Structure of tropical river food webs revealed by stable isotope ratios

Fish assemblages in tropical river food webs are characterized by high taxonomic diversity, diverse foraging modes, omnivory, and an abundance of detritivores. Feeding links are complex and modified by hydrologic seasonality and system productivity. These properties make it difficult to generalize about feeding relationships and to identify dominant linkages of energy flow. We analyzed the stable carbon and nitrogen isotope ratios of 276 fishes and other food web components living in four Venezuelan rivers that differed in basal food resources to determine 1) whether fish trophic guilds integrated food resources in a predictable fashion, thereby providing similar trophic resolution as individual species, 2) whether food chain length differed with system productivity, and 3) how omnivory and detritivory influenced trophic structure within these food webs. Fishes were grouped into four trophic guilds (herbivores, detritivores/algivores, omnivores, piscivores) based on literature reports and external morphological characteristics. Results of discriminant function analyses showed that isotope data were effective at reclassifying individual fish into their pre-identified trophic category. Nutrient-poor, black-water rivers showed greater compartmentalization in isotope values than more productive rivers, leading to greater reclassification success. In three out of four food webs, omnivores were more often misclassified than other trophic groups, reflecting the diverse food sources they assimilated. When fish δ¹⁵N values were used to estimate species position in the trophic hierarchy, top piscivores in nutrient-poor rivers had higher trophic positions than those in more productive rivers. This was in contrast to our expectation that productive systems would promote longer food chains. Although isotope ratios could not resolve species-level feeding pathways, they did reveal how top consumers integrate isotopic variability occurring lower in the food web. Top piscivores, regardless of species, had carbon and nitrogen profiles less variable than other trophic groups.     

Two-Level factorial screening of new plasmid/strain combinations for prodution of recombinant-DNA products

This article treats the basic problem of selection of experimental conditions for microbiological experiments for evaluation of newly isolated bacterial strains, mutants, or plasmid/strain combinations. For this purpose shake flask experiments in a 2(10-4)confounded factorial design at resolution IV with four blocks of 16 flasks were used. The design was used for testing of two new strain/plasmid combinations (E. coli MT 102/403-SD2 and W 3110/403-SD2) i.e., both strains with the same plasmid 403-SD2. Both strains were integrated in the design, so both strains were tested with nine factors (temperature, aeration, glucose, initial pH, pH regulation, reduced aeration, chloramphenicol, acetate, and glycerol). With both strains the interaction between initial pH and reduced aeration had a significant influence on the yield of the recombinant-DNA product nuclease. There was more than a factor of 10 between lowest and highest yield of product. In this interactive system the strains reacted differently. MT 102/403-SD2 had highest yields at high initial pH (8.4) and no reduction in aeration, whereas W 3110/403-SD2 had highest yields of nuclease at low initial pH (7.4) and reduced aeration (rubber stopper inserted after cultivation for 12 h). These data (and previous work) clearly demonstrate that it is impossible to suggest a simple set of experimental conditions for testing of new plasmid/strain combinations. It is clear that the exclusive application of a standardized growth technique e.g., LB-medium at 37 degrees C at an unspecified and uncontrolled aeration level, may lead to wrong conclusions on properties and potentials of now plasmid/strain combinations and may lead to rejection of useful strains or plasmids.     

Moth Outbreaks Reduce Decomposition in Subarctic Forest Soils

Ecosystems - Tree mortality from insect infestations can significantly reduce carbon storage in forest soils. In subarctic birch forests (Betula pubescens), ecosystem C cycling is largely affected...     

Genomic and exoproteomic analyses of cold‐ and alkaline‐adapted bacteria reveal an abundance of secreted subtilisin‐like proteases

Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography–tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin‐like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20°C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity.     

Time limitation, egg limitation, the cost of oviposition, and lifetime reproduction by an insect in nature

For more than 80 years, ecologists have debated whether reproduction by female insect herbivores and parasitoids is constrained by the time needed to find hosts (time limitation) or by the finite supply of mature eggs (egg limitation). Here we present the first direct measures of permanent time limitation and egg limitation and their influences on the cost of oviposition and lifetime reproduction for an insect in nature. We studied the gall midge Rhopalomyia californica, which neither matures nor resorbs eggs during the adult stage. By sampling females soon after their death and correcting for predation effects, we demonstrate that females lay a large proportion of their total complement of eggs (multiyear mean: 82.9%). The egg supplies of 17.1% of females were completely exhausted, with the remaining 82.9% of females being time limited. As predicted by theory, we estimate that even though egg limitation is a minority condition within the population, egg costs make a substantial contribution (57% of the total) to the cost of oviposition. We conclude that insect life histories evolve to produce a balanced risk of time and egg limitation and, therefore, that both of these constraining factors have important influences on insect oviposition behavior and population dynamics.     

Effect of boat noise and angling on lake fish behaviour

The effects of disturbances from recreational activities on the swimming speed and habitat use of roach Rutilus rutilus, perch Perca fluviatilis and pike Esox lucius were explored. Disturbances were applied for 4 h as (1) boating in short intervals with a small outboard internal combustion engine or (2) boating in short intervals combined with angling with artificial lures between engine runs. The response of the fish species was evaluated by high‐resolution tracking using an automatic acoustic telemetry system and transmitters with sub‐minute burst rates. Rutilus rutilus swimming speed was significantly higher during disturbances [both (1) and (2)] with an immediate reaction shortly after the engine started. Perca fluviatilis displayed increased swimming activity during the first hour of disturbance but not during the following hours. Swimming activity of E. lucius was not significantly different between disturbance periods and the same periods on days without disturbance (control). Rutilus rutilus increased their use of the central part of the lake during disturbances, whereas no habitat change was observed in P. fluviatilis and E. lucius. No difference in fish response was detected between the two types of disturbances (boating with and without angling), indicating that boating was the primary source of disturbance. This study highlights species‐specific responses to recreational boating and may have implications for management of human recreational activities in lakes.     

Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii

The prs gene encoding phosphoribosyl diphosphate (PRPP) synthase of the hyperthermophilic autotrophic methanogenic archaeon Methanocaldococcus jannaschii has been cloned and expressed in Escherichia coli. Subsequently, M.jannaschii PRPP synthase has been purified, characterised, crystallised, and the crystal structure determined. The enzyme is activated by phosphate ions and only ATP or dATP serve as diphosphoryl donors. The K(m) values are determined as 2.6 mM and 2.8 mM for ATP and ribose 5-phosphate, respectively, and the V(max) value as 2.20 mmol (minxmg of protein)(-1). ADP is a potent inhibitor of activity while GDP has no effect. A single ADP binding site, the active site, is present per subunit. The crystal structure of the enzyme reveals a more compact subunit than that of the enzyme from the mesophile Bacillus subtilis, caused by truncations at the N and C terminus as well as shorter loops in the M.jannaschii enzyme. The M.jannaschii enzyme displays a tetrameric quaternary structure in contrast to the hexameric quaternary structure of B.subtilis PRPP synthase. Soaking of the crystals with 5'-AMP and PRPP revealed the position of the former compound as well as that of ribose 5-phosphate. The properties of M.jannaschii PRPP synthase differ widely from previously characterised PRPP synthases by its tetrameric quaternary structure and the simultaneous phosphate ion-activation and lack of allosteric inhibition, and, thus, constitute a novel class of PRPP synthases.