Microbes are the unseen majority in soil and comprise a large portion of lifeÕs genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogenfixing bacteria are responsible for c. 5-20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

This paper (i) reviews temperature/development rate relationships in plants and poikilothermic invertebrates, (ii) argues that the relationship is often linear over much of the range up to the thermal optimum (T o ) and provides a possible mechanism, (iii) provides evidence of a trade-off between the base temperature (T b ) and the thermal constant (DD) that enables each species to adapt to its thermal environment, and (iv) indicates some of the practical and ecological implications. Where a linear relationship has been characterised it is possible to estimate the base temperature for development (T b , expressed in °C) and the thermal constant for development (DD, the reciprocal of the temperature coefficient (a), expressed in degree [°C] days accumulated above T b ). A possible basis for the linear relationship between rate and temperature is proposed based on the Arrhenius and Sharpe-Schoolfield equations involving activation enthalpy and progressive inactivation of the reactant molecules at both low and high temperatures. Knowledge of T b and DD enables rates of development of organisms/ processes to be calculated and compared at any given temperature between T b and T o . An analysis of published results for differentiation processes (differentiation = a change of state) in species of insects, Collembola, spiders, nematodes and plants showed that T b tended to vary with the temperature of the niche to which the organism is adapted, and that there was a trade-off between T b and DD. Tropical species had higher values of T b than temperate and DD decreased as T b increased (and vice versa). This conferred a competitive advantage on each species in the thermal environment to which it was adapted. The decrease in DD tended to be relatively greater than the increase in T b, further favouring a high T b in tropical species. A mechanism for the trade-off is suggested whereby DD and T b were shown to be correlated (P < 0.01) with the activation enthalpy (H A ) of an assumed, rate-limiting enzyme. Thermal time can also be applied to processes involving growth (= an increase in dry weight) when the DD requirement for development to maturity is the sum of the requirements for differentiation and growth. Rates of both differentiation and growth can vary greatly between species, depending upon the niche they inhabit, and the implications of such differences for resource requirements are considered. In insects and nematodes, but not in annual plants, development is usually coupled to growth. Consequently, when resources are inadequate, mature size in these animals varies less than in plants. Thermal time is shown to provide insight into the life strategies of species within their communities and to have practical implications.

Risk assessment procedures use toxicity tests in which organisms are subjected to chemicals under otherwise constant and favorable experimental conditions. Because variable and suboptimal environmental conditions are common aspects of natural ecosystems, the hazard of underestimation of risk arises. Therefore, an uncertainty factor is used in the extrapolation of results of standard toxicity tests to field situations. The choice for these uncertainty factors is based on little ecological evidence. This review discusses studies on the toxicity of various chemicals to aquatic organisms, modified by temperature, nutritional state and salinity, excluding papers on changes in bioavailability of compounds. Collected data were analyzed quantitatively to evaluate the validity of toxicity data obtained from standard toxicity tests in the laboratory under field conditions. Generally, organisms living under conditions close to their environmental tolerance limits appeared to be more vulnerable to additional chemical stress. Usually, increasing temperature and decreasing food or nutrient level raised toxicity. The influence of salinity was less clear; metal toxicity increased with decreasing salinity, toxicity of organophosphate insecticides increased with higher salinity, while for other chemicals no clear relationship between toxicity and salinity was observed. The interactions can be explained by several physical and physiological processes, acting on factors such as bioavailability, toxicokinetics, and sensitivity of organisms. Quantitative analysis of data indicated that an uncertainty factor for the laboratory to field extrapolation should be smaller than one for an ecosystem in a temperate region, while a factor greater than one would be appropriate for systems nearby discharge points of cooling water. The factor should be greater than one when varying nutritional state is concerned, but smaller than one with respect to salinity. Dependent on the effect parameter used, the differences in toxicity between laboratory and relevant field situations ranged from a factor of 2.6 to 130 and 1.7 to 15 for the two temperature conditions and 1.2 to 10 for nutritional state. A salinity increase from freshwater to marine water decreased toxicity by a factor of 2.1. However, as less extreme salinity changes are more relevant under field conditions, the change in toxicity is probably much smaller. To obtain uncertainty factors that sufficiently protect natural systems without being overprotective, additional research is required.

Organisms are able to control metal concentrations in certain tissues of their body to minimize damage of reactive forms of essential and nonessential metals and to control selective utilization of essential metals. These physiological aspects of organisms are not accounted for when assessing the risk of metals in the environment. The Critical Body Residue (CBR) approach relates toxicity to bioaccumulation and biomagnification and might at first sight provide a more accurate estimation of effects than the external concentration. When expressing CBRs on total internal concentrations, the capacity of organisms to sequester metals in forms that are not biologically reactive is neglected. The predictability of toxic effects will increase when knowledge on metal compartmentalization within the organisms' body is taken into account. Insight in metal compartmentalization sheds light on the different accumulation strategies organisms can follow upon metal exposure. Using a fractionation procedure to isolate metal-rich granules and tissue fragments from intracellular and cytosolic fractions, the internal compartmentalization of metals can be approximated. In this paper, current knowledge regarding metal compartmentalization in organisms is summarized, and metal fractions are identified that are indicators of toxicity. Guidance is provided on future improvement of models, such as the Biotic Ligand Model (BLM), for risk assessment of metal stress to biota.

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Standard toxicity tests are performed at one constant, optimal temperature (usually 20 degrees C), while in the field variable and suboptimal temperatures may occur. Lack of knowledge on the interactions between chemicals and temperature hampers the extrapolation of laboratory toxicity data to ecosystems. Therefore, the aim of this study was to analyze the effects of temperature on cadmium toxicity to the waterflea Daphnia magna and to address possible processes responsible for temperature-dependent toxicity. This was investigated by performing standard toxicity tests with D. magna under a wide temperature range. Thermal effects on accumulation kinetics were determined by estimating uptake and elimination rates from accumulation experiments. To study temperature dependency of the intrinsic sensitivity of the daphnids to cadmium, the DEBtox model was used to estimate internal threshold concentrations (ITCs) and killing rates from the toxicity and accumulation data. The results revealed that increasing temperature lowered the ITC and increased the killing rate and the uptake rate of the metal. Enhanced sensitivity of D. magna was shown to be the primary factor for temperature-dependent toxicity. Since temperature has such a major impact on toxicity, a temperature correction may be necessary when translating toxicity data from the laboratory to the field.

Background Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.ResultsWe applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster.ConclusionsThe expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3852-x) contains supplementary material, which is available to authorized users.