Carbon,nitrogen and phosphorus net mineralization in organic horizons of temperate forests: stoichiometry and relations to organic matter quality

The rates of mineralization processes influence C sequestration and soil fertility, but despite their importance for ecosystem functioning, C, N and P net mineralization rates are seldom investigated together. Hence, we studied the relationships between net mineralization rates and organic matter stoichiometry in an 8-week incubation experiment with Oi, Oe and Oa horizon material of six beech, one spruce and one pine site. We determined C, N and P net mineralization rates, organic C quality and C:N:P stoichiometry. Net N mineralization only occurred below molar organic matter C:N ratios of 40 (Oi) or 28 (Oa) and N:P ratios of 42 (Oi) or 60 (Oa), and increased with decreasing C:N and N:P ratios. Net P mineralization only occurred below C:P ratios of 1400 (Oi) and N:P ratios of 40 (Oi), and increased with decreasing C:P and N:P ratios. Net N and P mineralization were strongly positively correlated with each other (r = 0.64, p < 0.001), whereas correlations of both net N and net P mineralization with C mineralization were weak. The average C:N:P stoichiometry of net mineralization was 620:4:1 (beech, Oi), 15,350:5:1 (coniferous, Oi), 1520:8:1 (Oe) and 2160:36:1 (Oa). On average, ratios of C:N net mineralization were higher, and ratios of N:P net mineralization lower than organic matter C:N and N:P ratios. This difference contributed to the decrease of C:N ratios and increase of N:P ratios from the Oi to the Oa horizons. In conclusion, the study shows that C, N and P net mineralization rates were closely correlated with the organic matter stoichiometry and that these correlations were modified by the degree of decomposition of the organic matter.     

Analysis of trophic structure of two carnivore assemblages by means of guild identification

We evaluated the existence of trophic guild structure, considering seasonal and annual variation, in two terrestrial carnivore assemblages: one from Santa Cruz province (Argentinean Patagonia, composed by six carnivore species), and the other from Doñana National Park (SW Spain, composed by five carnivore species). To identify trophic guilds, we first studied seasonal and annual diets of predators, calculated trophic overlap among species pairs, and then constructed overlap matrices (similarity matrices). We determined guild membership objectively by entering the similarity matrices into the clustering technique unweighted pair-group method with arithmetic averaging. Carnivores from both assemblages were grouped, respectively, into four feeding guilds. Lagomorphs and rodents promoted the formation of two feeding guilds in both study sites, although the taxonomic composition of predator species that composed them was different. The ungulates-edentates feeding guild was only present at Santa Cruz, whereas the birds and reptiles feeding guild was only present at Doñana. Invertebrates and fruits were the base for the formation of a guild composed by species of the same taxonomic origin both in Santa Cruz and Doñana. Guild structure of Santa Cruz and Doñana assemblages did not exhibit seasonal or annual variation, although the specific guild composition changed over the two studied periods for both assemblages. This structure probably responded to discontinuities in resource spectra in Santa Cruz and fluctuations in rabbit abundance in Doñana. Our results support the hypothesis that establishes that guilds are originated by opportunistic convergence of species on abundant and energetically rewarding resources.     

Heat shock protein expression and change of cytochrome c oxidase activity: presence of two phylogenic old systems to protect tissues in ischemia and reperfusion

Induction of heat shock proteins (hsp) has been shown to protect cells from ischemia by providing transient tolerance against myocardial injury and improving postischemic functional recovery. Attenuation of ATP depletion and earlier restoration of ATP content on reperfusion are thought to play a role in this scenario. Hsp induction is accompanied by altered enzyme activity of the respiratory chain, the major generator of ATP under physiological conditions. This report addresses the question whether processing and final assembly of the active holoenzyme cytochrome c oxidase (CcO, complex IV), member of the respiratory chain, is compromised under hypoxic conditions unless protected by stress proteins. Special focus is laid on function of the enzyme’s subunits and importance of cellular energy availability and maintenance.     

Characterization of aerobic heterotrophic bacteria in cold and nutrient-poor freshwater ecosystems

Aerobic heterotrophic bacteria present in the surface water of three cold and nutrient-poor lakes in the Chilean Patagonia (Alto Reino, Las Dos Torres and Venus) were analysed for genetic similarity and metabolic diversity using 16S ribosomal DNA and the Biolog EcoPlate^TM system, respectively. Bacterial fingerprints of water samples in enriched and non-enriched nutrient broth demonstrated a >50% fingerprinting similarity between the lakes. Metabolic activity was also similar. However, the Biolog EcoPlate^TM system carbon substrates revealed functional diversity. Lake Las Dos Torres showed the most fingerprinting similarity between enriched and non-enriched cold water samples. The amounts of living and viable bacteria were also higher in this lake’s water sample, suggesting a predominance of facultative oligotrophic groups. DNA sequencing analysis demonstrated the presence of phylum Bacteroidetes in Lake Alto Reino; phyla Bacteroidetes and Gammaproteobacteria in Lake Las Dos Torres; and phyla Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria in Lake Venus. Although each lake had a unique bacterial community structure, the different bacterial groups may be performing similar metabolic functions, given the similarity in extreme environmental conditions.     

Habitat utilization by sympatric European mink<Emphasis Type="Italic">Mustela lutreola</Emphasis> and polecats<Emphasis Type="Italic">Mustela putorius</Emphasis> in south-western France

The European minkMustela lutreola Linnaeus, 1761 and the European polecatMustela putorius Linnaeus, 1758 are related species sympatric in southwestern France. The European mink is rapidly disappearing whereas the polecat maintains good populations. Seasonal habitat use of both species was compared in the Landes de Gascogne region to identify if some vulnerability factors of the European mink were associated with habitats occupied by this mustelid. Potential habitats were mapped using a satellite picture and 12 main types of habitats were defined. Animal locations were recorded by radiotracking 9 European mink and 14 polecats from March 1996 to August 1999. Resting animals were located by triangulation, and, when possible, resting places were described. Animals in activity were tracked by continuous monitoring. Data collected revealed a strong preference of European mink for flooded habitats, particularly open marshes, flooded woodlands and moorlands. They seldom left the corridor of the riparian forest and their resting places were mainly in flooded environments, above ground (under herbs or bushes) or in cavities between tree roots. European polecats were less tightly linked to wetlands. Most of their locations were in the pine forests outside the valleys and their resting places were mainly in burrows. The strong specialisation of European mink in aquatic habitats is probably one of the main reasons for its decline because wetlands suffer drastic damages throughout all of its range. Maintaining adequate water levels is crucial for satisfying habitat requirements of mink.     

Reproductive biology of female blue shark <Emphasis Type="Italic">Prionace glauca</Emphasis> in the southeastern Pacific Ocean

Polyandry is extremely common across a wide range of organisms. In promiscuous mating systems, females are often sexually harassed by males, but at the same time obtain benefits from multiple mating. It remains unclear whether polyandry is exclusively imposed by males or is also promoted by females. Here, we investigated this question by recording the time spent by female guppies near a single male or a group of males with similar size and colour patterns over three consecutive days. We accounted for the effect of shoaling by using a control treatment where a group of females was used instead of a group of males. Results showed that females spent significantly more time near the group of males, but not with the group of females. In the presence of a group of males, total female mating preference time did not change over the course of the study, but rather shifted from spending more time near the single male at the beginning of the experiment to spending more time near the group of males. The consequence of this female preference for associating with a group of males in a non-experimental setup would be to promote multiple mating. Our result indicates that polyandry in guppies is at least partially encouraged by females, and not entirely a consequence of male sexual behaviour.     

A halotolerant and thermotolerant <Emphasis Type="Italic">Bacillus</Emphasis> sp. degrades hydrocarbons and produces tensio-active emulsifying agent

A Bacillus sp. strain DHT, isolated from oil-contaminated soil, grew and produced biosurfactant when cultured in variety of substrate at salinities of up to 100 g l⁻¹ and temperatures up to 45°C. It was capable of utilizing crude oil, fuels, various pure alkanes and PAHs as a sole carbon and energy source across a wide range of temperature and salinity. Over the range evaluated, the degradation of hydrocarbon and biosurfactant production was not influenced by salinity (0–10% wv⁻¹) and temperature (30–45°C). The biosurfactant produced by the organism emulsified a range of hydrocarbons with hexadecane as the best substrate and toluene as the poorest. From 16S rDNA analysis, strain DHT was related to Bacillus licheniformis.     

Algorithms for matching partially labelled sequence graphs

Background

In order to find correlated pairs of positions between proteins, which are useful in predicting interactions, it is necessary to concatenate two large multiple sequence alignments such that the sequences that are joined together belong to those that interact in their species of origin. When each protein is unique then the species name is sufficient to guide this match, however, when there are multiple related sequences (paralogs) in each species then the pairing is more difficult. In bacteria a good guide can be gained from genome co-location as interacting proteins tend to be in a common operon but in eukaryotes this simple principle is not sufficient.

Results

The methods developed in this paper take sets of paralogs for different proteins found in the same species and make a pairing based on their evolutionary distance relative to a set of other proteins that are unique and so have a known relationship (singletons). The former constitute a set of unlabelled nodes in a graph while the latter are labelled. Two variants were tested, one based on a phylogenetic tree of the sequences (the topology-based method) and a simpler, faster variant based only on the inter-sequence distances (the distance-based method). Over a set of test proteins, both gave good results, with the topology method performing slightly better.

Conclusions

The methods develop here still need refinement and augmentation from constraints other than the sequence data alone, such as known interactions from annotation and databases, or non-trivial relationships in genome location. With the ever growing numbers of eukaryotic genomes, it is hoped that the methods described here will open a route to the use of these data equal to the current success attained with bacterial sequences.

     

Morpho-physiology and maize grain yield under periodic soil flooding in successive selection cycles

This study was carried out to evaluate maize plants of different recurrent selection cycles of the variety (Zea mays L.—Saracura-BRS-4154) regarded to genetic gains, morphophysiology, and grain yield, achieved over the selection cycles under intermittent flooding of the soil. This variety has the capacity to survive and produce in temporarily flooded soils and was developed by the National Maize and Sorghum Research Center (EMBRAPA). The experiment was conducted in greenhouse by using ten alternating selection cycles (Cycle 1–18) and BR 107 a variety known for its susceptibility to flooding. The flooding initiated at six-leaf stage by applying 50 mm of water three times a week. At flowering, the following parameters were evaluated: rate of leaf photosynthesis, stomatal conductance, intercellular CO₂ concentration, transpiration rate, photosynthetically active leaf area, root porosity, relative chlorophyll content, grain yield, harvest index, ear length, and interval between male and female flowering. Yield as a function of root porosity and photosynthesis were also evaluated. An index was created in this study, in order to help the discussion of the characteristics evaluated, it was called “Relative Tolerance Value—RTV”, only gaseous exchange measurements was not included in this index. By the way, it was observed throughout the selection cycles an increase in all gaseous exchange parameters, being the cycle 18, the one which presented the greatest averages. RTV for leaf area showed the greatest values for cycles 7 and 18, whereas root porosity, chlorophyll relative content, and harvest index, the greater RTV values were found in cycles 17 and 18. The largest grain yield RTV was observed in cycle 7, followed by cycles 13, 15, and 18. Flooding resulted in longer Anthesis-Silking Interval, especially for the first cycles. At flooding condition, grain yield was strongly related to root porosity (R ² = 0.66). These results showed that the selection cycles of “Saracura” maize improved some morphophysiologic characters, which favor their survival in flooded environments, also resulting in higher productivity.