Testate amoebae community structure in the moss biotopes of streams

The specific composition and community structure of testate amoebae in the moss biotopes of streams were studied in the Sura River basin (Middle Volga region). Twenty-nine species and forms were identified. The eurybiont species Trinema enchelys, Euglypha ciliata glabra, Centropyxis aerophila, Tracheleuglypha dentata, Crythion dubium, Centropyxis cassis, Trinema complanatum, and Trinema lineare are dominant. The species richness varies from 2 to 11 species per sample, the abundance is 100 to 4000 ind./g of absolutely dry moss. The degree of forest covering in the basin, hydrochemical peculiarities (the amount of biogenic elements and water hardness) of streams, the size of streams, and environmental contamination are possible factors that determine the specific character of the composition and structure of testate amoebae communities.     

Testate amoeba response to acid deposition in a Scottish peatland

Peatlands around the world are exposed to anthropogenic or volcanogenic sulphur pollution. Impacts on peatland microbial communities have been inferred from changes in gas flux but have rarely been directly studied. In this study, the impacts of sulphuric acid deposition on peatland testate amoebae were investigated by analysis of experimental plots on a Scottish peatland almost 7 years after acid treatment. Results showed reduced concentration of live amoebae and changes in community structure which remained significant even when differences in pH were accounted for. Several possible explanations for the impacts can be proposed including taphonomic processes and changes in plant communities. Previous studies have inferred a shift from methanogenic archaea to sulphate-reducing bacteria in sulphate-treated peats; it is possible that the impacts detected here might relate to this change, perhaps through testate amoeba predation on methanotrophs.     

Ecological indicators based on trophic spectrum as a tool to assess ecosystems fishing impacts

Trophic indicators were used to compare two Malian freshwater reservoirs whose main differences are based on their different fishing pressures. Data were collected from a scientific survey of small-scale fishery landings conducted in 2002/2003. The trophic levels of fish species caught by artisanal fisheries are estimated from observations of scientific fishing or from the metabase Fishbase. Important differences exist in the trophic structure of both reservoirs. In Selingue (with high fishing pressure), very few top predators are found in the catches while the low trophic level fishes increase in total catches. In Manantali (with low fishing pressure), the top predators contribute twice as much to catches compared to Selingue. Hence, the mean trophic level of catches in Selingue (2.80) is lower than in Manantali (2.97). When comparing these results with those of study made in 1994/1995, it clearly appears that the effects of the fishing pressure in Selingue are obvious through a decrease of 0.12 in the mean trophic level while in Manantali this mean level has increased by 0.33 due to a recent strategic targeting of top predators. Trophic spectra seem to be relevant tools to characterize exploited fish communities from multi-specific and multi-gear small-scale fisheries catch data.     

Palaeoecology of testate amoebae in a tropical peatland

We present the first detailed analysis of subfossil testate amoebae from a tropical peatland. Testate amoebae were analysed in a 4-m peat core from western Amazonia (Peru) and a transfer function developed from the site was applied to reconstruct changes in water table over the past ca. 8,000 years. Testate amoebae were in very low abundance in the core, especially in the lower 125 cm, due to a combination of poor preservation and obscuration by other organic matter. A modified preparation method enabled at least 50 testate amoebae to be counted in each core sample. The most abundant taxa preserved include Centropyxis aculeata, Hyalosphenia subflava, Phryganella acropodia and Trigonopyxis arcula. Centropyxis aculeata, an unambiguous wet indicator, is variably present and indicates several phases of near-surface water table. Our work shows that even degraded, low-abundance assemblages of testate amoebae can provide useful information regarding the long-term ecohydrological developmental history of tropical peatlands.     

Testate amoebae community pattern in different types of boundary structures at the water-land contact zone

The patterns of changes in the species richness, abundance, species composition, and species structure of the testate amoebae community along six different types of water-land boundaries in the Medveditsa River (Don river Basin) were studied, namely, a new boundary, terrigenous and reogeneous edges, reogeneous and terrigenous hemiecotones, and the full ecotone. The testate amoebae communities are divided into terrestrial and aquatic variants for all types of boundaries. Hydrophilic species of the genera Arcella, Diffugia, Cyphoderia, and Pseudodifflugia dominate in the aquatic types of communities while pedobiont and eurybiont groups from the genera Centropyxis, Euglypha, Plagiopyxis, and Trinema are characteristic of the terrestrial communities. A decrease in the abundance and species richness of testate amoebae in the boundary zones was detected.     

Evaluating the use of dominant microbial consumers (testate amoebae) as indicators of blanket peatland restoration

Peatlands represent globally-important ecosystems and carbon stores. However, large areas of peatland have been drained for agriculture, or peat has been harvested for use as fuel or in horticulture. Increasingly, these landscapes are being restored through ditch blocking and rewetting primarily to improve biodiversity and promote peat accumulation. To date we have little knowledge of how these interventions influence the microbial communities in peatlands. We compared the responses of dominant microbial consumers (testate amoebae) to drainage ditch restoration relative to unblocked ditches in a UK upland blanket peatland (Migneint, North Wales). Two techniques were used for restoration: (i) dammed ditches with re-profiling; and (ii) dammed ditches with pools of open water behind each dam. Testate communities in the inter-ditch areas changed markedly over time and between treatments illustrating the potential of this group of organisms as indicators of blanket peatland restoration status. However, the responses of testate amoebae to peat rewetting associated with restoration were partially obscured by inter-annual variability in weather conditions through the course of the experiment. Although there was considerable variability in the response of testate amoebae communities to peatland drain blocking, there were clearly more pronounced changes in samples from the dammed and reprofiled treatments including an increase in diversity, and the appearance of unambiguous wet-indicator species in relatively high abundances (including Amphitrema stenostoma, Archerella flavum, Arcella discoides type, Difflugia bacillifera and Difflugia bacillarium). This reflects a shift towards overall wetter conditions across the site and the creation of new habitats. However, water-table was not a significant control on testate amoebae in this case, suggesting a poor relationship between water table and surface moisture in this sloping blanket peatland. Our findings highlight the potential of testate amoebae as bioindicators of peatland restoration success; however, there is a need for caution as mechanisms driving change in the microbial communities may be more complex than first assumed. Several factors need to be taken into account when implementing biomonitoring studies in peatlands including: (i) the natural variability of the peatland ecosystem under changing weather conditions; (ii) any disturbance connected with the restoration procedures; and (iii) the timescales over which the ecosystem responds to the management intervention. Our results also suggest an indicator species approach based on population dynamics may be more appropriate for biomonitoring peatland restoration than examining changes at the community level.     

Testate amoebae colonizing a newly exposed land surface are of airborne origin

We hypothesized that at the very beginning of terrestrial ecosystem development, airborne testate amoebae play a pivotal role in facilitating organismic colonization and related soil processes. We, therefore, analyzed size and quantity of airborne testate amoebae and immigration and colonization success of airborne testate amoebae on a new land surface (experimental site “Chicken Creek”, artificial post-mining water catchment). Within an altogether 91-day exposure of 70 adhesive traps, 12 species of testate amoebae were identified to be of airborne origin. Phryganella acropodia (51% of all individuals found, diameter about 35–45 μm) and Centropyxis sphagnicola (23% of all individuals found, longest axis about 55–68 μm), occurred most frequently in the adhesive traps. We extrapolated an aerial amoeba deposition of 61 individuals d⁻¹ m⁻² (living and dead individuals combined). Although it would be necessary to have a longer sequence (some additional years), our analysis of the “target substrate” of aerial immigration (catchment site) may point to a shift from a stochastic (variable) beginning of community assembly to a more deterministic (stable) course. This shift was assigned to an age of seven years of initial soil development. Although experienced specialists are necessary to conduct these time-consuming studies, the presented data suggest that terrestrial amoebae are suitable indicators for initial ecosystem development and utilization.     

The utility of DNA barcoding as a tool to assess the success of ecological restoration using Hemiptera as a biological indicator

DNA barcoding uses a short, standardized DNA fragment to sort individuals into species. This molecular technique has applications in fields including ecology, evolution, conservation, and biogeography. In ecological applications such as species monitoring and habitat restoration, its potential has not been fully realized and implemented. Invertebrates are excellent biological indicators, as changes in species diversity or community assemblage provide important insights into the condition of, or changes in, the environment. This information is particularly useful within the context of restoration ecology. In this study, DNA barcoding is used to assess the potential of Hemiptera as a biological indicator of restoration success for the Buffelsdraai Landfill Site Community Reforestation Project (Durban, South Africa). A total of 393 Hemiptera specimens were collected from sites reforested at distinct phases (plots reforested in 2010, 2012, and 2015) and two reference sites (natural forest and grassland). The Hemiptera species composition and assemblage were assessed by analyzing diversity indices, ordination, unweighted pair‐group average cluster analysis, and phylogenetic analysis. Hemiptera species composition varied significantly across the chronologically different reforested sites, with a higher species richness observed in the older reforested plots. This suggests that Hemiptera diversity can be used to track restoration success, even over the small temporal scale used in this study. This study highlights the utility of DNA barcoding as a taxonomic sorting tool both to monitor ecological restoration and to discover specific taxa within Hemiptera that may be useful biological indicators.     

The feasibility of vibration as a tool to assess spinal integrity

As the majority of back pain is thought to be mechanical in origin, quantitative tests designed to assess spinal mechanics may provide information about its etiology and treatment. This paper describes the application of structural vibration testing in the spine, its reliability and ability to discriminate between different structural states. In each of five cadaveric pigs, tri-axial accelerometers were fixed to the spinouses of L1-5 and short-duration vibrations (0-2000Hz) were applied to the L3 spinous exclusively. The frequency response function (FRF) of each sensor axis was calculated and the process repeated. Additional FRF data were obtained after the creation of multiple structural alterations including joining of adjacent vertebrae and scalpel transections of each lumbar disc. To assess the reliability of structural vibration testing, the intra-class correlation coefficient was calculated for FRFs obtained from each structural state in each specimen. To determine if structural vibration testing could distinguish between different structural states, correlation coefficients were calculated between FRFs from each structural state and a baseline condition. Most intra-class correlation coefficients (3740) were in the excellent range (>0.75), while FRF data from each structural state were found to be significantly different from that of the baseline state (p<0.05). These results indicate that structural vibration testing can be used to obtain reliable FRFs that are sensitive to alterations in the spine's structure. In the future, we hope to refine this technique to obtain specific diagnoses of, and/or assess therapies for, common spinal disorders.     

A proposal to use plant demographic data to assess potential weed biological control agents impacts on non-target plant populations

Weed biocontrol programs aim to reduce the spread and population growth rate of the target plant while stabilizing or increasing populations of those native species considered under threat by invasive plants. This goal is not unique to weed biocontrol but applies to all other invasive plant management techniques, though such information is rarely collected. Without this information, success of management interventions can be ambiguous, and regulatory agencies, the public, policy makers, funders and land managers cannot be held accountable for chosen treatments. A fundamental reform, including use of demographic studies and long-term assessments, are essential to guide weed biocontrol programs. We propose to add use of plant demography (an assessment of how environmental factors and ecological interactions, for example competition, disease or herbivory, may affect plant populations by altering survival, growth, development and reproductive rates of plant individuals) during host specificity risk assessments of potential biological control agents. Demographic models can refine assessments of potential impacts for those plant species that experience some feeding or larval development during host specificity testing. Our proposed approach to focus on impact on plant demography instead of attack on plant individuals is useful in appropriately gauging threats potential weed biocontrol agents may pose to non-target species after field release.     

Testate amoebae analysis in ecological and paleoecological studies of wetlands: past, present and future

Testate amoebae are an abundant and diverse polyphyletic group of shelled protozoa living in aquatic to moist habitats ranging from estuaries to lakes, rivers, wetlands, soils, litter, and moss habitats. Owing to the preservation of shells in sediments, testate amoebae are useful proxy indicators complementary to long-established indicators such as pollen and spores or macrofossils. Their primary use to date has been for inferring past moisture conditions and climate in ombrotrophic peatlands and, to a lesser extent, to infer pH in peatlands and the trophic or nutrient status of lakes. Recent research on these organisms suggests other possible uses in paleoecology and ecology such as sea-level reconstruction in estuarine environments, as indicators of soil or air pollution, and monitoring recovery of peatland. We review the past and present use of testate amoebae, the challenges in current research, and provide some ideas on future research directions.     

Global characterisation factors to assess land use impacts on biotic production

Purpose

The inclusion of land-use activities in life cycle assessment (LCA) has been subject to much debate in the LCA community. Despite the recent methodological developments in this area, the impacts of land occupation and transformation on its long-term ability to produce biomass (referred to here as biotic production potential [BPP]) — an important endpoint for the Area of Protection (AoP) Natural Resources — have been largely excluded from LCAs partly due to the lack of life cycle impact assessment methods.

Materials and methods

Several possible methods/indicators for BPP associated with biomass, carbon balance, soil erosion, salinisation, energy, soil biota and soil organic matter (SOM) were evaluated. The latter indicator was considered the most appropriate for LCA, and characterisation factors for eight land use types at the climate region level were developed.

Results and discussion

Most of the indicators assessed address land-use impacts satisfactorily for land uses that include biotic production of some kind (agriculture or silviculture). However, some fail to address potentially important land use impacts from other life cycle stages, such as those arising from transport. It is shown that the change in soil organic carbon (SOC) can be used as an indicator for impacts on BPP, because SOC relates to a range of soil properties responsible for soil resilience and fertility.

Conclusions

The characterisation factors developed suggest that the proposed approach to characterize land use impacts on BBP, despite its limitations, is both possible and robust. The availability of land-use-specific and biogeographically differentiated data on SOC makes BPP impact assessments operational. The characterisation factors provided allow for the assessment of land-use impacts on BPP, regardless of where they occur thus enabling more complete LCAs of products and services. Existing databases on every country’s terrestrial carbon stocks and land use enable the operability of this method. Furthermore, BPP impacts will be better assessed by this approach as increasingly spatially specific data are available for all geographical regions of the world at a large scale. The characterisation factors developed are applied to the case studies (Part D of this special issue), which show the practical issues related to their implementation.     

The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny

Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.     

Fluctuation as a tool of biological molecular machines

The mechanism for biological molecular machines is different from that of man-made ones. Recently single molecule measurements and other experiments have revealed unique operations where biological molecular machines exploit thermal fluctuation in response to small inputs of energy or signals to achieve their function. Understanding and applying this mechanism to engineering offers new artificial machine designs.     

Statistical models of invertebrate distribution on Macquarie Island: a tool to assess climate change and local human impacts

Sub-Antarctic islands are good model systems in which to study the ecological effects of human impacts, particularly global climate change and alien species. Invertebrates form a central component of these ecosystems. We conducted a stratified survey of 69 sites on sub-Antarctic Macquarie Island and used logistic regression models to describe the distribution of 14 abundant invertebrate species. We also developed a statistical model of windspeed based on topography. The distributions of individual species were described by different combinations of aspect, altitude and vegetation type. Ordination of sites based on species composition showed strong effects of altitude and vegetation on invertebrate assemblages. The species distribution models provide a tool for detecting, monitoring and predicting effects of climate change and alien species on biota and ecosystem processes. Accepted: 30 August 1998     

Brevibacillus as a biological tool: a short review

The significance of Brevibacillus has been documented scientifically in the published literature and commercially in heterologous recombinant protein catalogs. Brevibacillus is one of the most widespread genera of Gram-positive bacteria, recorded from the diverse environmental habitats. The high growth rate, better transformation efficiency by electroporation, availability of shuttle vectors, production of negligible amount of extracellular protease, and the constitutive expression of heterologous proteins make some strains of this genus excellent laboratory models. Regarding biotechnological applications, this genus continues to be a source of various enzymes of great biotechnological interest due to their ability to biodegrade low density polyethylene, ability to act as a candidate bio-control agent, and more recently acknowledged as a tool for the overexpression. This article reviews the properties of Brevibacillus spp. as better biological tools with varied applications.     

The biological race concept as a research tool

In present day research in human biology, the validity of the concept of biological race rests on its utility as a research tool. The methodology of this research into human biological variability is a multidimensional application of the comparative method, utilizing, as one dimension, genetic distance. The body of this paper suggests two generalizing principles for the establishment of genetic distance. Genetic distance may occur due to physical or temporal isolation or in conjunction with environmental differences. A brief analysis of the fifteenth century human populations examines the relationship between these principles and presently used racial taxonomic systems. It is concluded that race may be defined operationally as a rough measure of genetic distance in human populations and as such may function as an informational construct in the multidisciplinary area of research in human biology.