Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Analysis of Bacterial Communities around the Adventdalen Landfill Site in Svalbard

Ecosystems are often resilient enough to fully recover following a natural disturbance, or to transform into a new equilibrium favourable to the surrounding flora and fauna. However, at a local level, whether this transformation will be beneficial or not depends strongly on the level of disturbance and the available mechanisms for recovery. The Arctic, however, provides a potentially extreme environment for microbial growth and this is reflected in the microbial biodiversity, the in-situ growth rates, the biogeochemical cycling and its sensitivity to environmental change. In this study, we evaluated the current microbial biodiversity and environmental conditions around the landfill site in Adventdalen, Svalbard to identify differences across bacterial communities that might promote or accelerate naturally occurring environmental recovery. Landfill sites can induce changes in the local environment through the input of exogenous chemicals (both organic and inorganic) and microorganisms. Leachate can flow with run-off from the primary location of the landfill site due to rain, snow or ice melt and spread material into soils surrounding the site. In this study we found a strong effect of the landfill site on the bacterial diversity in the local landscape. Intervention is highly desirable to enhance the environment and improve the restoration by subtly altering the conditions at the site (such as the pH or drainage courses) and by encouraging specific groups of naturally occurring indigenous microorganisms to bioremediate the site.

DIVERISTY and enzymatic potential of indigenous bacteria from unexplored contaminted soils in Faisalabad

Bacteria residing in contaminated waste soil degrade and utilize organic and inorganic material as a source of nutrients as well as reduce environmental contamination through their enzymatic machinery. This enzymatic potential of indigenous bacteria can be exploited at industrial level through detailed screening, characterization, optimization and purification. In present study, diversity and enzymatic potential of indigenous bacteria was investigated through qualitative and quantitative screening methods from unexplored contaminated soil waste sites in Faisalabad. Shannon diversity (H') index revealed that twenty-eight soil samples from four contaminated sites were highly diverse of amylase, protease and lipase producing bacteria. Maximum protease producing bacteria were detected in fruit waste (1.929 × 10⁷), whereas amylase and lipase producing bacteria were found in industrial (1.475 × 10⁷) and (5.38 × 10⁶), in household waste soil samples. Most of the indigenous bacterial isolates showed potential for multiple enzymes. An isolate OC5 exhibited capability for amylase production and optimization at a wider range of cultural conditions; pH (6-8), temperature (25 °C, 37 °C, 45 °C), incubation time (24-72 h), and NaCl concentrations 0.5-13%, using (1%) starch and lactose as substrates. An isolate OC5 was identified by molecular identification and phylogenetic analysis showed 99% sequence similarity with Bacillus spp. ANOVA was used to analyzed all data statistically. This study enhances the importance of initial screening and reporting of industrially potent indigenous bacteria from unexplored contaminated waste soils. In future, indigenous bacteria in contaminated wastes may be good candidates to solve various environmental pollution problems.

Aerobic biodegradation pathways of pentabromobiphenyl ethers (BDE-99) and enhanced degradation in membrane bioreactor system

A bacterial strain capable of efficiently degrading pentabromobiphenyl ether (BDE-99) was isolated from activated sludge and named as NLPSJ-22. This strain was highly close to Pseudomonas asplenii with 100% similarity. The degradation products of BDE-99 were analyzed by gas chromatography mass spectrometry. The biochemical degradation pathways analysis indicated that BDE-99 gradually transformed to diphenyl ether by meta-, para- and ortho-debromination. It became phenol under the action of ring-opening cracking and finally entered the tricarboxylic acid cycle. The degradation of BDE-99 by strain NLPSJ-22 conformed to the first-order reaction kinetics. Rhamnolipid significantly improved the cell-surface hydrophobicity and the degradation of BDE-99. The highest degradation efficiency (96%) was achieved when diphenyl ether as co-metabolic substrate was added. In the bioaugmentation membrane bioreactor (MBR) system, BDE-99 was intensively degraded, and the reactor reached a steady state in about 35 days. The degradation rate of BDE-99 was over 80%, which was significantly higher than that of the control system. MiSeq sequencing results indicated that the genera of Rhodococcus, Bacillus, Pseudomonas, Burkholderia, and Sphingobium were the predominant bacterial communities responsible for BDE-99 biodegradation in the MBR. Pseudomonas increased significantly in the bioaugmented reactor with the relative abundance increasing from 5% to 24%.

Metataxonomy and functionality of wood-tar degrading microbial consortia

Wood-tar is a liquid material obtained by wood gasification process, and comprises several polycyclic aromatic hydrocarbons (PAH). Tar biodegradation is a very challenging task, due to its toxicity and to its complex chemistry. The 'microbial resource management' concerns the use of environmental microbial communities potentially able to provide us services. We applied this concept in tar biodegradation. Tar composed by several PAH (including phenanthrene, acenaphthylene and fluorene) was subjected to a biodegradation process in triplicate microcosms spiked with a microbial community collected from PAH-rich soils. In 20 days, 98.9% of tar was mineralized or adsorbed to floccules, while negative controls showed poor PAH reduction. The dynamics of fungal and bacterial communities was assessed through Automated Ribosomal Intergenic Spacer Analysis (ARISA), 454 pyrosequencing of the fungal ITS and of the bacterial 16S rRNA. Quantification of the degrading bacterial communities was performed via quantitative Real Time PCR of the 16S rRNA genes and of the cathecol 2,3-dioxygenase genes. Results showed the importance of fungal tar-degrading populations in the first period of incubation, followed by a complex bacterial dynamical growth ruled by co-feeding behaviors.

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [¹³C]benzene enabled us to obtain ¹³C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities.

IMPORTANCE

Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.

Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing

Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.

Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas

Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems.

Quantitative approach to track lipase producing Pseudomonas sp. S1 in nonsterilized solid state fermentation

Proliferation of the inoculated Pseudomonas sp. S1 is quantitatively evaluated using ERIC-PCR during the production of lipase in nonsterile solid state fermentation an approach to reduce the cost of enzyme production. Under nonsterile solid state fermentation with olive oil cake, Pseudomonas sp. S1 produced 57·9 IU g(-1) of lipase. DNA fingerprints of unknown bacterial isolates obtained on Bushnell Haas agar (BHA) + tributyrin exactly matched with that of Pseudomonas sp. S1. Using PCR-based enumeration, population of Pseudomonas sp. S1 was proliferated from 7·6 × 10(4) CFU g(-1) after 24 h to 4·6 × 10(8) CFU g(-1) after 96 h, which tallied with the maximum lipase activity as compared to control. Under submerged fermentation (SmF), Pseudomonas sp. S1 produced maximum lipase (49 IU ml(-1) ) using olive oil as substrate, while lipase production was 9·754 IU ml(-1) when Pseudomonas sp. S1 was grown on tributyrin. Optimum pH and temperature of the crude lipase was 7·0 and 50°C. Crude enzyme activity was 71·2% stable at 50°C for 360 min. Pseudomonas sp. S1 lipase was also stable in methanol showing 91·6% activity in the presence of 15% methanol, whereas 75·5 and 51·1% of activity were retained in the presence of 20 and 30% methanol, respectively. Thus, lipase produced by Pseudomonas sp. S1 is suitable for the production of biodiesel as well as treatment of oily waste water.

SIGNIFICANCE AND IMPACT OF STUDY

This study presents the first report on the production of thermophilic organic solvent tolerant lipase using agro-industry waste in nonsterile solid state fermentation. Positive correlation between survival of Pseudomonas sp. S1 and lipase production under nonsterile solid state fermentation was established, which may emphasize the need to combine molecular tools and solid state fermentation in future studies. Our study brings new insights into the lipase production in cost-effective manner, which is an industrially relevant approach.

Bioresources for control of environmental pollution

Environmental pollution is one of the biggest threats to human beings. For practical reasons it is not possible to stop most of the activities responsible for environmental pollution; rather we need to eliminate the pollutants. In addition to other existing means, biological processes can be utilized to get rid of toxic pollutants. Degradation, removal, or deactivation of pollutants by biological means is known as bioremediation. Nature itself has several weapons to deal with natural wastage and some of them are equally active for eliminating nonnatural pollutants. Several plants, microorganisms, and some lower eukaryotes utilize environmental pollutants as nutrients and some of them are very efficient for decontaminating specific types of pollutants. If exploited properly, these natural resources have enough potential to deal with most elements of environmental pollution. In addition, several artificial microbial consortia and genetically modified organisms with high bioremediation potential were developed by application of advanced scientific tools. On the other hand, natural equilibria of ecosystems are being affected by human intervention. Rapid population growth, urbanization, and industrialization are destroying ecological balances and the natural remediation ability of the Earth is being compromised. Several potential bioremediation tools are also being destroyed by biodiversity destruction of unexplored ecosystems. Pollution management by bioremediation is highly dependent on abundance, exploration, and exploitation of bioresources, and biodiversity is the key to success. Better pollution management needs the combined actions of biodiversity conservation, systematic exploration of natural resources, and their exploitation with sophisticated modern technologies.

Molecular Characterization of camphor utilizing bacterial isolates from refinery sludge and detection of target loci-Cytochrome P-450 cam mono oxygenase (cam C gene) by PCR and gene probe

This study presents the isolation and molecular characterization of bacterial strains utilizing 1, 7, 7-Trimethylbicyclo (2.2.1) heptane-2-one (camphor) as a sole source of carbon, isolated from the biomass sludge sample collected from an effluent treatment plant of Mathura Refinery Limited (MRL), India. Initial screening was carried out where the 16S rDNA PCR was performed using reported eubacterial primer set followed by Amplified Ribosomal DNA Restriction Analysis (ARDRA). About 47% of the isolates have shown unique ARDRA pattern based on which, 15 distinct isolates were selected and tested for the presence of cam C gene that was successfully demonstrated by PCR using gene specific primers. A Dot-Blot experiment was designed to detect the cam C loci in the plasmid DNA of all camphor isolates based on non-radioactive “Biotin-Streptavidin” detection system. The bacterial identity with respect to partial 16S rDNA gene sequences of all camphor isolates placed them in 9 major genera viz., Pseudomonas sp., Staphylococcus sp., Alcaligenes sp., Agromyces sp., Stenotrophomonas sp., Reichenowia sp., Achromobacter sp., Brevibacterium sp. and Pseudaminobacter sp. A detailed phylogentic tree was also constructed to establish their evolutionary status from the gene sequence data.

Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases in the sediments from the Pearl River estuary, China

Bacterial community compositions were characterized using denaturing gradient gel electrophoresis analysis of bacterial 16S rRNA gene in the sediments of the Pearl River estuary. Sequencing analyses of the excised bands indicated that Gram-negative bacteria, especially Gammaproteobacteria, were dominant in the Pearl River estuary. The diversity of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) gene in this estuary was then assessed by clone library analysis. The phylogenetic analyses showed that all PAH-RHD gene sequences of Gram-negative bacteria (PAH-RHD[GN]) were closely related to the nagAc gene described for Ralstonia sp. U2 or nahAc gene for Pseudomonas sp. 9816-4, while the PAH-RHD gene sequences of Gram-positive bacteria (PAH-RHD[GP]) at sampling site A1 showed high sequence similarity to the nidA gene from Mycobacterium species. Meanwhile, molecular diversity of the two functional genes was higher at the upstream of this region, while lower at the downstream. Redundancy analysis indicated that environmental factors, such as NH₄--N, ∑PAHs, pH, SiO₃--Si, and water depth, affected the distribution of the PAH-RHD[GN] gene in the Pearl River estuary.

Pathogenesis of and strategies for preventing Edwardsiella tarda infection in fish

Edwardsiella tarda is one of the serious fish pathogens, infecting both cultured and wild fish species. Research on edwardsiellosis has revealed that E. tarda has a broad host range and geographic distribution, and contains important virulence factors that enhance bacterial survival and pathogenesis in hosts. Although recent progress in edwardsiellosis research has enabled the development of numerous, highly effective vaccine candidates, these efforts have not been translated into a commercialized vaccine. The present review aims to provide an overview of the identification, pathology, diagnosis and virulence factors of E. tarda in fish, and describe recent strategies for developing vaccines against edwardsiellosis. The hope is that this presentation will be useful not only from the standpoint of understanding the pathogenesis of E. tarda, but also from the perspective of facilitating the development of effective vaccines.

Characterization of the bacterial archaeal diversity in hydrocarbon-contaminated soil

A polyphasic approach combining culture-based methods with molecular methods is useful to expand knowledge on microbial diversity in contaminated soil. Microbial diversity was examined in soil samples from a former industrial site in the European Alps (mainly used for aluminum production and heavily contaminated with petroleum hydrocarbons) by culture-dependent and culture-independent methods. The physiologically active eubacterial community, as revealed by fluorescence-in-situ-hybridization (FISH), accounted for 6.7% of the total (DAPI-stained) bacterial community. 4.4% and 2.0% of the DAPI-stained cells could be attributed to culturable, heterotrophic bacteria able to grow at 20°C and 10°C, respectively. The majority of culturable bacterial isolates (34/48) belonged to the Proteobacteria (with a predominance of Alphaproteobacteria and Gammaproteobacteria), while the remaining isolates were affiliated with the Actinobacteria, Cytophaga-Flavobacterium-Bacteroides and Firmicutes. A high fraction of the culturable, heterotrophic bacterial population was able to utilize hydrocarbons. Actinobacteria were the most versatile and efficient degraders of diesel oil, n-alkanes, phenol and PAHs. The bacterial 16S rRNA gene clone library contained 390 clones that grouped into 68 phylotypes related to the Proteobacteria, Bacteroidetes, Actinobacteria and Spirochaetes. The archaeal 16S rRNA gene library contained 202 clones and 15 phylotypes belonging to the phylum Euryarchaeota; sequences were closely related to those of methanogenic archaea of the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales and Thermoplasmatales. A number of bacterial and archaeal phylotypes in the clone libraries shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Knowledge of the bacterial and archaeal diversity in the studied soil is important in order to get a better insight into the microbial structure of contaminated environments and to better exploit the bioremediation potential by identifying potential hydrocarbon degraders and consequently developing appropriate bioremediation strategies.

Monitoring of microbial hydrocarbon remediation in the soil

Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon-degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Provided the polluted soil has requisite values for environmental factors that influence microbial activities and there are no inhibitors of microbial metabolism, there is a good chance that there will be a viable and active population of hydrocarbon-utilizing microorganisms in the soil. Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved. Enumeration and characterization of hydrocarbon degraders, use of micro titer plate-based most probable number technique, community level physiological profiling, phospholipid fatty acid analysis, 16S rRNA- and other nucleic acid-based molecular fingerprinting techniques, metagenomics, microarray analysis, respirometry and gas chromatography are some of the methods employed in bio-monitoring of hydrocarbon remediation as presented in this review.

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.