Uncertainty in Diatom Assessment: Sampling, Identification and Counting Variation

Despite the widespread application of periphytic diatoms to water quality assessment at a regional level, there is no standard European sampling protocol or associated assessment metrics. Furthermore, relatively little is known about the uncertainty in the results of such assessments. One of the objectives of the European project for the Standardisation of River Classifications (STAR) is to improve and standardise diatom assessment methods. An extensive diatom ring test, together with an audit of the project results, provided a better understanding and quantification of the uncertainty in quality assessment of running waters using diatoms. The variation in multimetric analysis shows that the choice of site and substrate for sampling, the inter-operator differences in diatom taxonomy and the counting techniques are the primary sources of uncertainty. To some extent, this variation also reveals the robustness of specific metrics in relation to the sources of uncertainty. Of the three most common substrate types tested (stone, macrophyte and sediment), macrophytes emerge as the most preferred substrate for diatom sampling when performing multimetric water quality assessment.     

Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species

Size homoplasy was analyzed at microsatellite loci by sequencing electromorphs, that is, variants of the same size (base pairs). This study was conducted using five interrupted and/or compound loci in three invertebrate species, the honey bee Apis mellifera, the bumble bee Bombus terrestris, and the freshwater snail Bulinus truncatus. The 15 electromorphs sequenced turned out to hide 31 alleles (i.e., variants identical in sequence). Variation in the amount of size homoplasy was detected among electromorphs and loci. From one to seven alleles were detected per electromorph, and one locus did not show any size homoplasy in both bee species. The amount of size homoplasy was related to the sequencing effort, since the number of alleles was correlated with the number of copies of electromorphs sequenced, but also with the molecular structure of the core sequence at each locus. Size homoplasy within populations was detected only three times, meaning that size homoplasy was detected mostly among populations. We analyzed population structure, estimating F _st and a genetic distance, based on either electromorphs or alleles. Whereas little difference was found in A. mellifera, uncovering size homoplasy led to a more marked population structure in B. terrestris and B. truncatus. We also showed in A. mellifera that the detection of size homoplasy may alter phylogenetic reconstructions. Received: 21 July 1997 / Accepted: 29 January 1998     

The Seasonal Succession of Biotic Communities in Wetlands of the Tropical Wet-and-Dry Climatic Zone: V. Aquatic Invertebrate Communities in the Pantanal of Mato Grosso,Brazil

The results of a 3 1/2 year study in the Pantanal of Mato Grosso revealed that the life cycles of the invertebrates are profoundly influenced by the annual alternations between a period of very heavy rainfall and several months during which almost no rain falls. A very pronounced effect on the biota is the elimination of many species present in neighboring regions but without the ability to survive periods of adverse conditions resulting from the alternations between flood and dryness. However, those species with suitable adaptations are able to produce very large populations. The annual activity cycles of the invertebrates must not only be timed to the seasonal weather conditions but also to the activities of other species in the food web. They must be adapted to periods of surplus alternating with scarcity of food and predator pressure, which exert great influence on the development of the populations. Of the 256 species considered, most have the ability to produce offspring throughout the year whenever conditions are conducive, but there are also a considerable number which have life cycles apparently including only one reproductive period each year. The general effect of the seasonal changes on the aquatic community of the wetland is to greatly reduce species diversity but to allow the production of vast numbers of those species that have successfully adapted to the conditions. This adaptation of the aquatic species usually entails a dormant stage or a terrestrial one as well as a considerable rate of reproduction to offset losses during periods of unfavorable conditions. The invertebrate fauna includes several taxa represented overwhelmingly by cosmopolitan and circumtropical species, including Rotifera and Gastrotricha, but the great majority of the species are endemic to South America.     

Searching for Optimal Sensory Signals: Iterative Stimulus Reconstruction in Closed-Loop Experiments

Shaped by evolutionary processes, sensory systems often represent behaviorally relevant stimuli with higher fidelity than other stimuli. The stimulus dependence of neural reliability could therefore provide an important clue in a search for relevant sensory signals. We explore this relation and introduce a novel iterative algorithm that allows one to find stimuli that are reliably represented by the sensory system under study. To assess the quality of a neural representation, we use stimulus reconstruction methods. The algorithm starts with the presentation of an initial stimulus (e.g. white noise). The evoked spike train is recorded and used to reconstruct the stimulus online. Within a closed-loop setup, this reconstruction is then played back to the sensory system. Iterating this procedure, the newly generated stimuli can be better and better reconstructed. We demonstrate the feasibility of this method by applying it to auditory receptor neurons in locusts. Our data show that the optimal stimuli often exhibit pronounced sub-threshold periods that are interrupted by short, yet intense pulses. Similar results are obtained for simple model neurons and suggest that these stimuli are encoded with high reliability by a large class of neurons.     

Impacts of an Invasive Non-Native Annual Weed,Impatiens glandulifera,on Above- and Below-Ground Invertebrate Communities in the United Kingdom

Vegetation community composition and the above- and below-ground invertebrate communities are linked intrinsically, though few studies have assessed the impact of non-native plants on both these parts of the community together. We evaluated the differences in the above- (foliage- and ground-dwelling) and below-ground invertebrate communities in nine uninvaded plots and nine plots invaded by the annual invasive species Impatiens glandulifera, in the UK during 2007 and 2008. Over 139,000 invertebrates were identified into distinct taxa and categorised into functional feeding groups. The impact of I. glandulifera on the vegetation and invertebrate community composition was evaluated using multivariate statistics including principal response curves (PRC) and redundancy analysis (RDA). In the foliage-dwelling community, all functional feeding groups were less abundant in the invaded plots, and the species richness of Coleoptera and Heteroptera was significantly reduced. In the ground-dwelling community, herbivores, detritivores, and predators were all significantly less abundant in the invaded plots. In contrast, these functional groups in the below-ground community appeared to be largely unaffected, and even positively associated with the presence of I. glandulifera. Although the cover of I. glandulifera decreased in the invaded plots in the second year of the study, only the below-ground invertebrate community showed a significant response. These results indicate that the above- and below-ground invertebrate communities respond differently to the presence of I. glandulifera, and these community shifts can potentially lead to a habitat less biologically diverse than surrounding native communities; which could have negative impacts on higher trophic levels and ecosystem functioning.     

Searching for the Optimal Combinations of Regulatory Anxiolytic Peptides: A Theoretical Basis

A vector method is proposed to initially select the complexes of regulatory peptides (RPs) with certain functional characteristics. As the result of a theoretical search for the optimal combinations of anxiolytic RPs with different spectra of side effects, the following complexes are proposed for subsequent experimental investigation: NPY–ANP, NPY–SP, NPY–NT, NPY–CGRP, NPY–DSIP, NPY–MIF-1, NPY–SP–MIF-1, NPY–ANP–DSIP, and NPY–CGRP–DSIP.     

Protocol for Optimal Quality and Quantity Pollen DNA Isolation from Honey Samples

The present study illustrates an optimized sample preparation method for an efficient DNA isolation from low quantities of honey samples. A conventional PCR-based method was validated, which potentially enables characterization of plant species from as low as 3 ml bee-honey samples. In the present study, an anionic detergent was used to lyse the hard outer pollen shell, and DTT was used for isolation of thiolated DNA, as it might facilitate protein digestion and assists in releasing the DNA into solution, as well as reduce cross-links between DNA and other biomolecules. Optimization of both the quantity of honey sample and time duration for DNA isolation was done during development of this method. With the use of this method, chloroplast DNA was successfully PCR amplified and sequenced from honey DNA samples.     

Sampling Effects on Food Availability Estimates: Phenological Method,Sample Size,and Species Composition1

It is currently recognized that the method used to collect phenology data can affect the resulting pattern. However, to date, the underlying influences have not been examined. To examine potential methodological biases, we investigated the effects of phenological method, sample size, and species composition on phenological patterns using data collected to estimate food availability for three primate species in Ranomafana National Park, Madagascar. Two phenological methods were compared: selected tree observations and systematic transect monitoring. By generating bootstrapped subsamples derived from the transect tree data set, we simulated two selected tree data sets and subsequently compared the observed and bootstrapped values. Although the observed values fell within the bootstrapped confidence inrervals, suggesting no significant effects of sampling protocol or sample size, additional lines of evidence suggest otherwise. Observed samples composed of different plant species, whether based on species attributes such as life-form or categories such as food versus nonfood plants, consistently produced different phenological patterns. Wide confidence intervals of the bootstrapped samples indicate high individual variation in reproductive activity within the species sampled. Finally, we compared how well the selected tree and the transect methods represented food items used by all three primate species studied and found that transect methods sampled a wider diversity of food items, including rare foods, and a higher percentage of main primate food items than selected tree methods.     

Recovery in Diversity of Fish and Invertebrate Communities Following Remediation of a Polluted Stream: Investigating Causal Relationships

Spatial and temporal responses of biota to anthropogenic disturbance were measured over a 15 year period in a contaminated stream undergoing remediation and recovery. Along the spatial gradient of the stream, levels of contaminants decreased downstream along with improved responses of instream biota at several levels of biological organization. Recovery of the biota in this stream over the 15 year study period is demonstrated by the temporal relationships between levels of decreasing contaminants and the concomitant responses of the periphyton, macroinvertebrate, and fish communities and changes in the various bioindicators of individual fish health. Decreases in contaminants over a temporal scale were followed closely by an improvement in physiological and organismal-level indicators, increases in the diversity of macroinvertebrate and fish communities, and rapid increases in the chlorophyll a biomass and photosynthesis rate of the periphyton community. These results emphasize that field studies designed to assess and evaluate the effectiveness of restoration activities on stream recovery should incorporate a variety of response endpoints ranging from sensitive and short-term responses to long-term but ecological relevant indicators of change. The close spatial and temporal relationships observed between changes in physicochemical factors and positive responses in various components of the stream biota over the 15-year study period suggest a strong cause and effect relationship between remediation activities and stream recovery. Understanding causal relationships and the mechanistic processes between environmental stressors, stress responses of biota, and the recovery process is important in the effective management and restoration of aquatic ecosystems. An erratum to this article is available at .     

Searching for DNA lesions: structural evidence for lower- and higher-affinity DNA binding conformations of human alkyladenine DNA glycosylase

To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, like AAG, to interact with DNA using two affinities: a lower-affinity interaction in a searching process and a higher-affinity interaction for catalytic repair. Here, we present crystal structures of AAG trapped in two DNA-bound states. The lower-affinity depiction allows us to investigate, for the first time, the conformation of this protein in the absence of a tightly bound DNA adduct. We find that active site residues of AAG involved in binding lesion bases are in a disordered state. Furthermore, two loops that contribute significantly to the positive electrostatic surface of AAG are disordered. Additionally, a higher-affinity state of AAG captured here provides a fortuitous snapshot of how this enzyme interacts with a DNA adduct that resembles a one-base loop.     

Some Factors Influencing the Diversity and Species Composition of Benthic Invertebrate Communities in Twenty Arctic and Subarctic Lakes

The factors influencing the density, diversity and species composition of benthic invertebrate communities in 20 lakes in the Canadian arctic and subarctic were determined during 1975, 1976 and 1977. Despite small differences in nutrient and phytoplankton levels among the lakes, there was a strong positive correlation between these parameters and the density and diversity of the communities. Other factors, including maximum summer water temperature, lake depth and surface area had little overall effect on the communities. The densities of 2 ultra-oligotrophic chironomids (Heterotrissocladius oliveri and Micropsectra cf. groenlandica) increased markedly in cold deep lakes. However the abundance of the majority of species, most notably Procladius denticulatus, Tanytarsus sp., and Stictochironomus sp., was not effected by temperature. Other species, (Pontoporeia affinis, Monodiamesa bathyphila and Dicrotendipes nervosus) were probably restricted in their northern distribution by temperature. Surface area usually had little effect on the densities of all common species.     

Spatial Variation in Population Structure and Its Relation to Movement and the Potential for Dispersal in a Model Intertidal Invertebrate

Dispersal, the movement of an individual away from its natal or breeding ground, has been studied extensively in birds and mammals to understand the costs and benefits of movement behavior. Whether or not invertebrates disperse in response to such attributes as habitat quality or density of conspecifics remains uncertain, due in part to the difficulties in marking and recapturing invertebrates. In the upper Bay of Fundy, Canada, the intertidal amphipod Corophium volutator swims at night around the new or full moon. Furthermore, this species is regionally widespread across a large spatial scale with site-to-site variation in population structure. Such variation provides a backdrop against which biological determinants of dispersal can be investigated. We conducted a large-scale study at nine mudflats, and used swimmer density, sampled using stationary plankton nets, as a proxy for dispersing individuals. We also sampled mud residents using sediment cores over 3 sampling rounds (20–28 June, 10–17 July, 2–11 August 2010). Density of swimmers was most variable at the largest spatial scales, indicating important population-level variation. The smallest juveniles and large juveniles or small adults (particularly females) were consistently overrepresented as swimmers. Small juveniles swam at most times and locations, whereas swimming of young females decreased with increasing mud presence of young males, and swimming of large juveniles decreased with increasing mud presence of adults. Swimming in most stages increased with density of mud residents; however, proportionally less swimming occurred as total mud resident density increased. We suggest small juveniles move in search of C. volutator aggregations which possibly act as a proxy for better habitat. We also suggest large juveniles and small adults move if potential mates are limiting. Future studies can use sampling designs over large spatial scales with varying population structure to help understand the behavioral ecology of movement, and dispersal in invertebrate taxa.     

Variation between and within colonies in the termite: morphology, genomic DNA, and behaviour

We investigate the structure between and within colonies of Schedorhinotermes lamanianus (Isoptera: Rhinotermitidae) at a cluster of foraging galleries in Shimba Hills National Reserve, Kenya. Three independent methods (morphometrics of minor soldiers, multilocus fingerprinting from genomic DNA of workers, and aggression tests between workers) yielded concordant results concerning number and spatial extent of colonies as well as variation between and within colonies. At least three colonies exist in our study area. Genetic data reveal that the largest colony is genetically and spatially substructured in three subsidiary nests, which may form reproductive units. These subsidiary nests were not completely isolated as we were able to document exchange of workers. Subsidiary nests may facilitate foundation of colonies by budding which may generate isolation by distance (population viscosity).     

Antimicrobial Histones and DNA Traps in Invertebrate Immunity: EVIDENCES IN CRASSOSTREA GIGAS*

Although antimicrobial histones have been isolated from multiple metazoan species, their role in host defense has long remained unanswered. We found here that the hemocytes of the oyster Crassostrea gigas release antimicrobial H1-like and H5-like histones in response to tissue damage and infection. These antimicrobial histones were shown to be associated with extracellular DNA networks released by hemocytes, the circulating immune cells of invertebrates, in response to immune challenge. The hemocyte-released DNA was found to surround and entangle vibrios. This defense mechanism is reminiscent of the neutrophil extracellular traps (ETs) recently described in vertebrates. Importantly, oyster ETs were evidenced in vivo in hemocyte-infiltrated interstitial tissues surrounding wounds, whereas they were absent from tissues of unchallenged oysters. Consistently, antimicrobial histones were found to accumulate in oyster tissues following injury or infection with vibrios. Finally, oyster ET formation was highly dependent on the production of reactive oxygen species by hemocytes. This shows that ET formation relies on common cellular and molecular mechanisms from vertebrates to invertebrates. Altogether, our data reveal that ET formation is a defense mechanism triggered by infection and tissue damage, which is shared by relatively distant species suggesting either evolutionary conservation or convergent evolution within Bilateria.     

Spatial and Temporal Variation of Archaeal,Bacterial and Fungal Communities in Agricultural Soils

Background

Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

Methodology/Principal Findings

In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

Conclusions

Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.     

Variation in culture,isoenzyme patterns and plastid DNA in the genusDaucus

Summary To identify markers for fusion and transformation studies, cell suspension cultures of four members of theDaucus genus were examined to determine differences in culture conditions, isoenzyme patterns, and plastid DNA. The four were:D. carota subsp.sativus cv. Danvers,D. carota subsp.gummifer, D. capillifolius, andD. pusillus. Under appropriate conditions, all four grew well as liquid cell suspension cultures and regenerated from protoplasts into plants. Enzyme activities of homoserine dehydrogenase (HSDH) and alcohol dehydrogenase from cell culture extracts were analyzed on electrophoretic gels. Although only one form of HSDH was present in eachDaucus line, the rate of migration of HSDH from cv. Danvers was different from that of the other cell lines. Multiple isoenzymic forms of ADH were present in eachDaucus cultivar. Camparison of endonuclease restriction fragment patterns from plastid DNAs digested by BamHI revealed only small differences between plastid DNAs of cv. Danvers and subsp.Gummifer, whereas large differences were observed between cv. Danvers andD. pusillus plastid DNA patterns. No differences were found between cv. Danvers andD. capillifolius plastid DNA patterns when examined using eight different restriction enzymes. The data indicate that specific isoenzyme and organelle DNA restriction fragment patterns will be useful markers for precise identification of genomes of differentDaucus species in somatic hybridization experiments. This research was supported by the U.S. Department of Agriculture under Agreement 59-2246-1-1-737-0.     

Temporal Variation and Co-occurrence Patterns of Bacterial Communities in Eutrophic Lake Taihu,China

To understand the long-term and local variations of bacteria under the influence of annually re-occurred water bloom, bacterial community composition (BCC) was investigated monthly for 3 years (2009–2011) at four different sites located across Lake Taihu. The bacterial community composition was analyzed by 16S rRNA gene clone libraries and terminal restriction fragment length polymorphism. Co-occurrence patterns among bacterial taxa and environmental variables were determined through network analysis. Overall, strong seasonal variation patterns of BCC were observed whilst the spatial variations of BCC were slight in the long-term observation. However, core species bacteria persisted throughout the annual variations. Network analysis showed that the highly connected operational taxonomic units in bacteria-environment network included both the numerically dominant taxa and some functional groups with low abundance, such as Methylophilaceae and Nitrospira. Co-occurrence networks further revealed that the correlations of bacteria-bacteria could be more critical than those between environment and bacteria in structuring microbial communities, and would be a crucial driving factor of BCC in Lake Taihu.