the attachment process of AGAS even at extremely low concentrations. In addition, the acylated homoserine lactone (AHL)-based quorum sensing system, the content of extracellular polymeric substances and the relative hydrophobicity of the sludges were greatly influenced by metal ions. As all these parameters had close relationships with the microbial attachment process, the microbial attachment may be affected by changes of these parameters.

Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters

Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

Biodegradation of Phenol by Bacteria Strain Acinetobacter Calcoaceticus PA Isolated from Phenolic Wastewater

A phenol-degrading bacterium strain PA was successfully isolated from the effluent of petrochemical wastewater. Based on its morphological, physiological and biochemical characteristics, the strain PA was characterized as a Gram-negative, strictly aerobic, nonmotile and short rod-shaped bacterium that utilizes phenol as a sole carbon and energy source. 16S rDNA sequence analysis revealed that this strain is affiliated to Acinetobacter calcoaceticus in the group of Gammaproteobacteria. The strain was efficient in removing 91.6% of the initial 800 mg∙L⁻¹ phenol within 48 h, and had a tolerance of phenol concentration as high as 1700 mg∙L⁻¹. These results indicated that A. calcoaceticus possesses a promising potential in treating phenolic wastewater.

High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates

This paper describes the microfluidic streak plate (MSP), a facile method for high-throughput microbial cell separation and cultivation in nanoliter sessile droplets. The MSP method builds upon the conventional streak plate technique by using microfluidic devices to generate nanoliter droplets that can be streaked manually or robotically onto petri dishes prefilled with carrier oil for cultivation of single cells. In addition, chemical gradients could be encoded in the droplet array for comprehensive dose-response analysis. The MSP method was validated by using single-cell isolation of Escherichia coli and antimicrobial susceptibility testing of Pseudomonas aeruginosa PAO1. The robustness of the MSP work flow was demonstrated by cultivating a soil community that degrades polycyclic aromatic hydrocarbons. Cultivation in droplets enabled detection of the richest species diversity with better coverage of rare species. Moreover, isolation and cultivation of bacterial strains by MSP led to the discovery of several species with high degradation efficiency, including four Mycobacterium isolates and a previously unknown fluoranthene-degrading Blastococcus species.

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

Relative microorganism abundance is a parameter describing biodiversity, referring to how common a bacterial species is within the total bacterial flora. Anal, rectal, skin, mucal, and respiratory swabs are typical clinical samples where knowledge of relative bacterial abundance might make distinction between asymptomatic carriers and symptomatic cases. Assays trying to measure total bacterial load are usually based on the amplification of universal segments of 16S rRNA genes. Previous assays were not adoptable to "direct" PCR protocols, and/or they were not compatible with hydrolysis-based detection. Using the latest summary of universal 16S sequence motifs present in literature and testing our design with 500 liquid and 50 formed stool samples, we illustrate the performance characteristics of a new 16S quantitative PCR (qPCR) assay, which addresses well-known technical problems, including a) positive priming reaction in the absence of intended target due to self-priming and/or mispriming of unintended targets; b) amplification bias due to nonoptimal primer/probe coverage; and c) too large amplicons for clinical qPCR. Stool swabs ranked into bins of different bacterial loads show significant correlation with threshold cycle values of our new assay. To the best of our knowledge, this is the first description of qPCR assay measuring individual differences of total bacterial load present in human stool.

Diversity and phylogenetic analysis of endosymbiotic bacteria of the date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae)

BACKGROUND

The date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae) is one of the major pests of palms. In Saudi Arabia, both larvae and adults of Oryctes are particularly troublesome, especially during the establishment of young date palm orchards. Endosymbiotic bacteria are known to have a key role in food digestion and insecticide resistance mechanisms, and therefore are essential to their host insect. Identification of these bacteria in their insect host can lead to development of new insect pest control strategies.

RESULTS

Metagenomic DNA from larval midgut of the date palm root borer, O. agamemnon, was analyzed for endosymbiotic bacterial communities using denatured gradient gel electrophoresis (DGGE) utilizing 16S rRNA genes. The DGGE fingerprints with metagenomic DNA showed predominance of eleven major operational taxonomic units (OTUs) identified as members of Photobacterium, Vibrio, Allomonas, Shewanella, Cellulomonas, and Citrobacter, as well as uncultured bacteria, including some uncultured Vibrio members. DGGE profiles also showed shifts in the dominant bacterial populations of the original soil compared with those that existed in the larval midguts. The endosymbiotic bacterial community was dominated by members of the family Vibrionaceae (54.5%), followed by uncultured bacteria (18.2%), Enterobacteriaceae (9.1%), Shewanellaceae (9.1%), and Cellulomonadaceae (9.1%). Phylogenetic studies confirmed the affiliation of the dominant OTUs into specified families revealed by clustering of each phylotype to its corresponding clade. Relative frequency of each phylotype in larval midguts revealed predominance of Vibrio furnisii and Vibrio navarrensis, followed by uncultured bacterial spp., then Cellulomonas hominis, Shewanella algae, and Citrobacter freundii.

CONCLUSION

Analysis of metagenomic DNA for endosymbiotic bacterial communities from the midgut of Oryctes larvae showed strong selection of specific bacterial populations that may have a key role in digestion, as well as other benefits to the larvae of O. agamemnon. Determination of the distinct endosymbiotic community structure and its possible biological functions within the insect could provide us with basic information for future pest control research.

Assessment of the chemical, microbiological and toxicological aspects of post-processing water from underground coal gasification

The purpose of this paper is to provide a comprehensive characterisation (including chemical, microbiological and toxicological parameters) of water after the underground coal gasification (UCG) process. This is the first report in which these parameters were analysed together to assess the environmental risk of the water generated during the simulation of the underground coal gasification (UCG) process performed by the Central Mining Institute (Poland). Chemical analysis of the water indicated many hazardous chemical compounds, including benzene, toluene, ethylbenzene, xylene, phenols and polycyclic aromatic hydrocarbons (PAHs). Additionally, large quantities of inorganic compounds from the coal and ashes produced during the volatilisation process were noted. Due to the presence of refractory and inhibitory compounds in the post-processing water samples, the microbiological and toxicological analyses revealed the high toxicity of the UCG post-processing water. Among the tested microorganisms, mesophilic, thermophilic, psychrophilic, spore-forming, anaerobic and S-oxidizing bacteria were identified. However, the number of detected microorganisms was very low. The psychrophilic bacteria dominated among tested bacteria. There were no fungi or Actinomycetes in any of the water samples. Preliminary study revealed that hydrocarbon-oxidizing bacteria were metabolically active in the water samples. The samples were very toxic to the biotests, with the TU50 reaching 262. None of biotests was the most sensitive to all samples. Cytotoxicity and genotoxicity testing of the water samples in Vicia uncovered strong cytotoxic and clastogenic effects. Furthermore, TUNEL indicated that all of the water samples caused sporadic DNA fragmentation in the nuclei of the roots.

Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.

Bacterial and fungal community composition over time in chicken litter with high or low moisture content

1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.

Brassica napus hairy roots and rhizobacteria for phenolic compounds removal

Phenolic compounds are contaminants frequently found in water and soils. In the last years, some technologies such as phytoremediation have emerged to remediate contaminated sites. Plants alone are unable to completely degrade some pollutants; therefore, their association with rhizospheric bacteria has been proposed to increase phytoremediation potential, an approach called rhizoremediation. In this work, the ability of two rhizobacteria, Burkholderia kururiensis KP 23 and Agrobacterium rhizogenes LBA 9402, to tolerate and degrade phenolic compounds was evaluated. Both microorganisms were capable of tolerating high concentrations of phenol, 2,4-dichlorophenol (2,4-DCP), guaiacol, or pentachlorophenol (PCP), and degrading different concentrations of phenol and 2,4-DCP. Association of these bacterial strains with B. napus hairy roots, as model plant system, showed that the presence of both rhizospheric microorganisms, along with B. napus hairy roots, enhanced phenol degradation compared to B. napus hairy roots alone. These findings are interesting for future applications of these strains in phenol rhizoremediation processes, with whole plants, providing an efficient, economic, and sustainable remediation technology.

Characterization of aerobic granular sludge treating high strength agro-based wastewater at different volumetric loadings

Understanding the relationship between microbial community and mechanism of aerobic granulation could enable wider applications of granules for high-strength wastewater treatment. The majority of granulation studies principally determine the engineering aspects of granules formation with little emphasis on the microbial diversity. In this study, three identical reactors namely R1, R2 and R3 were operated using POME at volumetric loadings of 1.5, 2.5 and 3.5 kg COD m(-3) d(-1), respectively. Aeration was provided at a volumetric flow rate of 2.5 cms(-1). Aerobic granules were successfully developed in R2 and R3 while bioflocs dominated R1 until the end of experiments. Fractal dimension (D(f)) averaged at 1.90 suggesting good compactness of granules. The PCR-DGGE results indicated microbial evolutionary shift throughout granulation despite different operating OLRs based on decreased Raup and Crick similarity indices upon mature granule formation. The characteristics of aerobic granules treating high strength agro-based wastewater are determined at different volumetric loadings.

Influence of depth and sampling time on bacterial community structure in an upland grassland soil

Abstract Temporal and spatial variation of soil bacterial communities was evaluated with both molecular and metabolic profiling techniques. Soil cores (20 cm deep) were taken from an upland grassland in the Scottish Borders (UK) over 3 days in July 1999, and on single days in October 1999, April 2000, and August 2000. Cores were separated into four 5-cm depths to examine vertical spatial distribution. The 0-5-, 5-10- and 10-15-cm samples represented organic horizons whilst the 15-20-cm depths were from a mineral horizon. The potential metabolic activities were analysed using BIOLOG-GN plates, whereas genotypic diversity was evaluated using molecular profiling of amplified 16S rRNA and 16S rDNA gene fragments (denaturing gradient gel electrophoresis (DGGE)). BIOLOG-GN analysis revealed decreased substrate utilisation in the lowest depths, which was coupled with changes in the DNA and RNA DGGE profiles. Seasonal variation was pronounced in the 5-10-cm and 10-15-cm organic horizons for the July samplings whilst the 15-20-cm depths appeared more stable. Potential factors influencing the observed changes in bacterial communities resulting from soil depth and sampling time are discussed.

Factors influencing the detection of bacterial cells using fluorescence in situ hybridization (FISH): A quantitative review of published reports

Abstract Fluorescence in situ hybridization (FISH) is widely used to describe bacterial community composition and, to a lesser extent, to describe the physiological state of cells. One of the limitations of the technique is that the effectiveness of the detection of target cells appears to vary widely. Here, we present a quantitative review of published reports on the percentage of cells detected using the common EUB338 probe (%Eub) in aquatic ecosystems. The %Eub varies from 1 to 100% in the different published reports, with an average of 56%. There is a methodological component in this variation, with a significant effect of the fluorochrome type and the stringency conditions of the reaction. But there is also a strong environmental component, and the type of ecosystem and dominant phylogenetic group significantly influence %Eub. We argue that the optimization of the FISH protocol to describe the phylogenetic composition of bacterial assemblages will probably lead to techniques that are not effective to describe the physiological state of cells.

Poplar clones of different sizes, grown on a heavy metal polluted site, are associated with microbial populations of varying composition

We performed a field trial to evaluate the response of different poplar clones to heavy metals. We found that poplar plants of the same clone, propagated by cuttings, had a marked variability of survival and growth in different zones of the field that were characterized by very similar physical-chemical prosperities. Since metal uptake and its accumulation by plants can be affected by soil microorganisms, we investigated soil microbial populations that were collected in proximity to the roots of large and small poplar plants. We used microbiological and molecular tools to ascertain whether bacterial strains or species were associated with large, or small poplars, and whether these were different from those present in the bulk (without plants) soil. We found that the culturable fraction of the bacteria differed in the three cases (bulk soil, small or large poplars). While some taxa were always present, two species (Chryseobacterium soldanellicola and Variovorax paradoxus) were only found in the soil where poplars (large or small) were growing, independently from the plant size. Bacterial strains of the genus Flavobacterium were prevalent in the soil with large poplar plants. The existence of different microbial populations in the bulk and in the poplar grown soils was confirmed by the DGGE profiles of the bacterial culturable fractions. Cluster analysis of the DGGE profiles highlighted the clear separation of the culturable fraction from the whole microbial community. The isolation and identification of poplar-associated bacterial strains from the culturable fraction of the microbial community provided the basis for further studies aimed at the combined use of plants and soil microorganisms in the remediation of heavy metal polluted soils.

Coverage evaluation of universal bacterial primers using the metagenomic datasets

BACKGROUND

The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers.

RESULTS

The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were ≪6%, while in the metagenomic datasets, most were ≫10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed.

CONCLUSIONS

Our study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.

Isolation and characterization of a nitrobenzene-degrading bacterium Klebsiella ornithinolytica NB1 from aerobic granular sludge

Strain NB1 was isolated from aerobic granular sludge capable of degrading nitrobenzene. Effects of several factors including pH, temperature, salinity, and second carbon/nitrogen source as co-substrate on the biodegradation of nitrobenzene by strain NB1 were investigated. Results showed that the optimal conditions for the biodegradation of nitrobenzene by strain NB1 were at pH 7.0 and 28-35°C. Under these conditions, the biodegradation rate of nitrobenzene could reach 9.29mgl(-1)h(-1) when the initial nitrobenzene concentration was 600mgl(-1). The addition of 1840mgl(-1) glucose or 500mgl(-1) ammonium chloride could slightly enhance the biodegradation efficiency, but even more addition of glucose or ammonium chloride delayed the biodegradation. Strain NB1 could degrade nitrobenzene in the presence of less than 3% NaCl (w/v %). Based on morphological and physiological characteristics as well as the phylogenetic analysis of 16S rDNA sequences, strain NB1 was identified as Klebsiella ornithinolytica.

Soil dissipation of juvenile hormone analog insecticide pyriproxyfen and its effect on the bacterial community

This investigation was undertaken to examine the dissipation rate of pyriproxyfen as well as the change in the soil bacterial community. Residues of pyriproxyfen were measured using high performance liquid chromatography (HPLC) and the changes in bacterial community were determined by comparing the 16S rDNA bands on patterns by denaturing gradient gel electrophoresis (DGGE). The dissipation of pyriproxyfen was affected by both the concentration applied and incubation temperature. Lower concentrations (1 mg Kg(-1)) and higher incubation temperatures (30 and 40°C) showed more rapid dissipation rates. The population of microbial community decreased rapidly after incubation with 10 mg Kg(-1) of pyriproxyfen for 91 days, indicating the toxicity of pyriproxyfen toward bacterial communities in a closed soil ecosystem. Lower concentrations of pyriproxyfen showed less toxicity toward the microbial community. From cluster analysis, the structure of the bacterial community showed roughly a 60 % similarity throughout the experiment period in the control experiment, indicating the stability within soil microbiota without chemical agitation. However, the similarity was lower than 50 % both in the one and 10 mg Kg(-1) of insecticide pyriproxyfen spiked experiment, indicating the soil bacterial community changed after the insecticide pyriproxyfen was applied.

Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation

Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of the bacterial community in the bioremediated soils was significantly different from that of the native soil. The shift observed in the bacterial community structure using RISA analysis was in accordance with the monitored changes in the abundances of 11 targeted phyla and classes. Actinobacteria, Bacteriodetes and α- and γ-Proteobacteria were more abundant under all three bioremediation treatments, with Actinobacteria representing the dominant phylum. Altogether, our results indicate that bioremediation of PCB-contaminated soil induces significant changes in the structure and abundance of the total microbial community, which must be addressed to implement bioremediation practices in order to restore soil functions.

Isolation and characterization of four novel Gram-positive bacteria associated with the rhizosphere of two endemorelict plants capable of degrading a broad range of aromatic substrates

Four new Gram-positive, phenol-degrading strains were isolated from the rhizospheres of endemorelict plants Ramonda serbica and Ramonda nathaliae known to exude high amounts of phenolics in the soil. Isolates were designated Bacillus sp. PS1, Bacillus sp. PS11, Streptomyces sp. PS12, and Streptomyces sp. PN1 based on 16S rDNA sequence and biochemical analysis. In addition to their ability to tolerate and utilize high amounts of phenol of either up to 800 or up to 1,400 mg l(-1) without apparent inhibition in growth, all four strains were also able to degrade a broad range of aromatic substrates including benzene, toluene, ethylbenzene, xylenes, styrene, halogenated benzenes, and naphthalene. Isolates were able to grow in pure culture and in defined mixed culture on phenol and on the mixture of BTEX (benzene, toluene, ethylbenzene, and xylenes) compounds as a sole source of carbon and energy. Pure culture of Bacillus sp. PS11 yielded 1.5-fold higher biomass amounts in comparison to mixed culture, under all conditions. Strains successfully degraded phenol in the soil model system (2 g kg(-1)) within 6 days. Activities of phenol hydroxylase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase were detected and analyzed from the crude cell extract of the isolates. While all four strains use ortho degradation pathway, enzyme indicative of meta degradation pathway (catechol 2,3-dioxygenase) was also detected in Bacillus sp. PS11 and Streptomyces sp. PN1. Phenol degradation activities were induced 2 h after supplementation by phenol, but not by catechol. Catechol slightly inhibited activity of catechol 2,3-dioxygenase in strains PS11 and PN1.

Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol

The coking process produces great volumes of wastewater contaminated with pollutants such as cyanides, sulfides and phenolics. Chemical and physical remediation of this wastewater removes the majority of these pollutants; however, these processes do not remove phenol and thiocyanate. The removal of these compounds has been effected during bioremediation with activated sludge containing a complex microbial community. In this investigation we acquired activated sludge from an industrial bioreactor capable of degrading phenol. The sludge was incubated in our laboratory and monitored for its ability to degrade phenol over a 48 h period. Multiple samples were taken across the time-course and analysed by Fourier transform infrared (FT-IR) spectroscopy. FT-IR was used as a whole-organism fingerprinting approach to monitor biochemical changes in the bacterial cells during the degradation of phenol. We also investigated the ability of the activated sludge to degrade phenol following extended periods (2-131 days) of storage in the absence of phenol. A reduction was observed in the ability of the microbial community to degrade phenol and this was accompanied by a detectable biochemical change in the FT-IR fingerprint related to cellular phenotype of the microbial community. In the absence of phenol a decrease in thiocyanate vibrations was observed, reflecting the ability of these communities to degrade this substrate. Actively degrading communities showed an additional new band in their FT-IR spectra that could be attributed to phenol degradation products from the ortho- and meta-cleavage of the aromatic ring. This study demonstrates that FT-IR spectroscopy when combined with chemometric analysis is a very powerful high throughput screening approach for assessing the metabolic capability of complex microbial communities.

Phenol removal from hypersaline wastewaters in a Membrane Biological Reactor (MBR): operation and microbiological characterisation

In this study, two Membrane Biological Reactors (MBR) with submerged flat membranes, one at lab-scale conditions and the other at pilot-plant conditions, were operated at environmental temperature to treat an industrial wastewater characterised by low phenol concentrations (8-16 mg L(-1)) and high salinity (∼ 150-160 mS cm(-1)). During the operation of both reactors, the phenol loading rate was progressively increased and less than 1mg phenol L(-1) was detected even at very low HRTs (0.5-0.7 days). Membrane fouling was minimized by the cross flow aeration rate inside the MBRs and by intermittent permeation. Microbial community analysis of both reactors revealed that members of the genera Halomonas and Marinobacter (gammaproteobacteria) were major components. Growth-linked phenol degradation by pure cultures of Marinobacter isolates demonstrated that this bacterium played a major role in the removal of phenol from the bioreactors.