Determination of food sources and trophic position in Malaysian tropical highland streams using carbon and nitrogen stable isotopes

Stable isotope analysis has been extensively used as an effective tool in determination of trophic relationship in ecosystems. In freshwater ecosystem, aquatic invertebrates represent main component of a river food web. This study was carried out to determine potential food sources of freshwater organism together with pattern of trophic position along the river food web. In this study, rivers of Belum-Temengor Forest Complex (BTFC) has been selected as sampling site as it is a pristine area that contains high diversity and abundance of organisms and can be a benchmark for other rivers in Malaysia. Stable isotope ratios of carbon (δ¹³C) and nitrogen (δ¹⁵N) were applied to estimate trophic position and food web paradigm. Analysis of stable isotopes based on organic material collected from the study area revealed that the highest δ¹³C value was reported from filamentous algae (? 22.68 ± 0.126⁰/₀₀) and the lowest δ¹³C was in allocthonous leaf packs (? 31.58 ± 0.187⁰/₀₀). Meanwhile the highest δ¹⁵N value was in fish (8.45 ± 0.177⁰/₀₀) and the lowest value of δ¹⁵N was in autochthonous aquatic macrophyte (2.00 ± 1.234⁰/₀₀). Based on the δ¹⁵N results, there are three trophic levels in the study river and it is suggested that the trophic chain begins with organic matter followed by group of insects and ends with fish (organic matter < insects < fish).     

Parasites alter the topology of a stream food web across seasons

Relatively few published food webs have included parasites, and in this study we examined the animal community in a stream across eight contiguous seasons to test how inclusion of helminth parasites alters the topology or structure of the food web. Food webs constructed for each season and analyzed using common binary matrix measures show that species richness, linkage density, and the number of observed and possible links increased when parasites were included as individual species nodes. With parasite–parasite and predator–parasite links omitted, measures of community complexity, such as connectance (C), generally increased over multiple seasons. However, relative nestedness (n*) decreased when parasites were included, which may be a result of low resolution of basal resources inflating specialist-to-specialist links. Overall, adding parasites resulted in moderate changes in food web measures when compared to those of four other published food webs representing different ecosystems. In addition, including parasites in the food web revealed consistent pathways of energy flow, and the association of parasite life histories along these pathways suggest stable evolutionary groups of interacting species within the community. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of evolutionary changes in prey use on the relationship between food web complexity and stability

The relationship between food web complexity and stability has been the subject of a long-standing debate in ecology. Although rapid changes in the food web structure through adaptive foraging behavior can confer stability to complex food webs, as reported by Kondoh (Science 299:1388–1391, 2003), the exact mechanisms behind this adaptation have not been specified in previous studies; thus, the applicability of such predictions to real ecosystems remains unclear. One mechanism of adaptive foraging is evolutionary change in genetically determined prey use. We constructed individual-based models of evolution of prey use by predators assuming explicit population genetics processes, and examined how this evolution affects the stability (i.e., the proportion of species that persist) of the food web and whether the complexity of the food web increased the stability of the prey–predator system. The analysis showed that the stability of food webs decreased with increasing complexity regardless of evolution of prey use by predators. The effects of evolution on stability differed depending on the assumptions made regarding genetic control of prey use. The probabilities of species extinctions were associated with the establishment or loss of trophic interactions via evolution of the predator, indicating a clear link between structural changes in the food web and community stability.     

The relative importance of herbivory and carnivory on the distribution of energy in a stochastic tri-trophic food web

A three-state, discrete-time Markov chain is used to model the dynamics of energy flow in a tri-trophic food web. The distribution of energy in the three trophic levels is related to the rates of flow between the trophic levels and calculated for the entire range of possible flow values. These distributions are then analysed for stability and used to test the idea that plants are resource-limited and herbivores are predation-limited. Low rates of death and decomposition, when coupled with low rates of herbivory and carnivory, tend to destabilize this food web. Food webs with higher rates of death and decomposition are relatively more stable regardless of rates of herbivory and carnivory. Plants are more prone to resource-limitation and herbivores are, in general, limited by their predators, which supports Hairston et al. (Am. Nat. 94 (1960) 421). The rate of decomposition often mediates the roles of top-down and bottom-up control of energy flow in the food web.     

Experimental dietary manipulations for determining the relative importance of allochthonous and autochthonous food resources in tropical streams

1. Autochthonous sources of organic matter appear to make a minor contribution to food webs in temperate forest streams, but their roles in supporting consumer biomass in tropical lotic environments have received little attention. We investigated the importance of autochthonous and allochthonous food sources to Brotia hainanensis (Pachychilidae), a detritivorous and algivorous snail common in Hong Kong hillstreams, using experimental dietary manipulations and assimilation-based analyses, including stoichiometry, carbon (C) and nitrogen (N) stable isotopes and fatty acid (FA) profiles.
2. Juvenile B. hainanensis collected in Pak Ngau Shek Stream were cultured under controlled laboratory conditions and fed for 2 months with either conditioned Liquidambar formosana (Hamamelidaceae) leaf litter or periphyton. Samples of B. hainanensis were also collected from the stream at the end of the experiment for comparison with snails reared in the laboratory.
3. Periphyton and leaf litter exhibited marked differences in C/N ratios, δ ¹³C and δ ¹⁵N values and FA profiles. Stable isotope analysis and FA profiling of laboratory-reared and field-collected B. hainanensis both confirmed that snails relied primarily on autochthonous foods, especially periphytic diatoms and cyanobacteria. Stoichiometry results indicated that periphyton was a more nutritious food (with lower C/N ratio) than leaf litter.
4. This is the first study demonstrating that the combined use of stable isotopes and FA profiles is an effective diagnostic tool to trace the basal food sources of consumers in natural stream habitats. Our findings further support the hypothesis that primary production in tropical streams is generally more important to aquatic consumers than inputs of terrestrial detritus.     

Isotopic metrics as a tool for assessing the effects of mine pollution on stream food webs

Most tools used to assess pollution impacts are based on structural, or less frequently, functional aspects of biotic communities. However, the application of measures that take a food web approach to understand the effects of stress on stream ecosystems offers a new perspective and promising insights. We assessed quantitative isotopic metrics, which describe characteristics of food web structure, as indicators of acid mine drainage (AMD) in 12 streams along a stress gradient and compared these metrics with traditional structural and functional metrics. The gradient ranged from highly stressed (pH < 3) streams with elevated concentrations of dissolved metals (Fe and Al) to moderately acidic streams (pH 3.6–4.9) with substrata coated in metal hydroxide precipitates and circumneutral reference streams. Key differences in food web structure were detected by the isotopic metrics. Specifically, fewer trophic levels and reduced trophic diversity characterized food webs in all mining impacted streams but the differences were not significant along the gradient. In contrast, most structural and functional metrics were significant predictors of AMD as stress increased. Therefore, our results suggest that isotopic metrics offer little advantage over traditional metrics in terms of detecting impacts for biomonitoring purposes. However, they do provide additional insights into how whole food webs are disrupted, and are likely to be more useful for guiding stream management and rehabilitation strategies.     

应用稳定同位素技术构建胶州湾食物网的连续营养谱

根据2011年春季和秋季在胶州湾进行的渔业资源综合调查,应用稳定同位素示踪技术,分析了胶州湾主要渔业生物的碳、氮稳定同位素比值(δ13C,δ15N),并计算其营养级,进而构建胶州湾食物网的连续营养谱。分析的生物种类包括浮游植物、浮游动物、大型无脊椎动物和鱼类,其生物量之和占总渔获量的95%。结果表明,胶州湾食物网的δ13C值范围是-25.63‰—-17.16‰,跨度为8.47‰,平均值为(-19.42±1.80)‰;δ15N值范围是4.15‰—14.11‰,跨度为9.96‰,平均值为(11.98±1.77)‰。胶州湾食物网中的主要生物种类可以划分为4个营养组群,即初级生产者、初级消费者、次级消费者以及顶级捕食者。δ15N值分析显示,胶州湾主要生物种类的营养级范围是1.10—4.03。与文献中基于胃含物分析计算的营养级相比较,37个种类中有29种的营养级分析结果基本一致(在0.5个营养级的误差范围之内)。因此,氮稳定同位素法是一种研究水生生态系统食物网营养位置的有效方法。其中,有8种鱼类的营养级与历史文献相比有所下降,分析方法的不同可能是原因之一,此外,这些鱼种摄食饵料生物营养级的下降也是导致其营养级降低的另一个主要原因。根据营养级计算的结果,构建了胶州湾食物网的连续营养谱,胶州湾食物网中,绝大多数生物种类都属于初级和中级肉食性种类。     

Use of isotopic signatures to assess the food web in a tropical shallow marine ecosystem of Southeastern Brazil

A dual isotope approach was used to assess the relative importance of terrestrial vegetation detritus and other primary producers in the trophic web of Flamengo Sound (Ubatuba, SP), SE Brazil, surrounded by the Atlantic Rain Forest. Primary producers showed distinct C signatures and the observed values suggest that little terrestrial or bulk sediment organic matter enter the food web of the sound. Suspended particulate organic matter (POM, supports the bulk of the consumers, with some contribution by macroalgae . Consumers C values ranged from −17.4 to . At least three trophic levels were detectable in the food web. The N value of POM was , while that of sediment and detritus was . The N values of suspension feeding benthic invertebrates were 8.2–, deposit feeders 8.3–, and carnivores 10.7–. Values for fishes were for detritivore, 11.4– for benthic feeders, 12.4– for zooplanktivores, and for piscivores/benthic invertebrate feeders. Squid mean value was . There is a reasonable agreement between feeding habits information from the literature and N values from this study. In the sound, the first and second trophic steps seem to be about 1– higher than those of similar organisms studied in temperate waters and this may reflect an input of allochtonous anthropogenic nitrogen enriched in ¹⁵N from human activities.     

Effects of food quality on growth and biochemical composition of a calanoid copepod,Argyrodiaptomus furcatus,and its importance as a natural food source for larvae of two tropical fishes

Growth, reproduction and biochemical composition were analyzed for the copepod Argyrodiaptomus furcatus fed on the alga Ankistrodesmus gracilis grown in different media. The ingestion of this copepod by larvae of two species of tropical fishes was also evaluated. The mean peak density of the copepod population was 1369 individuals l^–1 for all four diets used, and the highest was 1387 individuals l^–1 on diet ARV (algae + ration + vitamins). A small copepod, A. furcatus tends to have a short life span. The smallest females did not attain maturity in the shortest time on all diets used. Food quality may play a major role in the dynamics of the biochemical composition of this copepod. Argyrodiaptomus furcatus was a more important food item for larvae of tambaqui (Colossoma macropomum) than of pacu (Piaractus mesopotamicus). However, it made up a large part of the gut contents of larvae of both species.     

Use of15N/14N rations to evaluate the food source of the mysid,Neomysis intermedia Czerniawsky,in a eutrophic lake in Japan

The stable isotope ratios of nitrogen were measured in the mysid,Neomysis intermedia, together with various biogenic materials in a eutrophic lake, Lake Kasumigaura, in Japan throughout a year of 1984/85. The mysid, particulate organic matter (POM, mostly phytoplankton), and zooplankton showed a clear seasonal change in ¹⁵N with high values in spring and fall, but the surface bottom mud did not. A year to year variation as well as seasonal change in ¹⁵N was found in the mysid. The annual averages of ¹⁵N of each material collected in 1984/85 are as follows: surface bottom mud, 6.3 (range: 5.7–6.9); POM, 7.9 (5.8–11.8); large sized mysid, 11.6 (7.7–14.3); zooplankton, 12.5 (10.0–16.4); prawn, 13.2 (9.9–15.4); goby, 15.1 (13.8–16.7). The degree of¹⁵N enrichment by the mysid was determined as 3.2 by the laboratory rearing experiments. The apparent parallel relationship between the POM and the mysid in the temporal patterns of ¹⁵N with about 3 difference suggests the POM (mostly phytoplankton) as a possible food source ofN. intermedia in this lake through the year.     

Trophic niche of the Pacific Sierra (Scomberomorus sierra) in the southeastern Gulf of California: Assessing its importance as a predator and prey (Mesopredator) in the food web

The identification of interspecific links (trophic niche) is important to characterize resource use of a predator, and to know its trophic role (for example, mesopredator or top predator) in the food web. In this study, we examined: a) the trophic ecology of Scomberomorus sierra as a predator (niche breadth, trophic overlap, and trophic position) and b) its presence as a prey in the diets of the region´s top predators, to evaluate the critical link of S. sierra as a probable mesopredator in the food web of the southeastern Gulf of California (GC). Based on %PSIRI, the dominant diet of S. sierra were engraulids and cephalopods. The diet was similar between sexes and among size-classes. However, the isotopic niche breadth values and δ¹⁵N variance (>1) reflect a broad niche for young adults likely related to a) changes in morphology (e.g., size of the mouth), b) development of the visual system, and c) changes in the energy requirements of the species reproductive stages. Seasonal changes in prey species’ availability and abundance resulted in isotopic variations, indicating that S. sierra is an opportunistic predator. A wide range in trophic position value (from 3.8 to 4.2) indicated that it also is an intermediary carnivore, with a high degree of trophic plasticity. Although S. sierra has not a dominant role in top predators’ diets, they share some prey species such as anchovies and other fish, depending on predator size. Therefore, S. sierra is a species with many prey-predator relationships in the southeastern GC food webs that may be considered a critical trophic link. This information is crucial for an ecosystem-based fisheries management in the Gulf of California.     

NL MIND-BEST: a web server for ligands and proteins discovery--theoretic-experimental study of proteins of Giardia lamblia and new compounds active against Plasmodium falciparum

There are many protein ligands and/or drugs described with very different affinity to a large number of target proteins or receptors. In this work, we selected Ligands or Drug-target pairs (DTPs/nDTPs) of drugs with high affinity/non-affinity for different targets. Quantitative Structure-Activity Relationships (QSAR) models become a very useful tool in this context to substantially reduce time and resources consuming experiments. Unfortunately most QSAR models predict activity against only one protein target and/or have not been implemented in the form of public web server freely accessible online to the scientific community. To solve this problem, we developed here a multi-target QSAR (mt-QSAR) classifier using the MARCH-INSIDE technique to calculate structural parameters of drug and target plus one Artificial Neuronal Network (ANN) to seek the model. The best ANN model found is a Multi-Layer Perceptron (MLP) with profile MLP 20:20-15-1:1. This MLP classifies correctly 611 out of 678 DTPs (sensitivity=90.12%) and 3083 out of 3408 nDTPs (specificity=90.46%), corresponding to training accuracy=90.41%. The validation of the model was carried out by means of external predicting series. The model classifies correctly 310 out of 338 DTPs (sensitivity=91.72%) and 1527 out of 1674 nDTP (specificity=91.22%) in validation series, corresponding to total accuracy=91.30% for validation series (predictability). This model favorably compares with other ANN models developed in this work and Machine Learning classifiers published before to address the same problem in different aspects. We implemented the present model at web portal Bio-AIMS in the form of an online server called: Non-Linear MARCH-INSIDE Nested Drug-Bank Exploration & Screening Tool (NL MIND-BEST), which is located at URL: http://miaja.tic.udc.es/Bio-AIMS/NL-MIND-BEST.php. This online tool is based on PHP/HTML/Python and MARCH-INSIDE routines. Finally we illustrated two practical uses of this server with two different experiments. In experiment 1, we report by first time Quantum QSAR study, synthesis, characterization, and experimental assay of antiplasmodial and cytotoxic activities of oxoisoaporphine alkaloids derivatives as well as NL MIND-BEST prediction of potential target proteins. In experiment 2, we report sampling, parasite culture, sample preparation, 2-DE, MALDI-TOF, and -TOF/TOF MS, MASCOT search, MM/MD 3D structure modeling, and NL MIND-BEST prediction for different peptides a new protein of the found in the proteome of the human parasite Giardia lamblia, which is promising for anti-parasite drug-targets discovery.     

Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA

Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison revealed in 45 antisense RNA control systems a 5' YUNR motif indicative for the formation of a U-turn structure in either an antisense or a target RNA loop and confirmed in the case of the hok/sok system of plasmid R1 its importance for regulation.Here, we demonstrate the importance of the 5' YUNR motif in the target RNA (RNAII) loop L1 of the replication control system of plasmid pIP501. The effect of four individual mutations in L1 was studied in vivo and in vitro. Mutations that maintained the putative U-turn or swapped it from sense to antisense RNA were silent, whereas mutations that eliminated the 5'-YUNR motif showed two- to threefold elevated copy numbers in vivo in correlation with three- to fourfold reduced inhibition rate constants of the complementary RNAIII species in vitro, whereas the half-lives of all RNAIII species were not affected. ENU probing experiments confirmed the U-turn structure for the silent mutation (N-C) and disruption of this structure upon alteration of the invariant U or inversion of the YUNR motif-containing loop. RNA secondary structure probing excluded loop size alterations as a reason for altered inhibition rates. Implications for the pathway and efficiency of RNAII/RNAIII interaction, and hence, pIP501 copy-number control, are discussed.