Soil Microbial Communities and Ecological Risk Assessment: Risk Assessors’ Perspective

In the past, ecological risk assessments (ERAs) have generally overlooked the soil microbial community when evaluating the impacts of contaminants in soil. However, the soil microbial community, which includes bacteria and fungi, performs functions necessary for overall ecosystem health, including nitrogen fixation, nutrient cycling, and even degradation of contaminants. The incorporation of the soil microbial community into ERA requires the compilation of adequate toxicity data to complete the hazard assessment phase of the risk assessment. A variety of soil microbial toxicity tests exist that provide rapid and inexpensive results. Surveys of the microbial community at a contaminated site may also provide insight as to their functioning in the presence of contaminants. This paper explores the use of toxicity tests and surveys to evaluate chemical toxicity to microbes. However, many questions related to the best methodological approach to an ERA of the soil microbial community have yet to be answered.     

Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances

Poly- and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.     

Zooplankters as indicators of ecosystem health: past findings and future directions

Both acute (ingestion, respiration) and chronic bioassays (reproduction, survival) have been used to identify sources of pollutants. A mass-balance analysis suggests that acute tests be paired, using important indicator species asDaphnia, Ceriodaphnia and potentially others, to estimate the impact of contaminants upon the zooplankton community. Eventually groups of community bioassays may be combined to approximate an ecosystem bioassay. Hormesis or the stimulation of a physiological process by a compound which is toxic at high concentrations is characteristic of several bioassays; in this paper the ecotoxicology community is challenged to keep detailed records of the species, toxic compound, and physiological response involving hormesis in order to understand it; and ultimately to use it to simplify interpretation of bioassays. Life history characteristics of the cladoceran zooplankton, including early reproduction, high net reproductive rates, and the potential for many parthenogenetic generations with constant genotypes and low mutation rates make good choices for environmental bioassays. In contrast, high mutation rates of rotifers make them questionable choices. Five innovations, one or more of which may improve our ability to detect and identify pollutants, are suggested for ecotoxicologists using zooplankton. These include (a) the use of strains of known genotype; (b) determination of the genetic adaptation of clones to common toxins; (c) the use of common behaviors, including responses to light in detection of non-lethal chemicals at ambient levels; (d) record keeping on occurrence of cladoceran tumors; and (e) the determination of precise toxins responsible for the inhibition of zooplankton function and behavior.     

From rumen to industry

ABSTRACT: The rumen is one of the most complicated and most fascinating microbial ecosystems in nature. A wide variety of microbial species, including bacteria, fungi and protozoa act together to bioconvert (ligno)cellulosic plant material into compounds, which can be taken up and metabolized by the ruminant. Thus, the rumen perfectly resembles a solution to a current industrial problem: the biorefinery, which aims at the bioconversion of lignocellulosic material into fuels and chemicals. We suggest to intensify the studies of the ruminal microbial ecosystem from an industrial microbiologists point of view in order to make use of this rich source of organisms and enzymes.     

Development of ecotoxicity assay based on inhibition of respiring activity in microbial community using XTT reduction

The aim of this study is to develop ecotoxicity assay for evaluating the influence of chemicals on a microbial ecosystem based on XTT reduction inhibition (XTT assay). XTT reduction method is used for quantification of the microbial respiratory activity. Since the XTT assay indicates the inhibition of microbial respiratory activity, it could evaluate the toxicity of chemicals. Suitable conditions for the XTT assay were determined to be 200 mg/L of particulate organic carbon as test microbe concentration and 15 min of assay time using activated sludge. Toxicities of several chemicals evaluated by activated sludge as test microbes were examined under these conditions. Sensitivity for the toxicity evaluated by the XTT assay using activated sludge microbes was almost the same value was that for the OECD activated sludge respiration inhibition test (ASRI test). XTT assay was also applied for evaluating the influence of chemicals on the soil microbial community and the XTT assay was used to evaluate a median effective concentration (EC(50)) value of 3,5-dichlorophenol (3,5-DCP). The EC(50) value of 3,5-DCP was almost the same as the value using activated sludge as test microbes. These results suggest that the XTT assay using both mixed cultures of non-contaminated environments and chemical extracts from various contaminated environments could evaluate the influence on microbial ecosystems affected by toxic chemicals.     

Dependence of Intake Fraction on Release Location in a Multimedia Framework

A defining feature of industrial ecology is the design of processes to minimize any disruption of the functioning of the natural ecosystem that supports life, including human beings. The extent of human exposure to anthropogenic contaminants in the environment is a complex function of the amount of chemical emitted, its physicochemical properties and reactivity, the nature of the environment, and the characteristics of the pathways for human exposure, such as inhalation, dermal contacts, and intake of food and water. For some chemicals, the location of emissions relative to areas of high population density or intense food production may also be an important factor. We explore the relative importance of these variables using the regionally segmented Berkeleyf-Trent (BETR) North America contaminant fate model and data for food production patterns and population density for North America. The model is applied to fourfff contaminants emitted to air: benzene, carbon tetrachloride, benzo-a-pyrene, and 2,3,7,8 tetrachlorodibenzo-pff-dioxin. The total continental intake fraction (iF), relating exposure quantity to emission quantity, is employed as a metric for assessing population exposure to these contaminants. Results show that the use of continentally averaged parameters for population density and food production provides an accurate estimate of the median of iF calculated for emissions in individual regions; however, iF can range from this median by up to 3 orders of magnitude, especially for chemicals transferred to humans through foods. The locations of population and food production relative to sources of chemicals are important variables that should be considered when assessing the possible human health impacts of chemical emissions as in life-cycle assessment.     

Phytoremediation of organochlorine pesticides: Concept,method, and recent developments

Rapid increase in industrialization of world economy in the past century has resulted in significantly high emission of anthropogenic chemicals in the ecosystem. The organochlorine pesticides (OCPs) are a great risk to the global environment and endanger the human health due to their affinity for dispersion, transportation over long distances, and bioaccumulation in the food chain. Phytoremediation is a promising technology that aims to make use of plants and associated bacteria for the treatment of groundwater and soil polluted by these contaminants. Processes known to be involved in phytoremediation of OCPs include phytoaccumulation, rhizoremediation, and phytotransformation. Vegetation has been accounted to considerably amplify OCP elimination from soil, in contrast to non-planted soil, attributable to both, uptake within plant tissues and high microbial degradation of OCP within the root zone. Developing transgenic plants is a promising approach to enhance phytoremediation capabilities. Recent advances in the application of phytoremediation technique for OCPs, including uptake by plants and plant–microbe association in the rhizosphere for the enhanced degradation and mineralization of these pollutants, is presented in this review. Additionally, some attempts to improve this technique using transgenesis and role of certain enzymes are also discussed.     

Contaminants in the Upper Mississippi River: historic trends,responses to regulatory controls,and emerging concerns

We synthesized information on selected contaminants in the Upper Mississippi River, summarized regulatory measures enacted to reduce pollution, and described biotic and ecosystem responses to regulatory actions. Contamination of the river with mercury and lead rapidly followed settlement of the basin by European immigrants in the mid-1800s. Metal contamination peaked in the 1960s and has since decreased substantially. DDT, its degradation product DDE, and PCBs biomagnified to concentrations that adversely affected wildlife in upper trophic levels. National (U.S.A.) environmental regulations enacted from 1972 to 1991 reduced discharges of wastes from point sources, improved wastewater treatment, and reduced or banned the production or usage of certain chemicals, such as DDT, PCBs, and lead. Responses to these regulatory measures include reductions in ecosystem contamination, reductions in biotic exposure, and recovery of affected wildlife populations. Recovery from pollution has been slow, however, and we conclude that proactive approaches focusing on prevention are highly preferable to reactive approaches in management of toxic substances. Past successes in reducing point-source pollution, which is greatest near urban areas, do not extend to nonpoint-source pollution, given that the existing regulatory framework does not adequately address nonpoint sources. The river continues to receive hundreds of recently synthesized chemicals, and the behavior and effects of most of these compounds in aquatic ecosystems are largely unknown. Emerging contaminants and recently discovered mechanisms of adverse biological effects, such as endocrine disruption, pose continuing challenges to scientists and environmental managers concerned with the ecological health of this riverine ecosystem.     

Chemical Contamination of Aquatic Organisms from an Urbanized River in the New York/New Jersey Harbor Estuary

The lower 6 miles of the tidal Passaic River, part of the New York/New Jersey (NY/NJ) Harbor Estuary system, are contaminated with a variety of organic and inorganic chemicals as a result of more than 150 years of heavy industrialization and urbanization. The River's ecology is substantially degraded due to habitat removal/alteration, and the organisms that reside in or utilize the River are exposed to and bioaccumulate chemicals from sediments and food web interactions. We quantify in this study the extent and magnitude of chemical contamination in several fish species (representing a range of trophic levels) and blue crab (Callinectes sapidus). In addition, the concentration of several contaminants of concern are compared to concentrations in similar organisms from other areas of the NY/NJ Harbor Estuary, as well as available tissue-based toxicological effects benchmarks that are reported in the literature. The results suggest that a variety of contaminants are present at elevated levels in each of the species collected from the River. Several contaminants, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), total DDT (2,2-bis[4-chlorophenyl]1,1-dichloroethene), copper, and mercury are present at average concentrations that exceed those from other waterways in the NY/NJ Harbor Estuary. However, the concentrations of contaminants in the River, with few exceptions do not exceed available toxic effects levels as reported in the literature for these or similar fish and crustaceans. This suggests that toxicological risks from bioaccumulative contaminants in the lower Passaic River are limited to select contaminants and species.     

Impaired ecosystem process despite little effects on populations: modeling combined effects of warming and toxicants

Freshwater ecosystems are exposed to many stressors, including toxic chemicals and global warming, which can impair, separately or in combination, important processes in organisms and hence higher levels of organization. Investigating combined effects of warming and toxicants has been a topic of little research, but neglecting their combined effects may seriously misguide management efforts. To explore how toxic chemicals and warming, alone and in combination, propagate across levels of biological organization, including a key ecosystem process, we developed an individual‐based model (IBM) of a freshwater amphipod detritivore, Gammarus pseudolimnaeus, feeding on leaf litter. In this IBM, life history emerges from the individuals’ energy budgets. We quantified, in different warming scenarios (+1–+4 °C), the effects of hypothetical toxicants on suborganismal processes, including feeding, somatic and maturity maintenance, growth, and reproduction. Warming reduced mean adult body sizes and population abundance and biomass, but only in the warmest scenarios. Leaf litter processing, a key contributor to ecosystem functioning and service delivery in streams, was consistently enhanced by warming, through strengthened interaction between the detritivorous consumer and its resource. Toxicant effects on feeding and maintenance resulted in initially small adverse effects on consumers, but ultimately led to population extinction and loss of ecosystem process. Warming in combination with toxicants had little effect at the individual and population levels, but ecosystem process was impaired in the warmer scenarios. Our results suggest that exposure to the same amount of toxicants can disproportionately compromise ecosystem processing depending on global warming scenarios; for example, reducing organismal feeding rates by 50% will reduce resource processing by 50% in current temperature conditions, but by up to 200% with warming of 4 °C. Our study has implications for assessing and monitoring impacts of chemicals on ecosystems facing global warming. We advise complementing existing monitoring approaches with directly quantifying ecosystem processes and services.     

A comparison of microbial community characteristics among petroleum-contaminated and uncontaminated subsurface soil samples

Measurements of microbial community size, including total cell counts and specific degrader enumerations, were conducted on subsurface soil samples from both petroleum-contaminated and pristine aquifers. Samples were collected from both uncontaminated and contaminated areas of the petroleum-contaminated sites. In pristine and uncontaminated samples, total cell counts (acridine orange direct counts) were related to depth. The deeper samples contained smaller total microbial populations. However, indices of microbial activity varied considerably from sample to sample and probably reflect soil and site heterogeneity. Exposure to petroleum contamination apparently altered the microbial community structure. In samples exposed to low levels of contaminants as vapors and/or dissolved phases (ppb concentrations), and not free product, the toluene-specific degrader populations were larger at greater depths, and the numbers of amino acid-specific degraders were highly correlated to the numbers of decane-specific degraders, indicating that petroleum-adapted microbial communities were present in the contaminated samples. In highly contaminated samples, total microbial population densities decreased with increasing depth; however, microbial activity tended to increase with depth. These results indicate that petroleum contaminants exert toxic effects on the active microbial community at high exposures and enrich specific degraders at ppb levels of dissolved contaminants. Correspondence to: S.C. Long     

The Role of Soil Microbial Tests in Ecological Risk Assessment: Differentiating between Exposure and Effects

The use of soil microorganisms in ecological risk assessment is hampered by an unclear dose-response relationship for most contaminants. Establishing dose-response curves for soil microbial communities requires that one have a clear estimate of exposure at the site of toxic action and a response free of confounding environmental factors. It is not clear what methods can estimate toxicant dose at the site of toxic action or determine microbial response to a toxicant. Pollution-induced community tolerance (PICT) is one possible estimate of microbial toxicant exposure. The PICT hypothesis is that the tolerance of a microbial community is proportional to the in situ dose. This method automatically corrects for differences due to differences in soil physical-chemical variables between samples. Various components of the soil nitrogen cycle can act as microbial bioindicators of toxicant impacts. Estimating denitrifica-tion activity presents a number of advantages over other components of the nitrogen cycle. Denitrifying bacteria come from a diversity of habitats, can be autotrophic or heterotrophic, and denitrification is a well-defined enzymatic system, which allows the use of molecular tools. Determining denitrification may be a good estimate of effects of toxicants on microbial communities. However, given the state of our ignorance regarding soil microbial community structure and function, redundant estimates of exposure and effect are necessary to adequately characterize the response of microbial communities to toxicants.     

An integrated biomarker-based strategy for ecotoxicological evaluation of risk in environmental management

Environmental impacts by both natural events and man-made interventions are a fact of life; and developing the capacity to minimise these impacts and their harmful consequences for biological resources, ecosystems and human health is a daunting task for environmental legislators and regulators. A major challenge in impact and risk assessment, as part of integrated environmental management (IEM), is to link harmful effects of pollution (including toxic chemicals) in individual sentinel animals to their ecological consequences. This obstacle has resulted in a knowledge-gap for those seeking to develop effective policies for sustainable use of resources and environmental protection. Part of the solution to this problem may lie with the use of diagnostic clinical-type laboratory-based ecotoxicological tests or biomarkers, utilising sentinel animals as integrators of pollution, coupled with direct immunochemical tests for contaminants. These rapid and cost-effective ecotoxicological tools can provide information on the health status of individuals and populations based on relatively small samples of individuals. In the context of ecosystem status or health of the environment, biomarkers are also being used to link processes of molecular and cellular damage through to higher levels (i.e., prognostic capability), where they can result in pathology with reduced physiological performance and reproductive success. Complex issues are involved in evaluating environmental risk, such as the effects of the physico-chemical environment on the speciation and uptake of pollutant chemicals and inherent inter-individual and inter-species differences in vulnerability to toxicity; and the toxicity of complex mixtures. Effectively linking the impact of pollutants through the various hierarchical levels of biological organisation to ecosystem and human health requires a pragmatic integrated approach based on existing information that either links or correlates processes of pollutant uptake, detoxication and pathology with each other and higher level effects. It is further proposed here that this process will be facilitated by pursuing a holistic or whole systems approach with the development of computational simulation models of cells, organs and animals in tandem with empirical data (i.e., the middle-out approach). In conclusion, an effective integrated environmental management strategy to secure resource sustainability requires an integrated capability for risk assessment and prediction. Furthermore, if such a strategy is to influence and help in the formulation of environmental policy decisions, then it is crucial to demonstrate scientific robustness of predictions concerning the long-term consequences of pollution to politicians, industrialists and environmental managers; and also increase stakeholder awareness of environmental problems.     

An evaluation of a water purification system for use in animal facilities

A commercially available water purification system was evaluated for its ability to minimize chemical and microbial contaminants. The reduction or removal of these impurities from the drinking water of experimental animals would reduce experimental variability. 3 strains of bacteria were collected from the processed water. An increase in the total number of bacteria was observed the longer the filters remained in use. Determinations of heavy metals in water samples before and after processing were made for lead, zinc, copper, nickel, manganese, iron, arsenic and mercury. Calcium and magnesium levels were also determined. The concentrations of these inorganic chemicals were reduced by the purification process except at 2 time points in which desorption of the chemical could have occurred. Bacterial colonization and desorption of these chemicals were controlled by installing new filter cartridges. Volatile halocarbon concentrations were determined for water samples before and after purification. All volatile halocarbons analyzed were less than 10 ppb before and after purification at all time points. Other organic chemicals were greatly reduced by the purification process. In a study of contaminants associated with installation of the unit, it was found that flushing the unit for 8 days reduced lead and methyl ethyl ketone concentrations to insignificant levels. The purification system was found to be effective in providing high quality drinking water as verified by a microbial and chemical testing program.     

A generalized physiologically-based toxicokinetic modeling system for chemical mixtures containing metals

Background  

Humans are routinely and concurrently exposed to multiple toxic chemicals, including various metals and organics, often at levels that can cause adverse and potentially synergistic effects. However, toxicokinetic modeling studies of exposures to these chemicals are typically performed on a single chemical basis. Furthermore, the attributes of available models for individual chemicals are commonly estimated specifically for the compound studied. As a result, the available models usually have parameters and even structures that are not consistent or compatible across the range of chemicals of concern. This fact precludes the systematic consideration of synergistic effects, and may also lead to inconsistencies in calculations of co-occurring exposures and corresponding risks. There is a need, therefore, for a consistent modeling framework that would allow the systematic study of cumulative risks from complex mixtures of contaminants.     

Effects of Picoxystrobin and 4-n-Nonylphenol on Soil Microbial Community Structure and Respiration Activity

There is widespread use of chemical amendments to meet the demands for increased productivity in agriculture. Potentially toxic compounds, single or in mixtures, are added to the soil medium on a regular basis, while the ecotoxicological risk assessment procedures mainly follow a chemical by chemical approach. Picoxystrobin is a fungicide that has caused concern due to studies showing potentially detrimental effects to soil fauna (earthworms), while negative effects on soil microbial activities (nitrification, respiration) are shown to be transient. Potential mixture situations with nonylphenol, a chemical frequently occurring as a contaminant in sewage sludge used for land application, infer a need to explore whether these chemicals in mixture could alter the potential effects of picoxystrobin on the soil microflora. The main objective of this study was to assess the effects of picoxystrobin and nonylphenol, as single chemicals and mixtures, on soil microbial community structure and respiration activity in an agricultural sandy loam. Effects of the chemicals were assessed through measurements of soil microbial respiration activity and soil bacterial and fungal community structure fingerprints, together with a degradation study of the chemicals, through a 70 d incubation period. Picoxystrobin caused a decrease in the respiration activity, while 4-n-nonylphenol caused an increase in respiration activity concurring with a rapid degradation of the substance. Community structure fingerprints were also affected, but these results could not be directly interpreted in terms of positive or negative effects, and were indicated to be transient. Treatment with the chemicals in mixture caused less evident changes and indicated antagonistic effects between the chemicals in soil. In conclusion, the results imply that the application of the fungicide picoxystrobin and nonylphenol from sewage sludge application to agricultural soil in environmentally relevant concentrations, as single chemicals or in mixture, will not cause irreversible effects on soil microbial respiration and community structure.     

微生物表面展示技术及其在环境污染治理中的应用

微生物表面展示技术是通过基因工程手段,将短的外源肽或蛋白质表达在微生物细胞表面,该技术可以应用于开发活的细菌疫苗、筛选抗体库、生产生物细胞吸附剂以及制备整细胞生物催化剂。通过金属高效结合肽的肽库筛选和微生物展示技术,将金属结合肽直接展示在微生物的表面,用于处理环境中的重金属污染,为环境中重金属污染的防治提供了一条崭新的途径。利用微生物表面展示技术制备整细胞催化剂,用于有毒有机污染物的处理,可以极大地加快污染物的降解速率。简要介绍了微生物表面展示技术及其在重金属污染治理和毒性有机污染物的脱毒等环境生物修复方面的最新研究进展。     

Hydrocarbon phytoremediation in the family Fabaceae--a review

Currently, studies often focus on the use of Poaceae species (grasses) for phytoremediation of hydrocarbon-contaminated soils. Research into the use of Fabaceae species (legumes) to remediate hydrocarbons in soils has been conducted, but these plants are commonly overlooked due to slower recorded rates of degradation compared with many grass species. Evidence in the literature suggests that in some cases Fabaceae species may increase total degradation of hydrocarbons and stimulate degradative capacity of the soil microbial community, particularly for contaminants which are normally more recalcitrant to degradation. As many recalcitrant hydrocarbons have negative impacts on human and ecosystem health, development of remediation options is crucial. Reconsideration of Fabaceae species for removal of such contaminants may lead to environmentally and economically sustainable technologies for remediation of contaminated sites.     

Prospects for a novel ultrashort pulsed laser technology for pathogen inactivation

ABSTRACT: The threat of emerging pathogens and microbial drug resistance has spurred tremendous efforts to develop new and more effective antimicrobial strategies. Recently, a novel ultrashort pulsed (USP) laser technology has been developed that enables efficient and chemical-free inactivation of a wide spectrum of viral and bacterial pathogens. Such a technology circumvents the need to introduce potentially toxic chemicals and could permit safe and environmentally friendly pathogen reduction, with a multitude of possible applications including the sterilization of pharmaceuticals, blood products, and the generation of attenuated or inactivated vaccines.