From tangled banks to toxic bunnies; a reflection on the issues involved in developing an ecosystem approach for environmental radiation protection.

The objective of this paper is to present the results of discussions at a workshop held as part of the International Congress of Radiation Research (Environmental Health stream) in Manchester UK, 2019. The main objective of the workshop was to provide a platform for radioecologists to engage with radiobiologists to address major questions around developing an Ecosystem approach in radioecology and radiation protection of the environment. The aim was to establish a critical framework to guide research that would permit integration of a pan-ecosystem approach into radiation protection guidelines and regulation for the environment. The conclusions were that the interaction between radioecologists and radiobiologists is useful in particular in addressing field versus laboratory issues where there are issues and challenges in designing good field experiments and a need to cross validate field data against laboratory data and vice versa. Other main conclusions were that there is a need to appreciate wider issues in ecology to design good approaches for an ecosystems approach in radioecology and that with the capture of 'Big Data', novel tools such as machine learning can now be applied to help with the complex issues involved in developing an ecosystem approach.

A Pipeline for Non-model Organisms for de novo Transcriptome Assembly, Annotation, and Gene Ontology Analysis Using Open Tools: Case Study with Scots Pine.

RNA sequencing (RNA-seq) has opened up the possibility of studying virtually any organism at the whole transcriptome level. Nevertheless, the absence of a sequenced and accurately annotated reference genome may be an obstacle for applying this technique to non-model organisms, especially for those with a complex genome. While de novo transcriptome assembly can circumvent this problem, it is often computationally demanding. Furthermore, the transcriptome annotation and Gene Ontology enrichment analysis without an automatized system is often a laborious task. Here we describe step-by-step the pipeline that was used to perform the transcriptome assembly, annotation, and Gene Ontology analysis of Scots pine (Pinus sylvestris), a gymnosperm species with complex genome. Using only free software available for the scientific community and running on a standard personal computer, the pipeline intends to facilitate transcriptomic studies for non-model species, yet being flexible to be used with any organism.

The response profile to chronic radiation exposure based on the transcriptome analysis of Scots pine from Chernobyl affected zone.

Radioactive contamination of the natural areas is one of the most long-lasting anthropogenic impacts on the environment. Scots pine (Pinus sylvestris L.) is a promising organism for radiation-related research because of its high radiosensitivity, but the genome size of Pinacea species has imposed obstacles for high-throughput studies so far. In this work, we conducted the analysis of the de novo assembled transcriptome of Scots pine populations growing in the Chernobyl-affected zone, which is still today contaminated with radionuclides because of the accident at the nuclear power plant in 1986. The transcriptome profiles indicate a clear pattern of adaptive stress response, which seems to be dose-dependent. The transcriptional response indicates a continuous modulation of the cellular redox system, enhanced expression of chaperones and histones, along with the control of ions balance. Interestingly, the activity of transposable element families is inversely correlated to the exposure levels to radiation. These adaptive responses, which are triggered by radiation doses 30 times lower than the one accepted as a safe for biota species by international regulations, suggest that the environmental management in radiation protection should be reviewed.

'Omic' technologies as a helpful tool in radioecological research.

This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.

Radiation exposure in the remote period after the Chernobyl accident caused oxidative stress and genetic effects in Scots pine populations.

Even 30 years after the Chernobyl accident, biological effects of irradiation are observed in the chronically exposed Scots pine populations. Chronic radiation exposure at dose rates above 50 mGy∙yr-1 caused oxidative stress and led to the increase of antioxidants concentrations in these populations. Genetic variability was examined for 6 enzymes and 14 enzymatic loci of 6 Scots pine populations. Dose rates over 10 mGy∙yr-1 caused the increased frequency of mutations and changes in genetic structure of Scots pine populations. However, the same dose rates had no effect on enzymatic activities. The results indicate that even relatively low dose rates of radiation can be considered as an ecological factor which should be taken into account for ecological management and radiation protection of biota species.

Ecological effects of exposure to enhanced levels of ionizing radiation.

Irradiation of plants and animals can result in disruption of ecological relationships between the components of ecosystems. Such effects may act as triggers of perturbation and lead to consequences that may differ essentially from expected ones based on effects observed at the organismal level. Considerable differences in ecology and niches occupied by different species lead to substantial differences in doses of ionizing radiation absorbed by species, even when they all are present in the same environment at the same time. This is especially evident for contamination with α-emitting radionuclides. Radioactive contamination can be considered an ecological factor that is able to modify the resistance in natural populations. However, there are radioecological situations when elevated radioresistance does not evolve or persist. The complexity and non-linearity of the structure and functioning of ecosystems can lead to unexpected consequences of stress effects, which would appear harmless if they were assessed within the narrower context of organism-based traditional radioecology. Therefore, the use of ecological knowledge is essential for understanding responses of populations and ecosystems to radiation exposure. Integration of basic ecological principles in the design and implementation of radioecological research is essential for predicting radiation effects under rapidly changing environmental conditions.

Genetic diversity in Scots pine populations along a radiation exposure gradient.

Polymorphisms of antioxidant enzymes were studied in the endosperm and embryos of seeds from Scots pine populations inhabiting sites in the Bryansk region of Russia radioactively contaminated as a result of the Chernobyl accident. Chronic radiation exposure at dose rates from 0.8 µGy/h led to a significant increase in the rate of enzymatic loci mutations. The main parameters of genetic variability of the affected Scots pine populations had considerably higher values than those from the reference site. Changes in the genetic makeup of Scots pine populations were observed at dose rates greater than 10.4 µGy/h. However, the higher mutation rate had no effect on the activities of antioxidant enzymes.

Effects on non-human species inhabiting areas with enhanced level of natural radioactivity in the north of Russia: a review.

Results of long-term radioecological investigations in areas with an enhanced level of natural radioactivity in the north of Russia are summarized. Deleterious changes within animal and plant populations inhabiting areas with an enhanced level of natural radioactivity in the Komi Republic were revealed. These changes are expressed in enhanced levels of mutagenesis, destructive processes in the tissues of animals, disturbances of reproductive functions and reduced offspring viability. Compensatory processes, resulting in animal and plant survival under extremely adverse conditions of radium and uranium-radium contamination, were observed as well. However, obvious signs of adaptation failed to be detected. The findings suggest that adverse somatic and genetic effects are possible in plants and animals in the dose range observed at sites with an enhanced level of natural radioactivity. In contrast, different plant species inhabiting an area with an enhanced level of natural radioactivity in the taiga zone of the Sakha Republic (Yakutia) reveal a stimulation of growth processes, photosynthesis, endogenous low molecular weight antioxidant synthesis as well as adaptive response. It is apparent from the data presented that naturally occurring differences in terrestrial radiation level could be of genetic and ecological consequence.

Cytogenetic effect of low dose gamma-radiation in Hordeum vulgare seedlings: non-linear dose-effect relationship.

The induction of chromosome aberrations in Hordeum vulgare germinated seeds was studied after ionizing irradiation with doses in the range of 10-1,000 mGy. The relationship between the frequency of aberrant cells and the absorbed dose was found to be nonlinear. A dose-independent plateau in the dose range from about 50 to 500 mGy was observed, where the level of cytogenetic damage was significantly different from the spontaneous level. The comparison of the goodness of the experimental data fitting with mathematical models of different complexity, using the most common quantitative criteria, demonstrated the advantage of a piecewise linear model over linear and polynomial models in approximating the frequency of cytogenetical disturbances. The results of the study support the hypothesis of indirect mechanisms of mutagenesis induced by low doses. Fundamental and applied implications of these findings are discussed.

Cytogenetic effects of combined radioactive (137Cs) and chemical (Cd, Pb, and 2,4-D herbicide) contamination on spring barley intercalar meristem cells.

The frequency of cytogenetic effects in spring barley intercalar meristem cells was studied in the presence of a range of different stressors. There was a non-linear dependence on the concentrations of 137Cs, Cd, Pb, and dichlorophenoxyacetic acid (2,4-D) herbicide contamination in the exposure ranges used. The frequency of cytogenetic effects increased at the lower concentrations of the pollutants more rapidly than at the higher concentrations. Contamination of the soil by lead at a concentration that meets the current standards for permissible content in soil, and by 2,4-D herbicide at the application levels recommended for agricultural use resulted in a significant increase in aberrant cell frequency. In these cases, the extent of the observed cytogenetic effects was comparable with the effect induced by a 137Cs soil contamination of 49.2 kBq/kg, a level that exceeds by 10-fold the maximum level permitted in radionuclide-contaminated areas where people are resident. In most cases, the experimentally observed combined effects of the pollutants studied differed from those expected from an additive hypothesis. When combined with 137Cs contamination, antagonistic effects became increasingly stronger when the second stressor was changed from cadmium to lead, and then to the herbicide, as measured both by tests of the 'frequency of aberrant cells' and the 'aberrations per cell'. Data from this study and previous reported literature suggest that synergistic increases in cytogenetic effects can be induced by the simultaneous influence of several stressors even at low intensities. This indicates that there is a capability for mutual intensification of the effects of environmental factors that actually occur in situations of low-level exposure.

Bio-monitoring the genotoxicity of populations of Scots pine in the vicinity of a radioactive waste storage facility.

Results of a long-term (1997-2002) study of the Scots pine populations growing in the vicinity of the radioactive waste storage facility ('Radon' LWPE) are presented. Cytogenetic disturbances in reproductive (seeds) and vegetative (needles) tissues sampled from Scots pine populations were studied to examine whether Scots pine trees have experienced environmental stress in areas with relatively low levels of pollution. The data clearly indicate the presence of mutagenic contaminants in the environment of the pine trees. An increased number of mitotic abnormalities, especially multipolar mitoses was found in the pine tree populations submitted to man-made exposure, which suggests that the cytogenetic damage is mainly caused by chemical contamination. A higher radioresistance of the Scots pine seeds from the impacted populations was shown by use of acute gamma-irradiation. During the observation period 1997-2002, pine trees exposed to anthropogenic pollution showed a steady increase of cytogenetic alterations in the root meristem cells.

Genotoxicity and cytotoxicity assay of water sampled from the underground nuclear explosion site in the north of the Perm region (Russia).

The results of our study revealed a local biologically relevant surface water contamination in the radionuclide anomaly in the north of Russia (Perm region) by means of Allium schoenoprasum L. anaphase-telophase chromosome aberration assay. This radionuclide anomaly was formed in 1971 as a result of an underground nuclear explosion with soil excavation. Specific activities of main dose-forming radionuclides in all examined reservoirs are below intervention levels officially adopted in Russia for drinking water. We found that (90)Sr significantly contributes to induction of cytogenetic disturbances. Our previous data and the data described here suggest that metal and radionuclide combined exposure (with the dose below permissible exposure limits for human) may cause substantial biological effects. These effects are in part due to synergic response. The findings described here indicated that development of a new concept of radiation protection for humans and biota should be based on the clear understanding of biological effects of low doses of radiation in chronic exposure to multi-pollutant mixtures.

Genotoxicity and toxicity assay of water sampled from a radium production industry storage cell territory by means of Allium-test.

Water from natural reservoirs located near the radium production industry storage cell were analyzed using the anaphase-telophase chromosome aberration assay that was carried out on Allium schoenoprasum L. meristematic root tip cells. (262)Ra, (228)U, (232)Th, (210)Pb and (210)Po concentrations in all samples were found not to exceed the radioactivity concentration guides. The concentrations of 10 heavy metal ions were measured in water samples, but only Zn and Mn levels exceeded the maximum permissible concentration for the natural reservoirs. All water samples caused a significant increase of the chromosome aberration frequency as compared to control. The chromosome aberration spectrum analysis shows that the genotoxic effect was a result of chemical toxicity mainly. Two samples from the brook springhead were found to be toxic. The regression analysis results show that the mitotic index increased in parallel to Zn ion levels, and decreased with higher (238)U concentrations. The water samples genotoxicity positively correlated with the Zn concentration. The present work demonstrates that in order to achieve pollutant screening, it is not sufficient to determine the pollutants concentration only. Adequate conclusions on the risk due to environment contamination need to be based on the additional simultaneous use of toxicity and genotoxicity tests. When bioassays indicate some genotoxic and toxic effects, the determination of the chemical composition of the samples is then required. A combination of these two methods allows the identification of the elements that require constant biological monitoring. In the study reported here, those elements are Zn and (238)U.