Analysis of structure, function, and activity of a benzene-degrading microbial community

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Mechanisms of benzene and benzo[a]pyrene biodegradation in the individually and mixed contaminated soils

There is a lack of knowledge on the biodegradation mechanisms of benzene and benzo [a]pyrene (BaP), representative compounds of polycyclic aromatic hydrocarbons (PAHs), and benzene, toluene, ethylbenzene, and xylene (BTEX), under individually and mixed contaminated soils. Therefore, a set of microcosm experiments were conducted to explore the influence of benzene and BaP on biodegradation under individual and mixed contaminated condition, and their subsequent influence on native microbial consortium. The results revealed that the total mass loss of benzene was 56.0% under benzene and BaP mixed contamination, which was less than that of individual benzene contamination (78.3%). On the other hand, the mass loss of BaP was slightly boosted to 17.6% under the condition of benzene mixed contamination with BaP from that of individual BaP contamination (14.4%). The significant differences between the microbial and biocide treatments for both benzene and BaP removal demonstrated that microbial degradation played a crucial role in the mass loss for both contaminants. In addition, the microbial analyses revealed that the contamination of benzene played a major role in the fluctuations of microbial compositions under co-contaminated conditions. Rhodococcus, Nocardioides, Gailla, and norank_c_Gitt-GS-136 performed a major role in benzene biodegradation under individual and mixed contaminated conditions while Rhodococcus, Noviherbaspirillum, and Phenylobacterium were highly involved in BaP biodegradation. Moreover, binary benzene and BaP contamination highly reduced the Rhodococcus abundance, indicating the toxic influence of co-contamination on the functional key genus. Enzymatic activities revealed that catalase, lipase, and dehydrogenase activities proliferated while polyphenol oxidase was reduced with contamination compared to the control treatment. These results provided the fundamental information to facilitate the development of more efficient bioremediation strategies, which can be tailored to specific remediation of different contamination scenarios.

Aerobic biodegradation of cycloalkanes in non-aqueous extracted oil sands tailings

Management of growing volumes of fluid fine tailings (FFT) is a significant challenge for oil sands industry. A potential alternative non-aqueous solvent extraction (NAE) process uses cycloalkane solvent such as cyclohexane or cyclopentane with very little water and generates smaller volumes of 'dry' solids (NAES) with residual solvent. Here we investigate remediation of NAES in a simulated bench-scale upland reclamation scenario. In the first study, microcosms with nutrient medium plus FFT as inoculum were amended with cyclohexane and incubated for ∼1 year, monitoring for cyclohexane biodegradation under aerobic conditions. Biodegradation of cyclohexane occurred under aerobic conditions with no metabolic intermediates detected. A second study using NAES mixed with FFT spiked with cyclohexane and cyclopentane, with or without additional nutrients (nitrogen and phosphorus), showed complete and rapid aerobic biodegradation of both cycloalkanes in NAES inoculated with FFT and supplemented with nutrients. 16S rRNA gene sequencing revealed dominance of Rhodoferax and members of Burkholderiaceae during aerobic cyclohexane biodegradation in FFT, and Hydrogenophaga, Acidovorax, Defluviimonas and members of Porticoccaceae during aerobic biodegradation of cyclohexane and cyclopentane in NAES inoculated with FFT and supplemented with nutrients. The findings indicate that biodegradation of cycloalkanes from NAES is possible under aerobic condition, which will contribute to the successful reclamation of oil sands tailings for land closure.

Study on characteristic and mechanism involved in the formation of N-nitrosodimethylamine precursors during microbial metabolism of amino acids

Amino acid metabolism by microorganisms is a new but important pathway for the formation of NDMA precursors in water. We investigated the properties of nitrosamine precursors produced through microbial metabolism of amino acids by polarity rapid assessment method and molecular weight fractionation by ultrafiltration method. The PRAM results showed that the positively charged fraction and the non-polar fraction accounted for most (45 %-79 % and 6 %-82 %, respectively) of the NDMA precursors. The MW fractionation results also indicate the dominant precursors had MWs <1 kDa or over 10 kDa. NDMA precursors produced through amino acid metabolism were identified and quantified. Dimethylamine, N-methyl-alanine and alanine methyl ester were produced during the metabolism of alanine and peptone. Together, N-methyl-alanine and dimethylamine averagely contributed 24 % (12 %-44 %) of the NDMA precursors in the alanine medium. The NDMA precursor formation pathway during alanine metabolism involves the methylation of alanine to form N-methyl-alanine and the decomposition of alanine anabolism products to form dimethylamine. Nitrosamine precursors are generally formed through anabolism or methylation, but biogenic amines or NH₃ can be produced through catabolism before nitrosamine precursor synthesis. Microbial community analysis was performed and Ralstonia was found to be a likely key genus contributing to NDMA precursor formation during alanine metabolism.

Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland

Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.

Indole metabolism by phenol-stimulated activated sludges: Performance, microbial communities and network analysis

Indole and phenol often coexist in the coking wastewater, while the effects of phenol on microbial communities of indole metabolism were less explored. In this study, the microbial interactions within activated sludge microbial communities stimulated by indole (group A) or by indole and phenol (group B) were systematically investigated in sequencing batch reactors (SBRs). The results showed that the removal of indole was increased by adding phenol. By using high-throughput sequencing technology, it was found that α-diversity was reduced in both groups. According to the relative abundance analysis, the indole-degrading genus Comamonas was the core genus in both groups (33.94% and 61.40%). But another indole-degrading genus Pseudomonas was only enriched in group A with 12.22% relative abundance. Meanwhile, common aromatic degrading genus Dyella and Thermomonas were enriched only in group B. It was found that the relative abundance of cytochrome P450 and styrene degradation enzymes were increased in group B by PICRUSt analysis. Based on the phylogenetic molecular ecological networks (pMENs), module hub OTU_1149 (Burkholderia) was only detected in group B, and the positive interactions between the key functional genus Burkholderia and other bacteria were increased. This study provides new insights into our understanding of indole metabolism communities stimulated by phenol, which would provide useful information for practical coking wastewater treatment.

Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation

To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.

Investigation into the bacterial diversity of sediment samples obtained from Berg River, Western Cape, South Africa

This study used conventional culturing and 16S rRNA metagenomics analyses to assess the diversity of bacterial communities in sediment samples obtained from the Berg River, Western Cape, South Africa. Samples were collected from six points: a residential and recreational area, an industrial area, an informal residential settlement, a point next to a wastewater treatment plant (WWTP), a pumping station, and a residential and agricultural farming area along the river. High bacterial counts recorded on general selective and differential culture media signify substantial microbial contamination along the sampling sites. The most prevalent bacterial phyla detected (through metagenomics analyses) along the sampling sites were Proteobacteria (61%), Planctomycetes (9.5%), Firmicutes (7.8%), Bacteroidetes (5%), Acidobacteria (4.6%), and Actinobacteria (4.6%). Some members of the identified predominant bacterial phyla, genera, and classes are important public health bacteria that have been implicated in human diseases and outbreaks, while some others are metal or hydrocarbon tolerant, indicating possible significant environmental pollution. Notable human pathogenic genera such as Bacillus, Clostridium, Shigella, Legionella, Mycobacterium, and Pseudomonas were identified in varying percentages at five of the six sampling areas. Fecal contamination was particularly rife at all residential areas, with the informal housing area being the most notably polluted. Diverse functional pathways were predicted for identified bacteria, such as those associated with different chronic and infectious human diseases as well as those related to hydrocarbon and metal remediation. The point next to a WWTP contained vastly diverse groups of bacterial contaminants as well as the most abundant pathway identities and titles.

Specific enrichment of hydrocarbonclastic bacteria from diesel-amended soil on biochar particles

Biochar has been proposed as a suitable biostimulant for the remediation of hydrocarbon contamination, and also has the potential to act as a carrier for hydrocarbonoclastic microorganisms which could bioaugment endogenous microbial communities. However, the evidence regarding the biostimulatory effects of biochars on hydrocarbon bioremediation is somewhat equivocal, possibly due to variability of the physicochemical properties of biochar and soil across studies. Here, we use standard biochars with defined properties produced from softwood pellets (SWP) and rice husk (RH) at pyrolysis temperatures of 550 °C or 700 °C to test the effects of biochar amendment on microbial community composition and hydrocarbon degradation in soil microcosms contaminated with diesel oil. Combining this approach for the first time with specific analysis of microbial community composition using amplicon sequence variants (ASVs), we find that oil contamination causes extreme short-term loss of soil microbial diversity, and highly-specific selection of a limited set of genera defined by 13 ASVs. Biochar ameliorates the short-term loss of diversity, and in the longer term (9 weeks), changes community composition in a type-specific manner. The majority of the 13 selected ASVs are further enriched on biochar particles, although SWP biochars perform better than RH biochar in enrichment of putative hydrocarbonoclastic Aquabacterium spp. However, complete degradation of normal (n) alkanes from the aliphatic hydrocarbon fraction is prevented in the presence of biochar amendment, possibly due to their adsorption onto the char surface. Furthermore, we show that putative hydrocarbon degraders released from diesel-amended soil can subsequently be enriched to high levels on SWP biochar particles in growth medium supplemented with diesel oil as the sole carbon source; these include selected ASVs representing the genera Rhodococcus, Aquabacterium, and Cavicella. This work suggests that use of biochar pre-enriched with endogenous, conditionally-rare hydrocarbon degrading bacteria is a promising strategy for bioaugmentation of diesel-contaminated soils.

Bacterial community colonization on tire microplastics in typical urban water environments and associated impacting factors

Only limited information is available on bacterial communities' dynamics on tire microplastics in urban water environments. This study exploited 16S rDNA high-throughput sequencing to characterize bacterial communities on tire microplastics, using three different tire brands and tire sizes, in two typical urban water environments, including an influent pond of constructed wetland (CW) and its subsequent effluent into a landscape river (LR) during three different periods, namely, 1 month, 3 and 6 months. Results showed that the abundance of bacterial colonization on tire microplastics will increase over time. Proteobacteria, Bacteroidetes were the dominant bacteria at a phylum level, although they exhibited dynamic changes. At a genus level, the identifiable bacteria found in tire microplastics was generally the common bacteria in wastewater discharge, such as Aquabacterium and Denitratisoma. Additionally, alpha diversity showed no significant differences in bacterial communities at the same locations. While beta diversity showed that the bacterial communities on the tire microplastics in the two locations was different. BugBase revealed that tire microplastics could support pathogenic bacteria in urban water environments. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) indicated that the abundance of microorganisms associated with metabolism and degradation increased with time. Moreover, the ambient environmental factors were the main influencing factors of bacterial communities on tire microplastics. Herein, the contribution rate of nutrient salts (NO₂-N, NO₃-N, NH₄-N, CODcr) was approximately 63%, and that of environmental physical factors of T and pH was 50%. While physicochemical factors, including particle size, contact angle, element content only had a slight impact. Accordingly, tire microplastics, as an emerging environmental pollutant, can act as carries for bacterial colonization and propagation, particularly harmful microorganisms. Therefore, the obtained findings can provide new insight into potential risks of harmful microorganisms that colonize tire microplastics in urban water environments.

Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis

The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.

Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain Buc^T was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z .  oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions.

Aerobic and Anaerobic Biodegradation of 1,2-Dibromoethane by a Microbial Consortium under Simulated Groundwater Conditions

This study was conducted to explore the potential for 1,2-Dibromoethane (EDB) biodegradation by an acclimated microbial consortium under simulated dynamic groundwater conditions. The enriched EDB-degrading consortium consisted of anaerobic bacteria Desulfovibrio, facultative anaerobe Chromobacterium, and other potential EDB degraders. The results showed that the biodegradation efficiency of EDB was more than 61% at 15 °C, and the EDB biodegradation can be best described by the apparent pseudo-first-order kinetics. EDB biodegradation occurred at a relatively broad range of initial dissolved oxygen (DO) from 1.2 to 5.1 mg/L, indicating that the microbial consortium had a strong ability to adapt. The addition of 40 mg/L of rhamnolipid and 0.3 mM of sodium lactate increased the biodegradation. A two-phase biodegradation scheme was proposed for the EDB biodegradation in this study: an aerobic biodegradation to carbon dioxide and an anaerobic biodegradation via a two-electron transfer pathway of dihaloelimination. To our knowledge, this is the first study that reported EDB biodegradation by an acclimated consortium under both aerobic and anaerobic conditions, a dynamic DO condition often encountered during enhanced biodegradation of EDB in the field.

Bioleaching conditioning increased the bioavailability of polycyclic aromatic hydrocarbons to promote their removal during co-composting of industrial and municipal sewage sludges

Conditioning treatments are extensively employed in wastewater treatment plants (WWTPs) to enhance sludge dewaterability, thereby improving the sludge dehydration during mechanical dewatering. However, it remains unclear whether the sludge conditioning treatments would influence the removal of polycyclic aromatic hydrocarbons (PAHs) during the dewatered sludge composting. In this study, the influences of three sludge conditioning methods, including bioleaching conditioning driven by Acidithiobacillus ferrooxidans, chemical conditioning with Fe[III]/CaO, and chemical conditioning with polyacrylamide (PAM), on the bioavailability of PAHs in dewatered sludge and the PAH removal during the co-compositing of industrial and municipal sewage sludges were investigated. The results showed that bioleaching conditioning was capable to significantly increase the bioavailability of PAHs in dewatered sludge, which was not attained by the other two conditioning methods. During the 39 days composting of dewatered sludge, the total removal efficiency of six detected PAHs (∑PAHs) including acenaphthylene, fluorene, phenanthrene, anthracene, chrysene and benzo(k)fluoranthene was 58.7% in raw sludge, 58.5% in PAM-conditioned sludge, 76.4% in bioleached sludge, and 60.4% in Fe[III]/CaO-conditioned sludge, respectively, and the removal of acenaphthylene, chrysene and benzo(k)fluoranthene was much higher in bioleached sludge than in other sludges. During dewatered sludge composting, PAHs may mainly be degraded by the bacteria belonging to the genera Luteimonas, Glutamicibacter, Alcanivorax, Dechloromonas, Ferribacterium, Truepera and Sphingobacterium. Linear correlation analysis between PAH removal and their bioavailability revealed that the promoted PAH removal during the composting of dewatered bioleached sludge may ascribe to the enhanced bioavailability of individual PAH. Therefore, the combination of bioleaching conditioning and subsequent dewatered sludge composting is effective to remove PAHs in sewage sludge, thus alleviating the loads of PAHs during the land application of sludge compost products.

Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota

While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of ¹³C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental “omics.” Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with ¹³C-labeled toluene under microoxic conditions. From the total sequencing reads (∼30 mio. reads per density-resolved RNA fraction), an average of 1.2% of reads per sample were identified as non-rRNA, including mRNA. Members of the Rhodocyclaceae (including those related to Quatrionicoccus spp.) were most abundant and enriched in ¹³C-rRNA, while well-known aerobic degraders such as Pseudomonas spp. remained unlabeled. Transcripts related to cell motility, secondary metabolite formation and xenobiotics degradation were highly labeled with ¹³C. mRNA of phenol hydroxylase genes were highly labeled and abundant, while other transcripts of toluene-activation were not detected. Clear labeling of catechol 2,3-dioxygenase transcripts supported previous findings that some of these extradiol dioxygenases were adapted to low oxygen concentrations. We introduce a novel combination of total RNA-SIP with calculation of transcript-specific enrichment factors (EFs) in ¹³C-RNA, enabling a targeted approach to process-relevant gene expression in complex microbiomes.

Stable isotope probing of hypoxic toluene degradation at the Siklós aquifer reveals prominent role of Rhodocyclaceae

The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro- or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but sustained oxygen supply, such as in the vicinity of groundwater monitoring wells, hypoxic degradation may take place. A large diversity of subfamily I.2.C extradiol dioxygenase genes has been previously detected in a BTEX-contaminated aquifer in Hungary. Older literature suggests that such catabolic potentials could be associated to hypoxic degradation. Bacterial communities dominated by members of the Rhodocyclaceae were found, but the majority of the detected C23O genotypes could not be affiliated to any known bacterial degrader lineages. To address this, a stable isotope probing (SIP) incubation of site sediments with 13C7-toluene was performed under microoxic conditions. A combination of 16S rRNA gene amplicon sequencing and T-RFLP fingerprinting of C23O genes from SIP gradient fractions revealed the central role of degraders within the Rhodocyclaceae in hypoxic toluene degradation. The main assimilators of 13C were identified as members of the genera Quatrionicoccus and Zoogloea, and a yet uncultured group of the Rhodocyclaceae.

Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond

Oil sands process-affected water (OSPW), produced by surface-mining of oil sands in Canada, is alkaline and contains high concentrations of salts, metals, naphthenic acids, and polycyclic aromatic compounds (PAHs). Residual hydrocarbon biodegradation occurs naturally, but little is known about the hydrocarbon-degrading microbial communities present in OSPW. In this study, aerobic oxidation of benzene and naphthalene in the surface layer of an oil sands tailings pond were measured. The potential oxidation rates were 4.3 μmol L^-1 OSPW d^-1 for benzene and 21.4 μmol L^-1 OSPW d^-1 for naphthalene. To identify benzene and naphthalene-degrading microbial communities, metagenomics was combined with stable isotope probing (SIP), high-throughput sequencing of 16S rRNA gene amplicons, and isolation of microbial strains. SIP using ¹³C-benzene and ¹³C-naphthalene detected strains of the genera Methyloversatilis and Zavarzinia as the main benzene degraders, while strains belonging to the family Chromatiaceae and the genus Thauera were the main naphthalene degraders. Metagenomic analysis revealed a diversity of genes encoding oxygenases active against aromatic compounds. Although these genes apparently belonged to many phylogenetically diverse taxa, only a few of these taxa were predominant in the SIP experiments. This suggested that many members of the community are adapted to consuming other aromatic compounds, or are active only under specific conditions. 16S rRNA gene sequence datasets have been submitted to the Sequence Read Archive (SRA) under accession number SRP109130. The Gold Study and Project submission ID number in Joint Genome Institute IMG/M for the metagenome is Gs0047444 and Gp0055765.

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations.

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes

Stable isotope probing of RNA has enthused researchers right from its first introduction in 2002. The concept of a labelling-based detection of process-targeted microbes independent of cellular replication or growth has allowed for a much more direct handle on functionally relevant microbiota than by labelling of other biomarkers. This has led to a widespread application of the technology, and breakthroughs in our understanding of carbon flow in natural microbiomes, autotrophic and heterotrophic physiologies, microbial food webs, host-microbe interactions and environmental biotechnology. Recent studies detecting labelled mRNA demonstrate that RNA-SIP is not limited to the analysis of rRNA, but is currently developing towards an approach for accessing targeted transcriptomes. In combination with next-generation sequencing and other methodological advances, RNA-SIP will continue to deliver invaluable insights into the functioning of microbial communities.

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.

Electrical stimulation on biodegradation of phenol and responses of microbial communities in conductive carriers supported biofilms of the bioelectrochemical reactor

Conductive carbon felts (Cf) were used as biofilm carriers in bioelectrochemical reactors to enhance the electrical stimulation on treatment of phenol-containing synthetic wastewater. In batch test, phenol biodegradation was accelerated under an optimum direct current (DC), which was 2mA for Cf biofilm carriers, lower than that for non-conductive white foam carriers. The stimulation effect was consistent with Adenosine Triphosphate contents in biofilms. The long-term operation further demonstrated that a high and stable phenol removal efficiency could be achieved with applied DC of 2mA, and intermittent DC application was better than continuous one, with phenol removal efficiency of over 97%. Although the quantities of whole microbial communities kept at a high level under all conditions, special microorganisms related with genera of Zoogloea and Desulfovibrio were distinctively enriched under intermittent applied DC pattern. This study shows that the electrical stimulation is potentially effective for biofilm reactors treating phenol-containing wastewater.

Occurrence of diverse alkane hydroxylase alkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water

Formation of specific oil degrading bacterial communities in diesel fuel, crude oil, heptane and hexadecane supplemented microcosms of the Baltic Sea surface water samples was revealed. The 475 sequences from constructed alkane hydroxylase alkB gene clone libraries were grouped into 30 OPFs. The two largest groups were most similar to Pedobacter sp. (245 from 475) and Limnobacter sp. (112 from 475) alkB gene sequences. From 56 alkane-degrading bacterial strains 41 belonged to the Pseudomonas spp. and 8 to the Rhodococcus spp. having redundant alkB genes. Together 68 alkB gene sequences were identified. These genes grouped into 20 OPFs, half of them being specific only to the isolated strains. Altogether 543 diverse alkB genes were characterized in the brackish Baltic Sea water; some of them representing novel lineages having very low sequence identities with corresponding genes of the reference strains.

Functional diversity and dynamics of bacterial communities in a membrane bioreactor for the treatment of metal-working fluid wastewater

An extensive microbiological study has been carried out in a membrane bioreactor fed with activated sludge and metal-working fluids. Functional diversity and dynamics of bacterial communities were studied with different approaches. Functional diversity of culturable bacterial communities was studied with different Biolog™ plates. Structure and dynamics of bacterial communities were studied in culturable and in non-culturable fractions using a 16S rRNA analysis. Among the culturable bacteria, Alphaproteobacteria and Gammaproteobacteria were the predominant classes. However, changes in microbial community structure were detected over time. Culture-independent analysis showed that Betaproteobacteria was the most frequently detected class in the membrane bioreactor (MBR) community with Zoogloea and Acidovorax as dominant genera. Also, among non-culturable bacteria, a process of succession was observed. Longitudinal structural shifts observed were more marked for non-culturable than for culturable bacteria, pointing towards an important role in the MBR performance. Microbial community metabolic abilities assessed with Biolog™ Gram negative, Gram positive and anaerobic plates also showed differences over time for Shannon's diversity index, kinetics of average well colour development, and the intensely used substrates by bacterial community in each plate.

The Analysis of a Microbial Community in the UV/O3-Anaerobic/Aerobic Integrated Process for Petrochemical Nanofiltration Concentrate (NFC) Treatment by 454-Pyrosequencing

In this study, high-throughput pyrosequencing was applied on the analysis of the microbial community of activated sludge and biofilm in a lab-scale UV/O₃- anaerobic/aerobic (A/O) integrated process for the treatment of petrochemical nanofiltration concentrate (NFC) wastewater. NFC is a type of saline wastewater with low biodegradability. From the anaerobic activated sludge (Sample A) and aerobic biofilm (Sample O), 59,748 and 51,231 valid sequence reads were obtained, respectively. The dominant phylotypes related to the metabolism of organic compounds, polycyclic aromatic hydrocarbon (PAH) biodegradation, assimilation of carbon from benzene, and the biodegradation of nitrogenous organic compounds were detected as genus Clostridium, genera Pseudomonas and Stenotrophomonas, class Betaproteobacteria, and genus Hyphomicrobium. Furthermore, the nitrite-oxidising bacteria Nitrospira, nitrite-reducing and sulphate-oxidising bacteria (NR-SRB) Thioalkalivibrio were also detected. In the last twenty operational days, the total Chemical Oxygen Demand (COD) and Total Organic Carbon (TOC) removal efficiencies on average were 64.93% and 62.06%, respectively. The removal efficiencies of ammonia nitrogen and Total Nitrogen (TN) on average were 90.51% and 75.11% during the entire treatment process.

Anaerobic biodegradation of nonylphenol in river sediment under nitrate- or sulfate-reducing conditions and associated bacterial community

Nonylphenol (NP) is a commonly detected pollutant in aquatic ecosystem and can be harmful to aquatic organisms. Anaerobic degradation is of great importance for the clean-up of NP in sediment. However, information on anaerobic NP biodegradation in the environment is still very limited. The present study investigated the shift in bacterial community structure associated with NP degradation in river sediment microcosms under nitrate- or sulfate-reducing conditions. Nearly 80% of NP (100 mg kg(-1)) could be removed under these two anaerobic conditions after 90 or 110 days' incubation. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi became the dominant phylum groups with NP biodegradation. The proportion of Gammaproteobacteria, Deltaproteobacteria and Choloroflexi showed a marked increase in nitrate-reducing microcosm, while Gammaproteobacteria and Firmicutes in sulfate-reducing microcosm. Moreover, sediment bacterial diversity changed with NP biodegradation, which was dependent on type of electron acceptor.

Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1

The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence.

Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated Buc(T), was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Buc(T) formed a distinct phyletic lineage within the genus Zoogloea. Its closest relative was found to be Zoogloea caeni EMB43(T) (97.2% 16S rRNA gene sequence similarity) followed by Zoogloea oryzae A-7(T) (95.9%), Zoogloea ramigera ATCC 19544(T) (95.5%) and Zoogloea resiniphila DhA-35(T) (95.4%). The level of DNA-DNA relatedness between strain Buc(T) and Z. caeni EMB43(T) was 31.6%. Cells of strain Buc(T) are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5-35 °C (optimum 25-28 °C), and at pH 6.0-9.0 (optimum 6.5-7.5). The predominant fatty acids were C16:0, C10 : 0 3-OH, C12:0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate Buc(T) is considered to represent a novel species of the genus Zoogloea, for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is Buc(T) ( =DSM 28387(T) =NCAIM B 02570(T)).

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.