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This study assessed the bacterial community composition of a drinking water system (DWS) serving a mid-sized city (120,000 inhabitants) in Brazil. Water samples, including raw and treated water, were collected at seven points throughout the DWS. DNA was extracted and analysed using high-throughput sequencing (Ion Torrent). Free chlorine and turbidity were measured in situ. Results showed that the highest relative abundance of 16S rRNA genes was from phyla Proteobacteria, followed by Bacteroidetes and Actinobacteria. The next most abundant phylum was Cyanobacteria, represented by Arthronema, Calothrix, and Synechococcus. An interesting observation was that the DNA-based analysis suggested a bacterial community change in the distribution network, with treated reservoir water being very different from the network samples. This suggests active microbiology within the distribution network and a tendency for bacterial diversity to decrease after chlorine disinfection but increase after pipeline distribution. In raw water, a predominance of Proteobacteria was observed with reduced Cyanobacteria, showing a negative correlation. In treated water, Proteobacteria were negatively correlated with Bacteroidetes. Finally, 16S rRNA genes from Firmicutes (especially Staphylococcus) had a high abundance in the chlorinated water, which may indicate the phylum's resistance to chlorine residuals. Opportunistic pathogens, e.g., Mycobacteria, Legionella, and Staphylococcus, were also observed. [ABSTRACT FROM AUTHOR]

Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10- seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol. [ABSTRACT FROM AUTHOR]

The use of activated carbon (AC) amendments to reduce exposure risks for hydrophobic contaminants like polycyclic aromatic hydrocarbons (PAHs) by adsorption is an innovative soil remediation approach. However, AC amendment side-effects on the pollution biodegradation are poorly understood. This study assessed for optimized nutrient ratio conditions, effects of 5% soil wet weight AC amendments, if added from the beginning or after five months, on the outcomes of one year of crude oil polluted soil bioremediation. CO 2 , residual hydrocarbon concentrations and microbial community structure analysis revealed how AC amendment hindered crude oil biodegradation much more, if added from the start, as compared to after 5 months, i.e. after the initial phase of biodegradation. Putative crude oil degrading microorganisms from the genera Marinobacter, Parvibaculum, Salinibacterium, Muricauda , and Alcanivorax were more sensitive to the AC amendment than those from the genus Rhodococcus. Rhodococci possess hydrophobic cell walls which may enable them to accumulate hydrocarbons in the AC amended soil, despite of their reduced availability. AC amendment from the start had the highest alkane and total US EPA PAH residues, but was more effective than one year of bioremediation, with or without AC amendment after 5 months, in reducing PAH availability in the soil. Image 1 • Crude oil biodegradation was studied with and without activated carbon (AC) addition. • If added from the start, AC slowed crude oil mineralisation. • If added from the start, AC reduced numbers of putative hydrocarbon degrading bacteria. • If added after 5 months, AC had only minor effects on crude oil biodegradation. • After 12 months, PAH availability was the lowest, if AC was added from the start. [ABSTRACT FROM AUTHOR]

We studied the effects of two percent by weight activated carbon versus biochar amendments in 93 cm long sand columns on the biofiltration of petroleum vapours released by a non-aqueous phase liquid (NAPL) source. Activated carbon greatly enhanced, whereas biochar slightly reduced, the biofiltration of volatile petroleum hydrocarbons (VPHs) over 430 days. Sorbent amendment benefitted the VPH biofiltration by retarding breakthrough during the biodegradation lag phase. Subsequently, sorbent amendment briefly reduced the mineralization of petroleum hydrocarbons by limiting their bioavailability. During the last and longest study period, when conditions became less supportive of microbial growth, because of inorganic nutrient scarcity, the sorbents again improved the pollution attenuation by preventing the degrading microorganisms from being overloaded with VPHs. A 16S rRNA gene based analysis showed sorbent amendment effects on soil microbial communities. Nocardioidaceae benefitted the most from petroleum hydrocarbons in activated carbon amended soil, whereas Pseudomonadacea predominated in unamended soil. Whilst the degrading microorganisms were overloaded with VPHs in the unamended soil, the reduced mobility and bioavailability of VPHs in the activated carbon amended soil led to the emergence of communities with higher specific substrate affinity, which removed bioavailable VPHs effectively at low concentrations. A numerical pollutant fate model reproduced these experimental observations by considering sorption effects on the pollutant migration and bioavailability for growth of VPH degrading biomass, which is limited by a maximum soil biomass carrying capacity. Activated carbon was a much stronger sorbent for VPHs than biochar, which explained the diverging effects of the two sorbents in this study. [ABSTRACT FROM AUTHOR]

We investigated the response of the dominant bacterial taxa in gravelly sand to the addition of biochar and/or mixtures of volatile petroleum hydrocarbons (VPHs) using denaturing gradient gel electrophoresis (DGGE) and sequencing of cut bands. Biochar addition alone had only weak effects on the soil bacterial community composition in batch study samples, while VPH addition had strong effects. Indirect effects of biochar on soil bacterial communities were apparent in column study samples, where biochar-enhanced sorption affected VPH spreading. Following VPH addition, cell abundance increased by no more than a factor of 2 and several Pseudomonas spp. became dominant in soil with and without biochar. We present a VPH fate model that considers soil bacterial biomass dynamics and a nutrient limited soil biomass carrying capacity. The model simulates an apparent lag phase before the onset of a brief period of intensive VPH biodegradation and biomass growth, which is followed by substantially slower VPH biodegradation, when nitrogen needs to be recycled between decaying and newly formed biomass. If biomass growth is limited by a factor other than the organic pollutant bioavailability, biochar amendment may enhance VPH attenuation in between a VPH source below ground and the atmosphere by reducing the risk of overloading the soil's biodegradation capacity. [ABSTRACT FROM AUTHOR]

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. [ABSTRACT FROM AUTHOR]

Volatile Petroleum Hydrocarbon (VPH) class effects on soil microbial composition were investigated using two next-generation sequencing (NGS) techniques – 454 pyrosequencing and ion torrent sequencing. Microbial activity was stimulated by adding different VPH compound classes to the sandy soil in comparison with live controls without VPH addition. Microbial community structure was significantly affected by the various VPH classes. At the genus level, Rhodococcus, Desulfosporosinus , Polaromonas, Mesorhizobium and Methylibium had the highest relative abundances in the straight-chain alkane (str-alk) treated soil as compared to the control (p < 0.05, 2 sample t-tests) while Pseudomonas was more dominant in the cyclic alkane (cyc-alk) contaminated soil. Pseudonocardia was significantly higher in relative abundance in the aromatic hydrocarbon (aro-H) treated batches as compared to the control (p < 0.05, 2 sample t-tests). A non-metric multidimensional scaling (NMDS) of the Bray Curtis similarity between microbial communities in the batches revealed at least 60% similarity for each treatment and also showed that VPH class was a statistically significant factor in shaping the bacterial communities in the soil treatments (Global R = 0.861, p < 0.01). The NGS platforms (454 GS Junior and Ion torrent) compared in this study did not appear to affect the outcomes of the microbial community structure and composition analysis. Image 1 • Volatile petroleum hydrocarbon (VPH) class mixtures stimulated microbial activity. • Microbial diversity decreased following addition of different VPH class mixtures. • VPH classes contributed to shaping the microbial communities in batch treatments. • Bacterial species demonstrated varying responses to different VPH class mixtures. • NGS platforms did not alter the outcomes of microbial community structures. 16S amplicon sequencing revealed how soil microbial communities respond to addition of different volatile petroleum hydrocarbons. [ABSTRACT FROM AUTHOR]

This study assessed the bacterial community composition of a drinking water system (DWS) serving a mid-sized city (120,000 inhabitants) in Brazil. Water samples, including raw and treated water, were collected at seven points throughout the DWS. DNA was extracted and analysed using high-throughput sequencing (Ion Torrent). Free chlorine and turbidity were measured in situ. Results showed that the highest relative abundance of 16S rRNA genes was from phyla Proteobacteria, followed by Bacteroidetes and Actinobacteria. The next most abundant phylum was Cyanobacteria, represented by Arthronema, Calothrix, and Synechococcus. An interesting observation was that the DNA-based analysis suggested a bacterial community change in the distribution network, with treated reservoir water being very different from the network samples. This suggests active microbiology within the distribution network and a tendency for bacterial diversity to decrease after chlorine disinfection but increase after pipeline distribution. In raw water, a predominance of Proteobacteria was observed with reduced Cyanobacteria, showing a negative correlation. In treated water, Proteobacteria were negatively correlated with Bacteroidetes. Finally, 16S rRNA genes from Firmicutes (especially Staphylococcus) had a high abundance in the chlorinated water, which may indicate the phylum's resistance to chlorine residuals. Opportunistic pathogens, e.g., Mycobacteria, Legionella, and Staphylococcus, were also observed.