Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring

Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world’s largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.     

Changes in the heavy metal and nutrient contents of dried feather mosses during long-term storage

This study measured heavy metal and nutrient concentrations of two feather mosses during the periods of dry storage. Samples (Hylocomium splendens, Pleurozium schreberi) were collected in the nationwide moss surveys carried out on the permanent sample plots of the 8th Finnish National Forest Inventory in 1985–86, 1990, 1995 and 2000. A small amount of each moss sample was analyzed soon after collection, and the remainder was dried and stored at the Paljakka environmental specimen bank (ESB). The 108 stored samples from 27 plots were reanalyzed in 2008. Concentrations of heavy metals (Cd, Cr, Cu, Fe, Ni, Pb, Zn) and nutrients (Ca, K, Mg, P) were determined and compared for each survey year. Overall, Fe, Pb and Cr concentrations decreased, and Cu concentrations increased significantly during storage. The greatest decrease was observed in samples from plots where their initial concentrations were the highest. Changes in the concentrations of Cd, Ni and Zn were less pronounced. The loss of heavy metals is likely due to drying when cell membranes rupture and some of the surface material is lost. K, P and, to some extent, Mg concentrations increased during storage, whereas Ca did not change significantly. Nutrient increase is probably due to their movement from older to younger growths during the initial phase of drying. Ca is mostly bound to cell walls and is not easily released. Results emphasize the importance of establishing the intended use of a stored moss prior to sampling, in order to select and optimize an appropriate storage technique.     

Deposition of gamma emitters from Chernobyl accident and their transfer in lichen–soil columns

Lichen–soil column samples were taken from several locations in the Southern Finland between 1986 and 2006. Columns were divided into three parts, upper lichen, lower lichen and underlying soil, and their gamma emitting radionuclides, ¹³⁴Cs, ¹³⁷Cs, ¹⁰³Ru, ⁹⁵Zr, ¹⁰⁶Ru, ^110mAg, ¹²⁵Sb and ¹⁴⁴Ce, were measured with gamma spectrometry. Deposition values were calculated as Bq/m² for each sampling site. Distribution of various radionuclides in the three compartments as a function of time was determined. Both effective and ecological half-lives of all radionuclides were calculated for upper lichen, whole lichen and whole lichen–soil column. A linear relation was derived between the physical half-lives and effective half-lives for whole lichen and for whole lichen–soil column. Reindeer meat activity concentrations of various radionuclides and ensuing radiation doses to reindeer-herding people were also estimated for a hypothetical case where a similar high radioactive pollution, as was taken place in the Southern Finland, would have occurred in the reindeer-herding areas in the Finnish Lapland.     

Avian flocking reduces starvation risk: an experimental demonstration

Summary Theory suggests that variance in individual food intake is lower during group foraging. Consequently, group foraging can at times reduce starvation risk. In aviary experiments using green-finches we demonstrate how intake variability decreases during group foraging because individuals use feeding by flock mates as a cue to locate food (local enhancement). Flocking preferences of greenfinches responded to variance in energy gain as predicted by theoretical models for foragers attempting to reduce starvation risk. While energy budget was positive the greenfinches were risk averse and foraged socially. Their preference shifted towards more risk prone solitary foraging when kept on a negative energy budget. We conclude that time or energy net gains are not necessary for foraging groups to form, but reductions in starvation risk may be sufficient.     

Development of a diffusive sampling method for determination of methyl isocyanate in air

A diffusive sampling method for determination of methyl isocyanate in air has been developed. A glass fibre filter impregnated with 1-(2-methoxyphenyl)piperazine in a commercially available diffusive sampling device was used to collect methyl isocyanate and the derivative formed was analysed with LC-MS/MS. The sampling rate was determined to be 15.6 ml min(-1), with a relative standard deviation of 7.3%. The sampler was validated for sampling periods from 15 min to 8 h, for relative humidities from 20% to 80% and for concentrations from I to 46 microg m(-3). A field validation was also made and the diffusive sampling results showed no difference compared to a pumped reference method. The impregnated filters have to be stored apart from the diffusive sampler housing and loaded into the sampler prior to each sampling.     

Alliances in winter flocks of willow tits; effects of rank on survival and reproductive success in male-female associations

Summary The value of being dominant in winter flocks of willow tits may not only be a matter of personal survival for males, although their survival probability was highest among flock members. Winter flocks of willow tits contain male-female subunits, and the dominant pair may be viewed as an alliance based on mutual benefits. Dominant males provide their mates with protection in winter, and females return the help in reproductive success. Survival was directly related to rank only within sexes. Mates of dominant males survived significantly better than low-ranked males even though these females were subordinate to these males in direct interactions. Mates of dominant males were relatively spared from costs of low rank as they were subject to aggression less often than expected. Presumably dominant males prevented such attacks, as they excluded other flock members from high tree sections where their mates fed. Males should gain from improving the survival probability of their mates since it was not always possible to replace lost mates in spring populations having a male-biased sex ratio. Dominance in avian winter flocks may thus have more indirect effects than merely to improve the personal survival probability through resource priority. The benefits of being a dominant suggest that subordinate willow tits join groups because there is no space available for them to take up a territory as dominants.     

Molecular orbital studies on brominated diphenyl ethers. Part I--conformational properties

Polybrominated diphenyl ethers (PBDEs) are widely used as additive flame retardants and quantities in the environment are on the rise. Because they are structurally related to polychlorinated biphenyls and also to thyroid hormones, there is serious concern that PBDEs may pose a danger to human health. Knowledge of their conformational properties is key to assessing their environmental fate and risk. The conformational properties of PBDEs were investigated by quantum chemical methods including semiempirical self-consistent field molecular orbital (SCF-MO), ab initio SCF-MO and density functional theory (DFT). Conformational analyses of model congeners 2,2',4,6'-tetrabromodiphenyl ether and 2,3,4,4',5,6-hexabromodiphenyl ether, based on energy maps calculated by semiempirical AM1 method, may indicate that all PBDE congeners except those with the tetra-ortho-bromination are conformationally flexible (or soft) due to low energy barriers for interconversion of stable conformers. The results of the conformational analyses are in conformity with recently published X-ray crystallographic data. For comparison with the results of the semiempirical method, higher level ab initio and DFT models were applied as well. The optimized geometries all lie well inside low energy regions on the maps and thus also ascertain the semiempirical calculations. According to computed geometric parameters and net atomic charges, the model B3LYP/3-21G* seemed to give better results than B3LYP/6-31G* and HF/6-31G*.     

Molecular orbital studies on brominated diphenyl ethers. Part II--reactivity and quantitative structure-activity (property) relationships

Polybrominated diphenyl ethers (PBDEs) are widely used as flame retardants and are increasingly turning up in the environment. Their structural similarities to polychlorinated biphenyls and thyroid hormones suggest they may be a risk to human health. The present study examines the reactivity of brominated diphenyl ethers (BDEs) on the basis of the electronic structures as calculated by semiempirical AM1 self-consistent field molecular orbital (SCF-MO) method. Frontier orbital energies were used to elucidate the reactivity of BDEs in electrophilic, nucleophilic and photolytic reactions. From an examination of the frontier electron densities, the regioselectivity, or orientation, of metabolic reactions of BDEs was predicted. Furthermore, satisfactory quantitative structure-activity (property) relationship (QSAR and QSPR) models were derived to calculate gas chromatographic and ultraviolet spectral properties and luciferase induction activities from the AM1-computed electronic parameters.     

Deposition of gamma emitters from Chernobyl accident and their transfer in lichen-soil columns

Lichen-soil column samples were taken from several locations in the Southern Finland between 1986 and 2006. Columns were divided into three parts, upper lichen, lower lichen and underlying soil, and their gamma emitting radionuclides, (134)Cs, (137)Cs, (103)Ru, (95)Zr, (106)Ru, (110m)Ag, (125)Sb and (144)Ce, were measured with gamma spectrometry. Deposition values were calculated as Bq/m(2) for each sampling site. Distribution of various radionuclides in the three compartments as a function of time was determined. Both effective and ecological half-lives of all radionuclides were calculated for upper lichen, whole lichen and whole lichen-soil column. A linear relation was derived between the physical half-lives and effective half-lives for whole lichen and for whole lichen-soil column. Reindeer meat activity concentrations of various radionuclides and ensuing radiation doses to reindeer-herding people were also estimated for a hypothetical case where a similar high radioactive pollution, as was taken place in the Southern Finland, would have occurred in the reindeer-herding areas in the Finnish Lapland.