Deconstructing occupancy frequency distributions in stream insects: effects of body size and niche characteristics in different geographical regions

1. Occupancy frequency distributions (OFDs) are one means to study species distribution patterns, allowing the delineation of rare and common species. Very few studies have deconstructed entire assemblages by ecological or biological characteristics and subsequently examined OFDs in subgroups of species. 2. The effect of deconstruction of entire assemblages by niche breadth, niche position or body size classes on OFDs in stream insects in three drainage basins was examined. It was hypothesized that OFDs should not vary between different drainage basins, but they should be affected by deconstruction into different niche breadth, niche position or body size classes. 3. The OFDs were typically strongly right‐skewed in all drainage basins. The set of small‐sized species was strongly dominated by rare species, whereas the importance of rare species decreased with increasing body size. Further, while the OFDs of sets of species with marginal niche position or small niche breadth were strongly dominated by rare species, those of species with non‐marginal niche position or large niche breadth showed highly variable degrees of occupancy. The OFDs of non‐marginal species were even uniform in the entire data and one drainage basin, providing partial support to the a priori hypothesis. 4. Niche‐based explanations are likely to account for occupancies of marginal and small‐niched species, whereas the distributions of non‐marginal and broad‐niched species may be not only affected by niche‐based mechanisms but also by spatial dynamics. Deconstruction of OFDs by ecological and biological traits thus showed that the patterns may vary between different subgroups of species.     

Three-dimensional perfused cell culture

Compelling evidence suggests the limitation and shortcomings of the current and well established cell culture method using multi-well plates, flasks and Petri dishes. These are particularly important when cell functions are sensitive to the local microenvironment, cell–cell and cell–extracellular matrix interactions. There is a clear need for advanced cell culture systems which mimic in vivo and more physiological conditions. This review summarises and analyses recent progress in three dimensional (3D) cell culture with perfusion as the next generation cell culture tools, while excluding engineered tissue culture where three dimensional scaffold has to be used for structural support and perfusion for overcoming mass transfer control. Apart from research activities in academic community, product development in industry is also included in this review.     

Experiments with artificial nests provide evidence for ant community stratification and nest site limitation in a tropical forest

Ants are dominant in tropical forests and many species nest in hollow cavities. The manner in which species are vertically stratified in these complex habitats is not known, with lack of nest sites being proposed to limit ant populations. Here, we assess ant community stratification and nest site limitation in a lowland rainforest in New Guinea using experimental addition of artificial bamboo nests of two cavity sizes (small: ~12 mm large: ~32 mm diameter) placed at ground level, in the understorey, and in the canopy. We also conducted a pilot experiment to test the utility of nest translocation. Nests were checked for occupancy after 10 weeks and half of the occupied nests were then translocated between forest plots, while keeping same vertical position. Occupancy of small nests was much higher in the understorey and canopy than at ground level (~75% vs. ~25%). Translocation was successful, as a majority of nests was inhabited by the same species before and after translocation and there was no impact of translocation to a different plot compared to the control, except for a reduction in colony size at ground level. Our experiment demonstrates a vertical stratification in community composition of ants nesting in hollow dead cavities and shows that these ants are more nest site limited in the higher strata than at ground level. Use of small artificial cavities has great potential for future experimental studies, especially for those focused on arboreal ants, as occupancy is high and translocation does not negatively affect their colony size. Abstract in Tok Pisin is available with online material.     

Fate of mouse carcasses in a Northern Woodland

1. Small, vertebrate carrion is a significant input into terrestrial ecosystems. The relative importance of different recyclers of carrion is poorly understood because of seasonal and habitat variation and methodological differences among studies. Many studies, in particular, do not account adequately for the activity of burying beetles (Nicrophorus spp.). 2. The present work, utilising a previously unstudied woodland, addresses this concern by: placing only two carcasses in the field at one time, using microsites only once, and providing a means to easily recover successful burying beetles. 3. Burying beetles buried 77.5% of experimental mouse carcasses over their breeding season, and typically did so within three activity periods after placement (30 of 31 burials). 4. The results and a brief review suggest that burying beetles are the dominant summer competitor for small, vertebrate carrion in mid‐ and northern latitude woodlands. Information on the age of carcasses utilised by burying beetles also provides an ecological context for laboratory studies of behaviour, life history, and microbial interactions.     

Identifying fern gametophytes using DNA sequences

Identification of fern gametophytes is generally hampered by low morphological complexity. Here we explore an alternative: DNA‐based identification. We obtained a plastid rbcL sequence from a sterile gametophyte of unknown origin (cultivated for more than 30 years) and employed blast to determine its affinities. Using this approach, we identified the gametophyte as Osmunda regalis. To evaluate the robustness of this determination, and the usefulness of rbcL in differentiating among species, we conducted a phylogenetic analysis of osmundaceous fern sequences. Based on our results, it is evident that DNA‐based identification has considerable potential in exploring the ecology of fern gametophytes.     

Survival of Escherichia coli in the environment: fundamental and public health aspects

In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism''s survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health.     

Structural Decomposition Analysis of Raw Material Consumption

The aim of this article is to quantify the drivers for the changes in raw material consumption (domestic material consumption expressed in the form of all materials extracted and used in the production phase) in terms of technology, which refers to the concept of sustainable production; the product structure of final demand, which refers to the concept of sustainable consumption; and the volume of final demand, which is related to economic growth. We also aim to determine to what extent the technological development and a shift in product structure of the final demand compensate for the growth in final consumption volume. Therefore, we apply structural decomposition analysis (SDA) to the change in raw material consumption (RMC) of the Czech Republic between 2000 and 2007. To present the study in a broader context, we also show other material flow indicators for the Czech Republic for 2000 and 2007. Our findings of SDA show that final demand structure has a very limited effect on the change in material flows. The rapid change in final demand volume was not compensated for crude oil, metal ores, construction materials, food crops, and timber. For the material category of non‐iron metal ores, even the change in technology contributes to an increase in material flows. The largest relative increases are reported for non‐iron metal ores (38%) and construction materials (30%). The main changes in material flows related to the Czech Republic are driven by exports and enabled by imports, the main source of these increased material flows. This emphasizes the increasing role of international trade.     

Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas‐fir forest

Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and Rhizopogon vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas‐fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. Rhizopogon vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared with xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes.