Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

<p>Abstract</p> <p>Background</p> <p>Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade <it>Milnesium tardigradum</it> were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress.</p> <p>Results</p> <p>In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration.</p> <p>Conclusions</p> <p>The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner.</p

High-temperature tolerance in anhydrobiotic tardigrades is limited by glass transition

Survival in microhabitats that experience extreme fluctuations in water availability and temperature requires special adaptations. To withstand such environmental conditions, tardigrades, as well as some nematodes and rotifers, enter a completely desiccated state known as anhydrobiosis. We examined the effects of high temperatures on fully desiccated (anhydrobiotic) tardigrades. Nine species from the classes Heterotardigrada and Eutardigrada were exposed to temperatures of up to 110 degrees C for 1 h. Exposure to temperatures of up to 80 degrees C resulted in a moderate decrease in survival. Exposure to temperatures above this resulted in a sharp decrease in survival, with no animals of the families Macrobiotidae and Echiniscidae surviving 100 degrees C. However, Milnesium tardigradum (Milnesidae) showed survival of >90% after exposure to 100 degrees C; temperatures above this resulted in a steep decrease in survival. Vitrification is assumed to play a major role in the survival of anhydrobiotic organisms during exposure to extreme temperatures, and consequently, the glass-transition temperature (T-g) is critical to high-temperature tolerance. In this study, we provide the first evidence of the presence of a glass transition during heating in an anhydrobiotic tardigrade through the use of differential scanning calorimetry

Freeze tolerance, supercooling points and ice formation: comparative studies on the subzero temperature survival of limno-terrestrial tardigrades

Many limno-terrestrial tardigrades live in unstable habitats where they experience extreme environmental conditions such as drought, heat and subzero temperatures. Although their stress tolerance is often related only to the anhydrobiotic state, tardigrades can also be exposed to great daily temperature fluctuations without dehydration. Survival of subzero temperatures in an active state requires either the ability to tolerate the freezing of body water or mechanisms to decrease the freezing point. Considering freeze tolerance in tardigrades as a general feature, we studied the survival rate of nine tardigrade species originating from polar, temperate and tropical regions by cooling them at rates of 9, 7, 5, 3 and 1 degrees Ch(-1) down to -30 degrees C then returning them to room temperature at 10 degrees Ch(-1). The resulting moderate survival after fast and slow cooling rates and low survival after intermediate cooling rates may indicate the influence of a physical effect during fast cooling and the possibility that they are able to synthesize cryoprotectants during slow cooling. Differential scanning calorimetry of starved, fed and cold acclimatized individuals showed no intraspecific significant differences in supercooling points and ice formation. Although this might suggest that metabolic and biochemical preparation are non-essential prior to subzero temperature exposure, the increased survival rate with slower cooling rates gives evidence that tardigrades still use some kind of mechanism to protect their cellular structure from freezing injury without influencing the freezing temperature. These results expand our current understanding of freeze tolerance in tardigrades and will lead to a better understanding of their ability to survive subzero temperature conditions

Stress Proteins (hsp70, hsp60) Induced in Isopods and Nematodes by Field Exposure to Metals in a Gradient near Avonmouth, UK

Heat shock proteins (hsps) are potential biomarkers for monitoring environmental pollution. In this study, the use of hsps as biomarkers in field bioassays was evaluated in terrestrial invertebrates exposed to a metal gradient near Avonmouth, UK. We investigated the hsp70 response in resident and transplanted isopods of the species Oniscus asellus and Porcellio scaber and the hsp60 response in transplanted nematodes of the species Plectus acuminatus in six field sites along the metal gradient. Considerable differences were detected in the stress responses between nematodes and isopods (isopods responded in a gradientspecific manner, nematodes did not), the two isopod species and the transplanted and resident specimens of each isopod species: in the sites closest to the smelter, O. asellus residents showed high hsp70 levels while O. asellus transplanted from an unpolluted site displayed comparatively low hsp70 levels. For P. scaber, it was just the opposite. In resident isopod populations of both species, tolerant phenotypes were revealed in the most contaminated field sites. The hsp70 level in both isopod species was a suitable biomarker of effect (but of exposure only in non-tolerant individuals) even in long-term metal -contaminated field sites. The hsp60 response in the nematode alone was not a suitable biomarker for heavily contaminated soils. However, it had indicative value when related to the hsp70 response in the isopods and could be a suitable biomarker for less heavily contaminated soils

European Atlas of Soil Biodiversity

The SOIL Action (22004) of the Joint Research Centre\u2019s Land Management and Natural Hazards Unit (H07) has just completed a comprehensive collaborative project focusing exclusively on life in the soil. One of the resulting outputs is the first ever European Atlas of Soil Biodiversity. This atlas is the result of a collaboration between the European Commission\u2019s Joint Research Centre in Ispra, Italy and world leading experts in soil biodiversity from Europe and beyond. The atlas is a visually stunning publication of 128 pages, using striking photographs, informative texts and maps to explain and illustrate the great diversity of life in the across Europe. The atlas functions as a comprehensive guide to soil biology, allowing non-specialists to access information about this unseen world. The first part of the book provides an overview of the below ground environment, soil biota in general, the ecosystem functions that soil organism perform, the important value it has for human activities and relevance for global biogeochemical cycles. The second part is more of an 'Encyclopedia of Soil Biodiversity'. Starting with the smallest organisms such as the bacteria, this segment works through a range of taxonomic groups such as fungi, nematodes, insects and macro-fauna to illustrate the astonishing levels of heterogeneity of life in soil