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The contamination of soil with petrogenic hydrocarbons represents a significant human health concern as a result of the carcinogenic and mutagenic properties of a number of compounds commonly found in petroleum products such as polycyclic aromatic hydrocarbons (PAHs). Although it is known that soil fungal communities play an important role in the degradation of highly branched petroleum hydrocarbons and high molecular weight PAHs, little information is available regarding the impact of petrogenic contamination on the structure and diversity of the fungal community and the impact of soil type on the fungal community response. Here, the aim of this study was to evaluate the impact of petrogenic contamination on fungal communities in two soil types. In sandy soils, the most contaminated test pit had the highest fungal diversity. Fungal profiles were dominated by species from the class Eurotiomycetes and included the well-known hydrocarbon-degrading species of Aspergillus and Eurotiales. The dominance of these species did not change with contamination concentration,suggesting a level of adaptability to multiple carbon sources. There appeared to be no correlation between fungal species diversity and contaminant concentration in the clayey soil. Similar dominant fungal species were identified in the clay and sandy soils, all of which were part of the phylum Ascomycota. The clayey soils had a higher species diversity and range-weighted richness compared to sandy soils, which may be a result of the pore connectivity theory i.e. as a result of low water connectivity in soils the formation of diverse communities is promoted through creation of microhabitats. Refereed/Peer-reviewed

The microbial contamination of surfaces presents a significant challenge due to the adverse effects associated with biofilm formation, particularly on implantable devices. Here, the attachment and ...

The dinitrotoluene isomers 2,4 and 2,6-dinitrotoluene (DNT) represent highly toxic, mutagenic, and carcinogenic compounds used in explosive manufacturing and in commercial production of polyurethane foam. Bioremediation, the use of microbes to degrade residual DNT in industry wastewaters, represents a promising, low cost and environmentally friendly alternative technology to landfilling. In the present study, the effect of different bioremediation strategies on the degradation of DNT in a microcosm-based study was evaluated. Biostimulation of the indigenous microbial community with sulphur phosphate (2.3 g/kg sludge) enhanced DNT transformation (82% transformation, from 300 g/L at Day 0 to 55 g/L in week 6) compared to natural attenuation over the same period at 25 °C. The indigenous microbial activity was found to be capable of transforming the contaminant, with around 70% transformation of DNT occurring over the microcosm study. 16S rDNA sequence analysis revealed that while the original bacterial community was dominated by Gammaproteobacteria (30%), the addition of sulphur phosphate significantly increased the abundance of Betaproteobacteria by the end of the biostimulation treatment, with the bacterial community dominated by Burkholderia (46%) followed by Rhodanobacter, Acidovorax and Pseudomonas. In summary, the results suggest biostimulation as a treatment choice for the remediation of dinitrotoluenes and explosives waste.

Balneotherapy is an ancient practice which remains commonplace throughout the world due to perceived health benefits that include relief of arthritis, fibromyalgia and relaxation. However, bathing environments are not sterile and natural spring waters may harbour natural microbial populations that include potential pathogens. We elucidated the microbial community from water taken from the borehole, pre-filter water (chlorinated, cold and post-bathing water) and post-filter water at a commercial Australian natural hot spring bathing facility. Thiobacillus, Sphingobium and Agrobacterium were the predominant genera in samples collected from the borehole. The predominant genera changed to Sphingobium, Parvibaculum and Achromobacter following chloride treatment and Azospira replaced the Achromobacter once the water reached ambient temperature and was stored ready to be used by bathers. The microbial community changed again following use by bathers, dominated by Pseudomonas, although Sphingobium persisted. No total or faecal coliforms were observed in any of the samples except for the post-bathing water, even there, their presence was at very low concentration (2.3 cfu/mL). These results confirm the lack of pathogens present in these hot spring waters but also suggests that good management of post-bathing water is required especially if the water is used for borehole water recharge.

Bioaugmentation or the addition of microbes to contaminated sites has been widely used to treat contaminated soil or water; however this approach is often limited to laboratory based studies. In the present study, large scale bioaugmentation has been applied to total petroleum hydrocarbons (TPH)-contaminated groundwater at a petroleum facility. Initial TPH concentrations of 1564 mg L?1 in the field were reduced to 89 mg L?1 over 32 days. This reduction was accompanied by improved ecotoxicity, as shown by Brassica rapa germination numbers that increased from 52 at day 0 to 82% by the end of the treatment. Metagenomic analysis indicated that there was a shift in the microbial community when compared to the beginning of the treatment. The microbial community was dominated by Proteobacteria and Bacteroidetes from day 0 to day 32, although differences at the genus level were observed. The predominant genera at the beginning of the treatment (day 0 just after inoculation) were Cloacibacterium, Sediminibacterium and Brevundimonas while at the end of the treatment members of Flavobacterium dominated, reaching almost half the population (41%), followed by Pseudomonas (6%) and Limnobacter (5.8%). To the author's knowledge, this is among the first studies to report the successful large scale biodegradation of TPH-contaminated groundwater (18,000 L per treatment session) at an offshore petrochemical facility.

The supplementation of agricultural soils with dewatered sewage sludge represents a technical solution not only to the disposal of the large quantities of biosolids generated daily, but also a potential means of increasing soil fertility and productivity. However, the presence of organic pollutants such as polycyclic aromatic hydrocarbons (PAHs) found in biosolids limits their application to agricultural soils. The application of Phanerochaete chrysosporium, its lignocelluloytic cell-free extract, a commercial preparation of the laccase enzyme for the enhanced removal of three PAHs (naphthalene, phenanthrene and pyrene) at two different concentrations (1 and 10 mg g−1 biosolids) from a biosolid sample was assessed in terms of both PAH degradation and their impact on the microbial community of the biosolids. The addition of P. chrysosporium biomass, a commercial laccase preparation, a P. chrysosporium cell-free extract at low PAH concentrations (1 mg g−1 biosolids) and high PAH concentrations (10 mg g−1 biosolids) resulted in a significant increase (P

Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active 13 C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event ( 14 C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community’s ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil. Refereed/Peer-reviewed

Graphical abstract, Soil-transmitted helminths (STHs) pose a significant public health problem, infecting approximately 2 billion people globally. Despite relatively low prevalence in developed countries, the removal of STHs from wastewater remains crucial to allow the safe use of biosolids or recycled water for agriculture. Wastewater helminth egg count data can contribute to an assessment of the need for, or success of, a parasite management program. Although the World Health Organisation (WHO) has recommended a standard method for counting helminth eggs in raw sewage based on the method of Bailenger (Ayres et al., 1996), the method generally results in low percentage egg recoveries. Given the importance of determining the presence of STHs, it is essential to develop novel techniques that optimise the recovery rate of eggs from raw sewage. In the present study: • The method described by Bowman et al. (2003) was optimized for the concentration and enumeration of helminth eggs in raw sewage from municipal sewage treatment plants. • The method is simple and reproducible and recovers a greater percentage of helminth eggs compared to the WHO method.

Abiotic and biotic processes can be used to remediate DDX (DDT, DDD, DDE, and DDNS) contaminated soils; these processes can be fostered using specific carbon-amendments to stimulate particular soil indigenous microbial communities to improve rates or extent of degradation. In this study, toluene and glycerol were evaluated as cosubstrates under aerobic and anoxic conditions to determine the degradation efficiencies of DDX and to elucidate possible degradation mechanisms. Slurry microcosms experiments were performed during 60 days using pretreated soil with zero-valent iron (ZVI). Toluene addition enhanced the percentage of degradation of DDX. DDNS was the main compound degraded (around 86%) under aerobic conditions, suggesting cometabolic degradation of DDX by toluene-degrading soil bacteria. Glycerol addition under anoxic conditions favored the abiotic degradation of DDX mediated by sulfate-reducing bacteria activity, where DDT was the main compound degraded (around 90%). The 16S rDNA metagenomic analyses revealed Rhodococcus ruber and Desulfosporosinus auripigmenti as the predominant bacterial species after 40 days of treatment with toluene and glycerol additions, respectively. This study provides evidence of biotic and abiotic DDX degradation by the addition of toluene and glycerol as cosubstrates in ZVI pretreated DDX-contaminated soil.

Nematode eggs are pervasive pathogens that infect billions of people and livestock every year. Adult parasitic nematode worms can be distinguished based on their size and morphology. However, their eggs, particularly their species Ascaris lumbricoides and Ascaris suum cannot be identified from each other. Identifying eggs of helminths from wastewater and sludge is important from a public health perspective to minimize the spread of Ascaris infections. Numerous methods exist for nematode identification, from a morphological-based approach to high throughput sequencing technology. However, these techniques are not consistent and often laborious and time-consuming. In this study, we demonstrate that non-invasive real-time identification of eggs is possible based on their intrinsic fluorescence. Using confocal microscopy, we investigate the autofluorescence properties of five species of nematode eggs and observe clear differences between genus and for the first time their species in sludge samples. This non-invasive imaging technique could lead to better understanding of these species and may assist in early control of diseases.

Bioremediation is a broadly applied environmentally friendly and economical treatment for the clean-up of sites contaminated by petroleum hydrocarbons. However, the application of this technology to contaminated soil in Libya has not been fully exploited. In this study, the efficacy of different bioremediation processes (necrophytoremediation using pea straw, bioaugmentation and a combination of both treatments) together with natural attenuation were assessed in diesel contaminated Libyan soils. The addition of pea straw was found to be the best bioremediation treatment for cleaning up diesel contaminated Libyan soil after 12 weeks. The greatest TPH degradation, 96.1% (18,239.6mgkg(-1)) and 95% (17,991.14mgkg(-1)) were obtained when the soil was amended with pea straw alone and in combination with a hydrocarbonoclastic consortium respectively. In contrast, natural attenuation resulted in a significantly lower TPH reduction of 76% (14,444.5mgkg(-1)). The presence of pea straw also led to a significant increased recovery of hydrocarbon degraders; 5.7log CFU g(-1) dry soil, compared to 4.4log CFUg(-1) dry soil for the untreated (natural attenuation) soil. DGGE and Illumina 16S metagenomic analyses confirm shifts in bacterial communities compared with original soil after 12 weeks incubation. In addition, metagenomic analysis showed that original soil contained hydrocarbon degraders (e.g. Pseudoxanthomonas spp. and Alcanivorax spp.). However, they require a biostimulant (in this case pea straw) to become active. This study is the first to report successful oil bioremediation with pea straw in Libya. It demonstrates the effectiveness of pea straw in enhancing bioremediation of the diesel-contaminated Libyan soil.

Green cincau (Premna oblongifolia Merr.) is a traditional food of Indonesia and provides a natural source of dietary fibre and antioxidants. This study evaluated the ability of green cincau, and other dietary fibres with or without the addition of anti-oxidant, epigallocatechin-3-gallate (EGCG), to prevent colorectal cancer in a 12 week azoxymethane (AOM) rat model. While all dietary treatments stimulated short chain fatty acid production (SCFA) in the digesta and faeces, no one treatment was able to significantly protect against aberrant crypt formation (ACF), when compared to the control diet. However, feeding green cincau leaves or extracts did not result in an increase in ACF compared to the control diet. Unexpectedly, when the dietary fibre source was pectin, 0.1% EGCG increased proliferative activity and liver lipid peroxidation when compared to the control diet containing cellulose. Examination of faecal microbial communities identified the presence of short chain acid producing bacteria, but a distinct community profile was not observed from any individual diet group. Overall, this research implies that combining dietary fibre with an antioxidant does not automatically equate to a beneficial response. Further work is required to investigate the health-promoting properties of green cincau.

Aburto-Medina, A., Ortiz, I., & Hernández, E. (mayo-junio, 2017). Prevalencia de Enterobacteriaceae y monitoreo de contaminantes en sedimentos del río Atoyac. Tecnología y Ciencias del Agua, 8(3), 27-37. Se identificó la comunidad bacteriana en sedimentos del río Atoyac por medio de biblioteca genómica de clones. Encontramos una baja diversidad bacteriana, ya que la familia Enterobacteriaceae, específicamente especies de Shigella, Escherichia fergusonii y E. coli dominan la comunidad bacteriana, lo cual es consistente con los valores obtenidos de coliformes totales por número más probable (NMP). No se encontraron los genes que codifican para toxinas Shiga (stx1 y stx2). Alcanos (C11-C16), ésteres, ácidos orgánicos, fenoles y ftalatos clasificados como potenciales disruptores endócrinos también fueron detectados en los sedimentos y la presencia de coprostanol indica contaminación fecal. Las concentraciones de elementos decrecieron de la siguiente manera: Ca > Fe > K > Ti > Sr > Ba > Mn > Zr > Zn > Cu > Rb, mientras que As, Mo y Pb estuvieron por debajo del límite de detección. Todos los elementos, excepto el Cu, no sobrepasan los límites de la Agencia de Protección Ambiental de los Estados Unidos (USEPA, 1977). Este estudio demuestra la dominancia de Enterobacteriaceae y la baja diversidad bacteriana con la habilidad de degradar contaminantes orgánicos en los sedimentos del río en un área previa a la presa Ávila Camacho, cuyas aguas son usadas para irrigar cultivos en tierras arriba.

The dinitrotoluene (DNT) isomers 2,4- and 2,6-DNT are highly toxic compounds, and their occurrence in groundwater and soils is a widespread problem mainly due to the explosive manufacturing industry and from the commercial production of polyurethane foam. Moreover, these compounds have mutagenic and carcinogenic properties making them a great hazard to the public health. Thus, their removal from the environment is paramount, and bioremediation strategies can be applied for the environmental cleanup. Pure cultures of microorganisms able to degrade at least 2,4-DNT have been recently isolated as well as a consortium and different plant species. The pure cultures are an Arthrobacter strain isolated from crude oil-contaminated soil, a Rhodococcus pyridinovorans NT2, and Shewanella marisflavi EP1, while the consortium named UHasselt Sofie 3 (UHS3) was formed by Burkholderia HC114, Variovorax paradoxus VM685, Bacillus, Pseudomonas mandelii HC88, and Ralstonia HC90. These microorganisms perform the degradation of the dinitrotoluenes in aerobic conditions except the marine strain Shewanella marisflavi. The plant species able to grow in the presence of 2,4-DNT and proposed for phytoremediation are hemp, flax, sunflower, and mustard. The intermediates reported in the majority of successful biodegradation studies are 4-methyl-5-nitrocatechol (4M5NC) and 2-hydroxy-5-methylquinone (2H5MQ) under aerobic conditions, while 2,4-diaminotoluene is obtained as an end product via the formation of 2-amino-4-nitrotoluene (2A4NT) and 4-amino-2-nitrotoluene (4A2NT) under anaerobic conditions. These microorganisms add to the growing number of isolates with the ability to degrade these types of compounds since strain DNT was isolated. This mini-review focuses on the microorganisms involved in the degradation of the dinitrotoluene isomers 2,4- and 2,6-DNT in recent years. Information related to the degradation of these contaminants is critical to understanding and predicting their fate in the environment.

Benzene is a highly toxic compound. Moreover, benzene-contaminated groundwater is a widespread problem caused mainly by the lack of oxygen in the subsurface. Long-term exposure may cause leukaemia. However, pure cultures of microorganisms with the ability to degrade benzene anaerobically have recently been isolated from novel enrichment cultures. The novel pure cultures include the hyperthermophilic archaeon Ferroglobus placidus and the Geobacter strains Ben and metallireducens which degrade benzene anaerobically coupled to the reduction of Fe(III). Syntrophic interactions have been suggested in enrichments where members of the Peptococcaceae within the class Clostridia are the dominant organisms and suggested as being responsible for the first attack on the benzene ring. Laboratory enrichment studies have also resulted in the development of consortia which degrade benzene, with different terminal electron acceptors supporting the syntrophy. Other benzene-degrading microorganisms have been identified under methanogenic conditions, involving the reduction of humic acids by, for example, the deltaproteobacterium Hasda-A and members of the Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria, respectively. This review focuses on the microorganisms involved in anaerobic benzene degradation under conditions involving several electron acceptors in recent years. Information related to the anaerobic degradation of benzene is critical to understanding and predicting the fate of this contaminant in groundwater.

Aims: To achieve the functional specialization of a microalgae community through operational tuning of an open photobioreactor used for biogas upgrading under alkaline conditions. Methods and Results: An open photobioreactor was inoculated with an indigenous microalgae sample from the Texcoco Soda Lake. A microalgae community was adapted to fix CO2 from synthetic biogas through different culture conditions reaching a maximum of 220 mg CO2 l?1 per day. Picochlorum sp. and Scenedesmus sp. were identified as the prominent microalgae genera by molecular fingerprinting (partial sequencing of 16S rRNA and 18S rRNA genes) but only the first was detected by microscopy screening. Changes in the microalgae community profile were monitored by a range-weighted richness index, reaching the lowest value when biogas was upgraded. Conclusions: A robust microalgae community in the open photobioreactor was obtained after different culture conditions. The specialization of microalgae community for CO2 fixation under H2S presence was driven by biogas upgrading conditions. Significance and Impact of the Study: The alkaline conditions enhance the CO2 absorption from biogas and could optimize specialized microalgae communities in the open photobioreactor. Denaturing gradient gel electrophoresis fingerprinting and richness index comparison are useful methods for the evaluation of microalgae community shifts and photosynthetic activity performance, particularly in systems intended for CO2 removal from biogas where the CO2 assimilation potential can be related to the microbial richness.

In this study, a number of slurry-phase strategies were trialled over a 42 day period in order to determine the efficacy of bioremediation for long-term hydrocarbon-contaminated soil (145 g kg−1 C10–C40). The addition of activated sludge and nutrients to slurries (bioaugmentation) resulted in enhanced hydrocarbon removal (51.6 ± 8.5 %) compared to treatments receiving only nutrients (enhanced natural attenuation [ENA]; 41.3 ± 6.4 %) or no amendments (natural attenuation; no significant hydrocarbon removal, P < 0.01). This data suggests that the microbial community in the activated sludge inoculum contributed to the enhanced removal of hydrocarbons in ENA slurries. Microbial diversity in slurries was monitored using DGGE with dominant bands excised and sequenced for identification. Applying the different bioremediation strategies resulted in the formation of four distinct community clusters associated with the activated sludge (inoculum), bioaugmentation strategy at day 0, bioaugmentation strategy at weeks 2–6 and slurries with autoclaved sludge and nutrient additions (bioaugmentation negative control). While hydrocarbon-degrading bacteria genera (e.g. Aquabacterium and Haliscomenobacter) were associated with the hydrocarbon-contaminated soil, bioaugmentation of soil slurries with activated sludge resulted in the introduction of bacteria associated with hydrocarbon degradation (Burkholderiales order and Klebsiella genera) which presumably contributed to the enhanced efficacy for this slurry strategy. Refereed/Peer-reviewed

Chlorinated ethenes are of environmental concern with most reports of successful microbial-mediated remediation being associated with major dechlorinating groups such as Dehalococcoides (Dhc) species. However, limited information is available on the community dynamics and dechlorinating activities of indigenous non-Dhc groups. Here, we present evidence of dechlorination of tetrachloroethene (perchloroethylene, PCE) in groundwater samples by indigenous microbial communities. 100 % PCE conversion to ethene was observed in acetate-stimulated 24 week-microcosms (controls; 15 %). Microbial community profiles showed dominance by groups such as Proteobacteria, Spirochaetes, Firmicutes, Methanomicrobiaceae and Methanosarcinaceae. Pareto-Lorenz (PL) analyses suggested an adapted (45 % PL value) but variable bacterial community (55.5 % Δ t(week)) compared to Archaea (25 % PL value; 46.9 % Δ t(week)). Our findings provide evidence of dechlorinating potential of indigenous microorganisms and useful information on their dynamics which may be exploited for in situ groundwater bioremediation.