Effect of investigator disturbance in experimental forensic entomology: succession and community composition

Carrion insect succession studies have historically used repeated sampling of single or a few carcasses to produce data, either weighing the carcasses, removing a qualitative subsample of the fauna present, or both, on every visit over the course of decomposition and succession. This study, conducted in a set of related experimental hypotheses with two trials in a single season, investigated the effect that repeated sampling has on insect succession, determined by the number of taxa collected on each visit and by community composition. Each trial lasted at least 21 days, with daily visits on the first 14 days. Rat carcasses used in this study were all placed in the field on the same day, but then either sampled qualitatively on every visit (similar to most succession studies) or ignored until a given day of succession, when they were sampled qualitatively (a subsample) and then destructively sampled in their entirety. Carcasses sampled on every visit were in two groups: those from which only a sample of the fauna was taken and those from which a sample of fauna was taken and the carcass was weighed for biomass determination. Of the carcasses visited only once, the number of taxa in subsamples was compared to the actual number of taxa present when the carcass was destructively sampled to determine if the subsamples adequately represented the total carcass fauna. Data from the qualitative subsamples of those carcasses visited only once were also compared to data collected from carcasses that were sampled on every visit to investigate the effect of the repeated sampling. A total of 39 taxa were collected from carcasses during the study and the component taxa are discussed individually in relation to their role in succession. Number of taxa differed on only one visit between the qualitative subsamples and the actual number of taxa present, primarily because the organisms missed by the qualitative sampling were cryptic (hidden deep within body cavities) or rare (only represented by very few specimens). There were no differences discovered between number of taxa in qualitative subsamples from carcasses sampled repeatedly (with or without biomass determinations) and those sampled only a single time. Community composition differed considerably in later stages of decomposition, with disparate communities due primarily to small numbers of rare taxa. These results indicate that the methods used historically for community composition determination in experimental forensic entomology are generally adequate.     

Behavior of filamentous cyanobacteria in laboratory culture

The observations of a laboratory culture of filamentous cyanobacteria revealed a complex of behavioral responses of their community, which maintain their activity as an integrated entity. A number of structures formed in the course of filament regrouping were revealed and described; their possible structural and functional analogues in eukaryotic organisms were determined. It is assumed that the behavioral reactions of the filaments help to maintain the integrity of the community at the stage prior to the formation of the structural bonds between its elements.     

Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.     

Effects of continuous cucumber cropping and alternative rotations under protected cultivation on soil microbial community diversity

The diversity of soil microbial communities as affected by continuous cucumber cropping and alternative rotations under protected cultivation were evaluated using community level physiological profiles (CLPP) and random amplified polymorphic DNA (RAPD) analysis. The soils were selected from six cucumber cropping systems, which cover two cropping practices (rotation and continuous cropping) and a wide spectrum for cucumber cropping history under protected cultivation. Shannon–Weaver index and multivariate analysis were performed to characterize variations in soil microbial communities. Both CLPP and RAPD techniques demonstrated that cropping systems and plastic-greenhouse cultivation could considerably affect soil microbial functional diversity and DNA sequence diversity. The open-field soil had the highest Shannon–Weaver index (3.27 for CLPP and 1.50 for RAPD), whereas the lowest value occurred in the 7-year continuous protected cultivation soil (3.27 for CLPP and 1.50 for RAPD). The results demonstrated that continuous plastic-greenhouse cultivation and management can cause the reduction in the species diversity of the biota. Higher Shannon–Weaver index and coefficients of DNA sequence similarity were found in soils under rotation than those under continuous cropping. Cluster analysis also indicated that microbial community profiles of continuous cultivation soils were different from profiles of rotation soils. The reduction in diversity of microbial communities found in continuous cultivation soils as compared with rotation soils might be due to the differences in the quantity, quality and distribution of soil organic matter. Section Editor: D. E. Crowley     

Competition may determine the diversity of transposable elements

Transposable elements are genomic parasites that replicate independently from their hosts. They harm their hosts by causing mutations or genomic rearrangements, and most organisms have evolved various mechanisms to suppress their activity. The evolutionary dynamics of transposons in insects, fish, birds and mammals are dramatically different. Mammalian genomes contain few, very abundant but relatively inactive transposon strains, while Drosophila and fish species harbour diverse strains, which typically have low abundance but are much more virulent. We hypothesise that the variation in the diversity and activity of transposable elements between various animal genomes is caused by the differences in the host defence mechanisms against transposon activity. In recent years RNAi, a mechanism capable of gene, virus and transposon silencing has been discovered. We model RNAi as a density dependant mechanism of defence, which can cause competition among transposons depending on its specificity, and test its predictions using the complete Caenorhabditis elegans, Drosophila melanogaster, Fugu rubripes, chicken, mouse, rat and human genome sequences.     

Persistence and stability of macroinvertebrate communities in streams of Denali National Park, Alaska: implications for biological monitoring

1. Macroinvertebrate communities were studied from 1994 to 2001/2002 (except 1997) in six streams in Denali National Park, interior Alaska. All six streams were potential reference streams with no known impairment. 2. Abundance of individual taxa varied markedly from year to year. Overall, abundance decreased over the study period, particularly with respect to mayflies. Stonefly taxa showed lower persistence and were sometimes absent from a stream in any particular year. 3. Mean community persistence for the six streams, as measured by Jaccard's similarity coefficients between years, varied from 0.48 in the year pair 1999–2000 to 0.78 in 1998–99. Tattler Creek (a small stable stream) supported the most persistent macroinvertebrate community and Highway Pass Creek (a small, unstable creek) the least. Mean community persistence showed a significant relationship with mean winter snowfall (November to March) for the six streams. 4. The highest community compositional stability was found in Tattler Creek and the lowest in Highway Pass Creek, but stability varied markedly over time for the six streams, peaking in 1994–95 and reaching a minimum in 2000–01. Compositional stability was significantly related to the Pfankuch Index of channel stability. 5. The composition metrics % Chironomidae, % dominant taxa, %EPT, % Ephemeroptera and % Plecoptera, employed as part of the Alaska Stream Condition Index, varied over almost their entire range in these pristine streams across the 9 years of the study. 6. This study demonstrates the wide range of natural variation that occurs in benthic macroinvertebrate communities in these pristine central Alaskan streams, potentially limiting the applicability of composition metrics for the biological monitoring of water quality in these systems.     

Spatial patterns of fish communities along two estuarine gradients in southern Florida

In tropical and subtropical estuaries, gradients of primary productivity and salinity are generally invoked to explain patterns in community structure and standing crops of fishes. We documented spatial and temporal patterns in fish community structure and standing crops along salinity and nutrient gradients in two subtropical drainages of Everglades National Park, USA. The Shark River drains into the Gulf of Mexico and experiences diurnal tides carrying relatively nutrient enriched waters, while Taylor River is more hydrologically isolated by the oligohaline Florida Bay and experiences no discernable lunar tides. We hypothesized that the more nutrient enriched system would support higher standing crops of fishes in its mangrove zone. We collected 50 species of fish from January 2000 to April 2004 at six sampling sites spanning fresh to brackish salinities in both the Shark and Taylor River drainages. Contrary to expectations, we observed lower standing crops and density of fishes in the more nutrient rich tidal mangrove forest of the Shark River than in the less nutrient rich mangrove habitats bordering the Taylor River. Tidal mangrove habitats in the Shark River were dominated by salt-tolerant fish and displayed lower species richness than mangrove communities in the Taylor River, which included more freshwater taxa and yielded relatively higher richness. These differences were maintained even after controlling for salinity at the time of sampling. Small-scale topographic relief differs between these two systems, possibly created by tidal action in the Shark River. We propose that this difference in topography limits movement of fishes from upstream marshes into the fringing mangrove forest in the Shark River system, but not the Taylor River system. Understanding the influence of habitat structure, including connectivity, on aquatic communities is important to anticipate effects of construction and operational alternatives associated with restoration of the Everglades ecosystem.     

Stability and Persistence of Alpine Stream Macroinvertebrate Communities and the Role of Physicochemical Habitat Variables

Macroinvertebrate communities in alpine streams have rarely been examined over more than two consecutive years or at sub-monthly temporal resolution during the summer melt season, in relation to a range of stream physicochemical habitat measurements. This paper addresses these research gaps by investigating the inter- (late melt season, 1996–2003) and intra-annual (bi-weekly; June–September, 2002–2003) community compositional stability and persistence of three alpine streams fed from different water sources (snow, glaciers and groundwater) in the Taillon–Gabiétous catchment, French Pyrénées. Inter-annual community stability and persistence decreased from 1996 to 2003; however, groundwater stream communities changed less than those in the main glacial stream. Intra-annual community stability varied spatially and temporally, particularly in relation to water quality variables (water temperature and suspended sediment concentration); water quantity (stream discharge) was less important perhaps due to taxa possessing adaptations to flow variability. The 15 most abundant taxa were consistently more stable and persistent than the entire stream community suggesting a common pool of taxa in these streams. Overall, the results support the view that streams originating from different alpine water sources are characterised by distinct benthic macroinvertebrate assemblages, and demonstrate the value of sampling at nested temporal scales (inter-annual to bi-weekly) for understanding how these stream ecosystems function.     

The Effects of Hydrology on Plankton Biomass in Shallow Lakes of the Pampa Plain

Climatic and hydrological variability is usually high in the Pampa Plain (Argentina). However it has not studied yet how this variability may affect the phytoplankton and zooplankton biomass and community structure in aquatic systems of this region. The main purpose of this study was to assess flushing effects on nutrient and plankton dynamics in two interconnected very shallow lakes of the Pampa Plain. In order to study the impact of hydrology on the plankton biomass and community structure, we compared the summer plankton community among three consecutive years with contrasting hydrological characteristics. Water residence time varied an order of magnitude among years and this variability was correlated to strong changes in physicochemical and biological lake characteristics. Depending on the water discharge level, the hydrological regime within the lakes ranged from lentic to more lotic conditions. Nutrient and phytoplankton biomass were positively related to water discharges. During high flushing periods, nutrients import from intensive agriculture lands leads to a dramatic increase in trophic conditions. On the other hand, macrozooplankton biomass was positively related to water residence time and showed a dramatic decrease during high flushing years. Rotifers biomass was not affected by interannual water discharge variability during the study period. Our results support that in case of lakes with high flushing rates, zooplankton development is dependent on water residence time and that hydrology may have stronger effects on macrozooplankton biomass than top-down control by planktivores.     

Relationship between Riparian Vegetation and Stream Benthic Communities at Three Spatial Scales

We examined the influence of riparian vegetation on macroinvertebrate community structure in streams of the Upper Thames River watershed in southwestern Ontario. Thirty-three μ-basins (129–1458 ha) were used to identify land cover variables that influenced stream macroinvertebrates. Micro-basins represented the entire drainage area of study streams and were similar in stream order (first, second) and land cover (agricultural or forest; no urban). We described the structure and composition of riparian vegetation and benthic macroinvertebrate communities at the outflow reach. The nature of the land cover was quantified for the stream network buffer (30 m) and the whole μ-basin. The objective of this study was to measure the magnitude and nature of the relationship between the riparian vegetation and benthic macroinvertebrate community at the outflow reach, stream network buffer, and whole μ-basin scales. Taxon richness (including total number of Ephemeroptera, Plecoptera, and Trichoptera taxa) and Simpson’s diversity of the macroinvertebrate community all increased with increased tree cover in the riparian zone at the outflow reach scale. Simpson’s equitability was lower with greater agricultural land cover in the stream network buffer. No relationship between the macroinvertebrate community and land cover was found at the whole μ-basin scale. Analysis of the influence of land cover on stream communities within a spatial hierarchy is important for understanding the interactions of stream ecosystems with their adjacent landscapes.