Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic ...plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET substrate. Future research is required to investigate microscale functional interactions at the plastic surface.
Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the ...environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.
Synthetic microplastics (≤5-mm fragments) are emerging environmental contaminants that have been found to accumulate within coastal marine sediments worldwide. The ecological impacts and fate of ...microplastic debris are only beginning to be revealed, with previous research into these topics having primarily focused on higher organisms and/or pelagic environments. Despite recent research into plastic-associated microorganisms in seawater, the microbial colonization of microplastics in benthic habitats has not been studied. Therefore, we employed a 14-day microcosm experiment to investigate bacterial colonization of low-density polyethylene (LDPE) microplastics within three types of coastal marine sediment from Spurn Point, Humber Estuary, U.K.
Bacterial attachment onto LDPE within sediments was demonstrated by scanning electron microscopy and catalyzed reporter deposition fluorescence in situ hybridisation (CARD-FISH). Log-fold increases in the abundance of 16S rRNA genes from LDPE-associated bacteria occurred within 7 days with 16S rRNA gene numbers on LDPE surfaces differing significantly across sediment types, as shown by quantitative PCR. Terminal-restriction fragment length polymorphism (T-RFLP) analysis demonstrated rapid selection of LDPE-associated bacterial assemblages whose structure and composition differed significantly from those in surrounding sediments. Additionally, T-RFLP analysis revealed successional convergence of the LDPE-associated communities from the different sediments over the 14-day experiment. Sequencing of cloned 16S rRNA genes demonstrated that these communities were dominated after 14 days by the genera Arcobacter and Colwellia (totalling 84-93% of sequences). Attachment by Colwellia spp. onto LDPE within sediments was confirmed by CARD-FISH.
These results demonstrate that bacteria within coastal marine sediments can rapidly colonize LDPE microplastics, with evidence for the successional formation of plastisphere-specific bacterial assemblages. Although the taxonomic compositions of these assemblages are likely to differ between marine sediments and the water column, both Arcobacter and Colwellia spp. have previously been affiliated with the degradation of hydrocarbon contaminants within low-temperature marine environments. Since hydrocarbon-degrading bacteria have also been discovered on plastic fragments in seawater, our data suggest that recruitment of hydrocarbonoclastic bacteria on microplastics is likely to represent a shared feature between both benthic and pelagic marine habitats.
Abstract
Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic ...surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type.
We investigated structural and taxonomical variation of microbial biofilm communities on plastic fragments in coastal and offshore Northern European waters, with respect to season, geographical location and plastic type.
We investigated structural and taxonomical variation of microbial biofilm communities on plastic fragments in coastal and offshore Northern European waters, with respect to season, geographical location and plastic type.
High-quality drinking water from treatment works is degraded during transport to customer taps through the Drinking Water Distribution System (DWDS). Interactions occurring at the pipe wall-water ...interface are central to this degradation and are often dominated by complex microbial biofilms that are not well understood. This study uses novel application of confocal microscopy techniques to quantify the composition of extracellular polymeric substances (EPS) and cells of DWDS biofilms together with concurrent evaluation of the bacterial community. An internationally unique, full-scale, experimental DWDS facility was used to investigate the impact of three different hydraulic patterns upon biofilms and subsequently assess their response to increases in shear stress, linking biofilms to water quality impacts such as discolouration. Greater flow variation during growth was associated with increased cell quantity but was inversely related to EPS-to-cell volume ratios and bacterial diversity. Discolouration was caused and EPS was mobilised during flushing of all conditions. Ultimately, biofilms developed under low-varied flow conditions had lowest amounts of biomass, the greatest EPS volumes per cell and the lowest discolouration response. This research shows that the interactions between hydraulics and biofilm physical and community structures are complex but critical to managing biofilms within ageing DWDS infrastructure to limit water quality degradation and protect public health.
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•Analysis of drinking water biofilm physical structure and bacterial communities•Biofilms developed naturally in full-scale drinking water distribution facility.•Hydraulic conditions influence cohesive strength of EPS.•Biofilm structure differs between Varied Flow and Steady State conditioned biofilms.•Understanding biofilms, including EPS, is key to safeguarding water quality.
Prebiotics (commonly oligosaccharides) added to infant feeds have the potential to prevent sensitisation of infants to dietary allergens.
To determine the effect of prebiotic given to infants for the ...prevention of allergy.
We performed an updated search in August 2012 of the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 8), MEDLINE, EMBASE, conference proceedings, citations, expert informants and clinical trials registries.
Randomised and quasi-randomised controlled trials that compared the use of a prebiotic to no prebiotic, or a specific prebiotic compared to a different prebiotic in infants for prevention of allergy.
Assessment of trial quality, data extraction and synthesis of data were performed using the standard methods of The Cochrane Collaboration.
The 2012 update identified 13 studies classified as ongoing or awaiting classification (yet to report allergy outcomes). Forty-three studies were excluded, primarily as no allergy data were reported, although none of these enrolled infants were at high risk of allergy. Four studies enrolling 1428 infants were eligible for inclusion. All studies were at high risk of attrition bias. Allergy outcomes were reported from four months to two years of age.Meta-analysis of two studies (226 infants) found no significant difference in infant asthma although significant heterogeneity was found between studies. Meta-analysis of four studies found a significant reduction in eczema (1218 infants, typical risk ratio 0.68, 95% CI 0.48 to 0.97; typical risk difference -0.04, 95% CI -0.07 to -0.00; number needed to treat to benefit (NNTB) 25, 95% CI 14 to > 100; P = 0.03). No statistically significant heterogeneity was found between studies. One study reported no significant difference in urticaria.No statistically significant subgroup differences were found according to infant risk of allergy or type of infant feed. However, individual studies reported a significant reduction in asthma and eczema from supplementation with a mixture of galacto- and fructo-oligosaccharide (GOS/FOS 9:1 ratio) (8 g/L) in infants at high risk of allergy; and in eczema from supplementation with GOS/FOS (9:1) (6.8 g/L) and acidic oligosacccharide (1.2 g/L) in infants not selected for allergy risk.
Further research is needed before routine use of prebiotics can be recommended for prevention of allergy in formula fed infants. There is some evidence that a prebiotic supplement added to infant feeds may prevent eczema. It is unclear whether the use of prebiotic should be restricted to infants at high risk of allergy or may have an effect in low risk populations; or whether it may have an effect on other allergic diseases including asthma.
Depression is one of the most frequently reported psychological problems following TBI, however prevalence estimates vary widely. Methodological and sampling differences may explain some of this ...variability, but it is not known to what extent.
Data from 99 studies examining the prevalence of clinically diagnosed depression (MDD/dysthymia) and self-reports of depression (clinically significant cases or depression scale scores) following adult, non-penetrating TBI were analysed, taking into consideration diagnostic criteria, measure, post-injury interval, and injury severity.
Overall, 27% of people were diagnosed with MDD/dysthymia following TBI and 38% reported clinically significant levels of depression when assessed with self-report scales. Estimates of MDD/dysthymia varied according to diagnostic criteria (ICD-10: 14%; DSM-IV: 25%; DSM-III: 47%) and injury severity (mild: 16%; severe: 30%). When self-report measures were used, the prevalence of clinically significant cases of depression differed between scales (HADS: 32%; CES-D: 48%) method of administration (phone: 26%; mail 46%), post-injury interval (range: 33-42%), and injury severity (mild: 64%; severe: 39%).
Depression is very common after TBI and has the potential to impact on recovery and quality of life. However, the diagnostic criteria, measure, time post-injury and injury severity, all impact on prevalence rates and must therefore be considered for benchmarking purposes.
Dumping wastes generated from the oil industry to the local waste disposal facilities remains the most common means of oil waste management. In industrial landfills, the most serious ecological ...problem is the contamination of soil and local groundwater by landfill leachate. Polycyclic aromatic hydrocarbons (PAHs) represent a hazardous group of harmful chemical compounds that threaten human and ecosystem health. This study focuses on a PAH-contaminated soil from a landfill site in New South Wales, Australia. Soil was exposed to two different bioremediation treatments, natural attenuation and biostimulation using pea straw. The bacterial community composition and diversity of the PAH-contaminated soil were also examined using high throughput Illumina MiSeq sequencing. The results revealed that PAHs were degraded naturally by indigenous microorganisms; however, the addition of plant residues led to enhanced degradation (66.6%) at the beginning of the treatment, although in all treatments a degradation plateau occurred between 43 and 102 days of incubation during bioremediation. Quantitative PCR analysis showed an increase in the number of 16S rRNA and ITS gene copies as well as genes associated with Gram-positive PAH-degrading bacteria in the soil amended with pea straw. Next generation sequencing results and diversity indices revealed that a high proportion of the sequences from all soil samples belonged to the Proteobacteria phyla; gammaprotobacteria was the dominant class in all the investigated samples. Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria were the most dominant in the natural attenuation and pea straw treated soil bacterial communities. The largest shift in bacterial communities was in the pea straw amended soils with increased abundances by Day 42 of Pseudomonas, Pseudoxanthomonas, Lewinella and Parvibaculum; these organisms are all known for their abilities to degrade petroleum hydrocarbons. However by Day 102, these organisms were decreased or not detected in both NA and PS treated soil samples at the end of incubation which may explain the degradation plateau. These findings suggest that Gram-negative PAH-degrading bacteria, mainly Pseudomonas sp., may be the key contributor to PAH-degradation in the landfill-polluted soil.
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•Biodegradation rate of PAHs in landfill soil was investigated.•Degradation plateau occurred in day 43 and 102.•PS increased the number of 16S rDNA, ITS and Gram-positive PAH-degrading genes.•PS displayed higher diversity of bacterial species.
Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the ...attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS.
The composition of the intestinal microflora may be different in individuals with atopic eczema from those without this condition, and such differences may precede the development of eczema. ...Prebiotics are nondigestible food components that benefit the host by selectively stimulating the growth or activity of non-pathogenic bacteria in the colon. Prebiotics (commonly oligosaccharides) added to infant feeds have the potential to prevent sensitisation of infants to dietary allergens.
To determine the effect of prebiotics given to infants for the prevention of allergic disease or food hypersensitivity.
This included searches of the Cochrane Central Register of Controlled Trials (Issue 1, 2007), MEDLINE (1966 - February 2007), EMBASE, PREMEDLINE, abstracts of conference proceedings and citations of published articles, and expert informants.
Randomised and quasi-randomised controlled trials that compared the use of a prebiotic to no prebiotic; or the use a specific prebiotic compared to a different prebiotic.
Assessment of trial quality, data extraction and synthesis of data were performed using standard methods of the Cochrane Neonatal Review Group.
Seven studies were eligible for inclusion. Only two studies reported an allergic disease outcome for 432 infants. Study quality was reasonable, although Moro 2006 reported 20% post-randomisation losses. Moro 2006 enrolled hydrolysed formula fed infants at high risk of allergy and reported a significant reduction in eczema in infants up to six months of age (RR 0.42, 95% CI 0.21, 0.84). Ziegler 2007 enrolled formula fed infants who were not selected on the basis of risk for allergy and reported no significant difference in eczema up to four months of age (RR 1.62, 95% CI 0.62, 4.26). Meta-analysis of the two studies found no significant difference in eczema, but significant heterogeneity was detected. Differences were potentially attributable to differences in infant risk, prebiotic formulation or measurement of eczema. Analysis of five studies reporting measures of infant growth found no consistent adverse effects.
There is insufficient evidence to determine the role of prebiotic supplementation of infant formula for prevention of allergic disease and food hypersensitivity. One small trial of prebiotic oligosaccharides with excess losses reported a reduction in eczema in high risk formula fed infants. Further trials are needed to determine whether this finding persists over a longer period of time, applies to other manifestations of allergic disease, is associated with reductions in allergen sensitisation, and is reproducible.
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