A multi-disciplinary approach to the characterization of waterlogged burial environments : assessing the potential for the in situ preservation of organic archaeological remains

The aim of this study was to characterise waterlogged burial environments and to assess their potential for the in situ preservation of organic archaeological remains. To characterise these environments, environmental parameters were monitored through the soil profile and integrated with a study of the composition and activity of the microbial community.Soil cores were taken from two wetland sites located in the Humberhead Levels in Yorkshire: Hatfield Moor and Sutton Common. Cores were subsampled at depth intervals down to 100 cm depth, to allow for the examination of the vertical distributions of the variables being studied. Redox potential, water level variation and other physico-chemical parameters were measured down the soil profile. Bacterial abundance was determined by direct counts; activity was assayed by extracellular enzyme activity and leucine assimilation. The physiological profile of the microbial community was analysed using BIOLOG and the bacterial community structure was examined by PCR-DGGE.Redox potential readings were positive above the water table and negative below. The bacterial abundance and activity were greatest at the soil surface and, in general, decreased with depth. BIOLOG showed both depth variation and between site variation in microbial physiological profile. DGGE gels presented a different bacterial community structure with depth and between-sites.The results from monitoring of redox potential combined with water table height and determination of bacterial abundance and activity allowed the recognition of stratigraphic horizon where there was less potential for microbial degradation of organic archaeological artefacts. The information from BIOLOG and DGGE holds the potential for the development of a more subtle understanding of between-depth and between-site differences in the degradation process.The physico-chemical and the conventional and molecular microbiological results presented in this thesis have shown that microbial activity is implicated as a key factor that could lead to compromised in situ preservation conditions at the sites studied

A methodological proposal to investigate the long term storage of pollutants in freshwater sediment biofilms and their response to environmental disturbances.

This research will review novel methodologies for understanding the behaviour of microbial communities and their role in pollution storage. Freshwater sediments are inhabited by attached microbial communities (biofilms) which are responsible for the majority of a river's metabolic activity. Biofilms thus provide valuable information on the environmental quality of the river and its surrounding areas. Despite remediation of freshwater sediments, biofilms can still store large quantities of pollutants. Biofilms have the exceptional capacity to adjust to new conditions including natural and anthropogenic environmental disturbances. Gaining a more comprehensive understanding of biofilm behaviour is therefore fundamental to developing improved management strategies. The initial focus of this research will be in the River Doe Lea in North East Derbyshire. The River Doe Lea extends 18km from the South at its source near Tibshelf, to the North at its discharge at the River Rother. In the 1990s the River was famed for having the highest level of dioxins in the world, 27 times higher than the second most polluted. The acute cause of this was a single pollutant event, however the river has also been subjected to long term anthropogenic pollution through industry, agriculture, transport (railways, M1) and wastewater pollution. While previous studies by the Environment Agency have focused on the flow, chemical, biological and ecological quality of the river, no research has been conducted into the role and behaviour of biofilms

Understanding microbial ecology to improve management of drinking water distribution systems

Microorganisms in Drinking Water Distribution Systems (DWDS) and in particular the microbial communities that form biofilms on infrastructure surfaces, drive critical processes impacting water quality. This paper reviews knowledge, research approaches and monitoring methods to consolidate understanding of the microbial ecology of DWDS. The review highlights how microbial characteristics and subsequent behaviour can be broadly classified as common or complex. Common behaviour relates to the ubiquitous and continual development of biofilms, consistent core communities and mediated material accumulation. In contrast, the complex aspect relates to the shape, structure and composition of the microbiome, defined by site specific properties such as supplied source water, pipe material and hydraulic regimes. It is shown how the latest microbial tools and techniques can be applied to increase our understanding of DWDS ecology and how water utilities are starting to use this knowledge. This is not because of regulatory requirements, but in recognition that they provide valuable information facilitating pro-active management and operation benefits to these critical yet ageing systems, protecting water quality and public health in the process

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System

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 ismobilised 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 analysismethod, 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 inmaterial accumulation within the DWDS

Methodological approaches for studying the microbial ecology of drinking water distribution systems

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects

Soil microbial community response to land-management and depth, related to the degradation of organic matter in English wetlands: implications for the in situ preservation of archaeological remains

Wetlands are important habitats not only for their unique ecological value but also because they contain organic material that is fundamental to our understanding of precedent landscape and human past. This study compares the effects of two different land-management regimes on metabolic diversity and bacterial community structure with depth in order to relate them to the process of organic matter degradation and the potential for preservation in situ of organic archaeological artefacts in wetland soils. Soil cores were collected at five depths down to 100 cm from two wetlands sites in England. Environmental variables were monitored and the metabolic capabilities of the microbial community were studied using Biolog Ecoplates (R). DNA was extracted from soil, and the bacterial community structure was examined by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE). To determine compositional changes in the bacterial community with depth, information about specific groups of bacteria at the site with higher water table (Hatfield Moor) was obtained by cloning and sequencing of 16S rRNA genes. Biolog and DGGE analyses showed depth variation and between-site variation. Carbon substrate utilization and bacterial diversity decreased with increasing depth. The wetland soil under an arable regime in which the water levels were kept elevated, showed higher metabolic capability and bacterial richness when compared with the soil under pasture and subjected to long-standing drainage. Cloning and sequencing showed that Proteobacteria and Acidobacteria were the predominant taxa within the soil profile, but there was a clear shift in bacterial community composition with increasing depth as several taxonomic groups (delta-Proteobacteria and Spirochaetes) were only detectable at 50 cm depth. Because the site with a high and stable water table presented higher metabolic activity and bacterial diversity, it may be that saturated conditions and a high water table are not sufficient to guarantee the preservation in situ of organic material such as archaeological artefacts. (C) 2010 Elsevier B.V. All rights reserved

Response of the microbial community to water table variation and nutrient addition and its implications for in situ preservation of organic archaeological remains in wetland soils

Wetland environments can preserve organic archaeological remains because of their anaerobic nature. The ongoing discovery of archaeological sites in wetlands is associated with a lack of funds for excavation and preservation. This situation has led to the consideration of preservation in situ the preferred option for dealing with the majority of waterlogged archaeological remains in England. To expand our understanding of the burial environment, we studied changes in environmental variables along with counts of total bacteria and microbial C-14-leucine assimilation down the soil profile at two wetlands in the North of England. Soil cores were sampled at five depth intervals between 10 and 100 cm. To test whether the addition of nutrients induces bacterial activity in the soil, inorganic phosphate and combined nitrogen were added to soil samples and the rate of C-14-leucine assimilation was recorded. Redox potential readings were positive above the water table and negative below. The total number of bacteria and the C-14-leucine assimilation rates differed among sites, but always decreased with increasing soil depth. Nutrient availability was limiting for the microbial communities in the upper soil horizons, but did not appear to limit those in the lower soil. These results allow a better understanding of the physico-chemical and microbiological conditions that potentially favour or inhibit the decomposition of organic archaeological remains at the studied wetlands. (C) 2009 Elsevier Ltd. All rights reserved

Biofilm and Related Amoebas in an UK Chlorinated Drinking Water System

Drinking water distribution systems (DWDS) can host pathogenic amoebae, but the role of biofilms in supporting the occurrence of these organisms needs to be fully explored in the UK systems. The presence of amoebae and associated bacteria in biofilms attached to inner pipe surfaces was studied in an experimental full-scale chlorinated distribution system in the UK. Quantitative polymerase change reaction (qPCR) was used to identify and quantify amoebae, whilst the bacterial communities in the biofilms were characterised by sequencing the 16S rRNA gene. Despite the maintenance of a chlorine residual in the network (free chlorine ≥ 0.24 mg/L), several species of amoebae belonging to the genera Acanthamoeba, Vermamoeba, and Naegleria were identified in 30-day-old biofilm samples; however, no amoebae were detected in the water samples analysed. The dominant bacterial communities present in the biofilm samples were Variovorax, Pseudomonas, and Aquabacterium. These results indicate that the biofilm samples contained potential pathogenic amoebae and bacteria, such as Acanthamoeba and Pseudomonas, respectively, which implies a potential public health risk if the biofilms are mobilised into the bulk water. Several of the amoebae identified in this study are able to support the presence of resistant bacteria that can remain viable within these prokaryotic organisms until they reach people’s taps. The identification of the microorganisms associated with the pathogenic amoeba species in biofilms could be used to improve the surveillance of DWDS in order to protect public health

Cluster analysis of similarity using fingerprint profiles to show the similarity between A) bacterial, B) archaeal and C) fungal drinking water biofilm communities.

<p>Relative abundance data was derived from T-RFLP or ARISA analysis, sample identification numbers are shown and clusters are indicated with a bracket and number. Red lines indicate profiles not significantly dissimilar according to SIMPROF analysis.</p