The effects of substrate composition, quantity, and diversity on microbial activity

Variation in organic matter inputs caused by differences in plant community composition has been shown to affect microbial activity, although the mechanisms controlling these effects are not entirely understood. In this study we determine the effects of variation in substrate composition, quantity, and diversity on soil extracellular enzyme activity and respiration in laboratory microcosms. Microbial respiration responded predictably to substrate composition and quantity and was maximized by the addition of labile substrates and greater substrate quantity. However, there was no effect of substrate diversity on respiration. Substrate composition significantly affected enzyme activity. Phosphatase activity was maximized with addition of C and N together, supporting the common notion that addition of limiting resources increases investment in enzymes to acquire other limiting nutrients. Chitinase activity was maximized with the addition of chitin, suggesting that some enzymes may be stimulated by the addition of the substrate they degrade. In contrast, activities of glucosidase and peptidase were maximized by the addition of the products of these enzymes, glucose and alanine, respectively, for reasons that are unclear. Substrate diversity and quantity also stimulated enzyme activity for three and four of the six enzymes assayed, respectively. We found evidence of complementary (i.e., non-additive) effects of additions of different substrates on activity for three of the six enzymes assayed; for the remaining enzymes, effects of adding a greater diversity of substrates appeared to arise from the substrate-specific effects of those substrates included in the high-diversity treatment. Finally, in a comparison of measures of microbial respiration and enzyme activity, we found that labile C and nutrient-acquiring enzymes, not those involved in the degradation of recalcitrant compounds, were the best predictors of respiration rates. These results suggest that while composition, quantity, and diversity of inputs to microbial communities all affect microbial enzyme activity, the mechanisms controlling these relationships are unique for each particular enzyme.     

Precipitation and elephants,not fire,shape tree community composition in Serengeti National Park,Tanzania

Savannas are spatially diverse, variable and are susceptible to high rates of disturbance from fire and herbivory. There is significant interest in woody cover dynamics in relation to disturbance regimes. Less effort has been devoted to understand processes that drive tree community composition. In this study, tree species composition data collected at the landscape scale in the Serengeti were used to identify key environmental factors driving variation in species composition. A system of 38 plots clustered within 10 sites spanning the mean annual precipitation (MAP) gradient was used to assess the relative role of bottom‐up (precipitation, soil nutrients and soil texture) vs. top‐down factors (fire and elephant herbivory) on tree community composition. We developed candidate models relating tree species composition (based on multivariate community analysis) to different combinations of plot‐level environmental covariates. Results suggest that tree community composition is largely driven by MAP and is associated with elephant population density. Strikingly, we found no evidence that fire influences species compositional turnover. In a second analysis, we used structural equation model (SEM) to explore the possible direction of association between elephant density and tree species composition. We compared a model that included elephant effects on composition to one that included community composition effects on elephant density. Results suggest that variation in elephant population density across space is more likely to drive tree community composition and not vice versa. We propose that precipitation and herbivory, rather than fire, determine tree species composition in Serengeti Acacia tree community.     

Relating belowground microbial composition to the taxonomic,phylogenetic, and functional trait distributions of trees in a tropical forest

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot‐level variability in belowground microbial communities.     

Polyunsaturated fats,membrane lipids and animal longevity

Fatty acids are essential for life because they are essential components of cellular membranes. Lower animals can synthesize all four classes of fatty acids from non-lipid sources, but both omega-6 and omega-3 cannot be synthesized de novo by ‘higher’ animals and are therefore essential components of their diet. The relationship between normal variation in diet fatty acid composition and membrane fatty acid composition is little investigated. Studies in the rat show that, with respect to the general classes of fatty acids (saturated, monounsaturated and polyunsaturated) membrane fatty acid composition is homeostatically regulated despite diet variation. This is not the case for fatty acid composition of storage lipids, which responds to diet variation. Polyunsaturated fatty acids are important determinants of physical and chemical properties of membranes. They are the substrates for lipid peroxidation and it is possible to calculate a peroxidation index (PI) for a particular membrane composition. Membrane PI appears to be homeostatically regulated with respect to diet PI. Membrane fatty acid composition varies among species and membrane PI is inversely correlated to longevity in mammals, birds, bivalve molluscs, honeybees and the nematode Caenorhabditis elegans.     

Parsimony analysis and ecological communities, phytosociology, nested subsets analysis, forest fragmentation: a reply to Giannini and Keller

We suggested using parsimony analysis to study community evolution in terms of species composition and to apply these results in the context of forest fragmentation as a replacement for the so‐called “nested subsets analysis” or other phenetic synecological or phytosociological methods ( Pellens et al., 2005 ). Giannini and Keller (2007 ) took issue with this new application on the basis of three misunderstandings. We re‐emphasize that communities themselves are analyzed, not landscape parts such as forest fragments. Therefore, it must be clear that communities are analogous to taxa and landscape parts such as fragments are analogous to distributions of taxa. Community evolution is the change in community composition by immigration, emigration and local extinction. Thus, gains and losses of species should not be confused with horizontal transfer. Parsimony analysis does not necessarily group communities based on shared absences of rare species. Rare species are not necessarily absent in the same communities and these absences are not necessarily inferred to be synapomorphies after rooting. This is the main advance expected when cladistics is used instead of the previously cited phenetic methods working with overall similarity. © The Willi Hennig Society 2007.     

Dietary practices,site-specific tumors,and age-at-death relationships

When rats are given freedom of dietary choice, the quantity and composition of the diet selected varies from animal to animal, but the risk to the individual of developing a variety of neoplasms is greatly increased over that of rats fed fixed diets. The increase in frequency of tumors cannot be explained on the basis of the amount or the composition of the diet selected. However, the application of “variable selection” statistical procedures shows that there are combinations of temporal-specific interacting dietary and dietary-dependent variables that are closely linked with cancer mortality. The multi-variable statistical model for animals dying with one type of tumor is not applicable to those dying with tumors of other types or sites. In every case, the only data required to characterize the dates of death of tumor-bearing individuals are those describing the dietary practices and growth responses prior to maturity. The model for animals with pancreatic tumors is used to illustrate the extent to which dietary practices of early life are linked with the animals’ survival.     

Differential responses of soil bacteria,fungi, archaea and protists to plant species richness and plant functional group identity

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454‐pyrosequencing to analyse the soil microbial community composition in a long‐term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.     

Anthropometric measures, body composition, body fat distribution, and knee osteoarthritis in women

Objective: Increased BMI is a well‐recognized risk factor for radiographic knee osteoarthritis (rKOA); however, the contributions of the components of body composition, body fat distribution, and height to this association are not clear. Research Methods and Procedures: We examined 779 women ≥45 years of age from the Johnston County Osteoarthritis Project. Body composition was assessed using DXA, and rKOA was defined as Kellgren‐Lawrence grade ≥2. Logistic regression models examined the association between rKOA and the fourth compared with the first quartiles of anthropometric, body composition, and fat distribution measures adjusting for age, ethnicity, and prior knee injury. Results: The adjusted odds ratios and 95% confidence interval of BMI and weight were 5.27 (3.05, 9.13) and 5.28 (3.05, 9.16), respectively. In separate models, higher odds of rKOA were also found for fat mass [4.54 (2.68, 7.69)], percent fat mass [3.84 (2.26, 6.54)], lean mass [3.94 (2.22, 6.97)], and waist circumference [4.15 (2.45, 7.02)]. Waist‐to‐hip ratio was not associated with rKOA [1.45 (0.86, 2.43)], and percent lean mass was associated with lower odds [0.20 (0.11, 0.35)]. Taller women had higher odds of rKOA after adjustment for BMI [1.77 (1.05, 3.00)]. Discussion: This study confirms that BMI and weight are strongly associated with rKOA in women and suggests that precise measurements of body composition and measures of fat distribution may offer no advantage over the more simple measures of BMI or weight in assessment of risk of rKOA.     

Pollen,ovules, and pollination in pea: Success,failure, and resilience in heat

Field pea (Pisum sativum), a major grain legume crop, is autogamous and adapted to temperate climates. The objectives of this study were to investigate effects of high temperature stress on stamen chemical composition, anther dehiscence, pollen viability, pollen interactions with pistil and ovules, and ovule growth and viability. Two cultivars (“CDC Golden” and “CDC Sage”) were exposed to 24/18°C (day/night) continually or to 35/18°C for 4 or 7 days. Heat stress altered stamen chemical composition, with lipid composition of “CDC Sage” being more stable compared with “CDC Golden.” Heat stress reduced pollen viability and the proportion of ovules that received a pollen tube. After 4 days at 35°C, pollen viability in flower buds decreased in “CDC Golden,” but not in “CDC Sage.” After 7 days, partial to full failure of anthers to dehisce resulted in subnormal pollen loads on stigmas. Although growth (ovule size) of fertilized ovules was stimulated by 35°C, heat stress tended to decrease ovule viability. Pollen appears susceptible to stress, but not many grains are needed for successful fertilization. Ovule fertilization and embryos are less susceptible to heat, but further research is warranted to link the exact degree of resilience to stress intensity.     

Dynamics, diversity, and resource gradient relationships in the herbaceous layer of an old-growth Appalachian forest

The ecological drivers of herbaceous layer composition and diversity in deciduous forests of eastern North America are imperfectly understood. We analyzed the herbaceous layer, across the growing season, in a central Appalachian old-growth forest to examine dynamics, diversity, and relationships to resource gradients. We found clear variation in herb species composition over the growing season. We identified intermingled resource gradients, including soil nutrients, light availability, and topography, that were related to herbaceous composition. We found that herb layer diversity was different among previously identified tree communities, but was not variable over the growing season. We identified a unimodal relationship between diversity and productivity in the herb flora that held throughout the growing season despite changing composition and levels of productivity. Diversity and distributions in the herbaceous community of our study site are linked to a complex of resource gradients.     

Functionally different pools of Shiga toxin receptor, globotriaosyl ceramide, in HeLa cells

Many studies have investigated the intracellular trafficking of Shiga toxin, but very little is known about the underlying dynamics of its cellular receptor, the glycosphingolipid globotriaosyl ceramide. In this study, we show that globotriaosyl ceramide is required not only for Shiga toxin binding to cells, but also for its intracellular trafficking. Shiga toxin induces globotriaosyl ceramide recruitment to detergent-resistant membranes, and subsequent internalization of the lipid. The globotriaosyl ceramide pool at the plasma membrane is then replenished from internal stores. Whereas endocytosis is not affected in the recovery condition, retrograde transport of Shiga toxin to the Golgi apparatus and the endoplasmic reticulum is strongly inhibited. This effect is specific, as cholera toxin trafficking on GM(1) and protein biosynthesis are not impaired. The differential behavior of both toxins is also paralleled by the selective loss of Shiga toxin association with detergent-resistant membranes in the recovery condition, and comparison of the molecular species composition of plasma membrane globotriaosyl ceramide indicates subtle changes in favor of unsaturated fatty acids. In conclusion, this study demonstrates the dynamic behavior of globotriaosyl ceramide at the plasma membrane and suggests that globotriaosyl ceramide-specific determinants, possibly its molecular species composition, are selectively required for efficient retrograde sorting on endosomes, but not for endocytosis.     

The Bushmeat Harvest Alters Seedling Banks by Favoring Lianas, Large Seeds, and Seeds Dispersed by Bats, Birds, and Wind

We evaluated predictions that hunters favor lianas, large seeds, and seeds dispersed by bats, small birds, and mechanical means for seedling banks in central Panama. We censused 3201 trees in 20 1-ha plots and 38,250 seedlings in the central 64 m² of each plot. We found significant differences in the species composition of the seedling bank between nine protected sites in the Barro Colorado Nature Monument and 11 hunted sites in the contiguous Parque Nacional Soberanía. Lianas, species with large seeds, and species with seeds dispersed by bats, small birds, and mechanical means were all overrepresented at hunted sites. The latter two findings could also be evaluated relative to the species composition of reproductively mature adults for canopy trees. The tree species present in the seedling bank had significantly heavier seeds than the tree species present as adults at hunted sites but not at protected sites. The representation of seed dispersal modes among the species present in the seedling bank did not reflect pre-existing differences in the local species composition of adults. We hypothesize that hunting large seed predators favors large seeds by reducing predation and increasing survival. We also hypothesize that the harvest of large birds and mammals that disperse many seeds favors other species whose seeds are dispersed by bats, small birds, and mechanical means. This process also favors lianas because the seeds of disproportionate numbers of liana species are dispersed by wind.     

Peptidoglycan composition and taxonomy of group D, E, and H streptococci, and Streptococcus mutans

The qualitative and quantitative composition of the peptidoglycan from the cell wall of groups D, E, and H streptococci, and Streptococcus mutans, was determined. In group D, S. faecalis and the closely related species S. liquefaciens and S. zymogenes were separated from S. faecium and the closely related species S. durans on the basis of their peptidoglycan composition. A relationship among S. bovis, S. equinus, and some strains of S. mutans was indicated by the presence in each of a similar peptidoglycan containing threonine. Threonine was released from the S. mutans polymer as a threonine-lysine dipeptide. Hydrolysis of the dipeptide at 100 C for 24 hr in 6 n HC1 was required to break the peptide bond. Motile group D streptococci possessed a peptidoglycan of the same composition as S. faecium. Group E and H strains were also similar in the composition of their peptidoglycan. The results demonstrate that peptidoglycan composition can be used to (i) aid in the division of members of an immunological group into subgroups, and (ii) indicate a relationship between members of the same genus which are not related on an immunological basis.     

Climate change,woodpeckers, and forests: Current trends and future modeling needs

The structure and composition of forest ecosystems are expected to shift with climate‐induced changes in precipitation, temperature, fire, carbon mitigation strategies, and biological disturbance. These factors are likely to have biodiversity implications. However, climate‐driven forest ecosystem models used to predict changes to forest structure and composition are not coupled to models used to predict changes to biodiversity. We proposed integrating woodpecker response (biodiversity indicator) with forest ecosystem models. Woodpeckers are a good indicator species of forest ecosystem dynamics, because they are ecologically constrained by landscape‐scale forest components, such as composition, structure, disturbance regimes, and management activities. In addition, they are correlated with forest avifauna community diversity. In this study, we explore integrating woodpecker and forest ecosystem climate models. We review climate–woodpecker models and compare the predicted responses to observed climate‐induced changes. We identify inconsistencies between observed and predicted responses, explore the modeling causes, and identify the models pertinent to integration that address the inconsistencies. We found that predictions in the short term are not in agreement with observed trends for 7 of 15 evaluated species. Because niche constraints associated with woodpeckers are a result of complex interactions between climate, vegetation, and disturbance, we hypothesize that the lack of adequate representation of these processes in the current broad‐scale climate–woodpecker models results in model–data mismatch. As a first step toward improvement, we suggest a conceptual model of climate–woodpecker–forest modeling for integration. The integration model provides climate‐driven forest ecosystem modeling with a measure of biodiversity while retaining the feedback between climate and vegetation in woodpecker climate change modeling.     

Disturbance,fish, and variation in the predatory insect guild of coastal streams

Species distributions, and thus the composition of communities, are determined by many interacting biotic and abiotic factors. We analyzed the variation in composition of the invertebrate predator guild across eight small, steep coastal streams in eastern Canada, in relation to variation in several broad categories of environmental variables: disturbance-related physical characteristics, top-down effects (fish), and bottom-up effects (prey composition and productivity-related physical/chemical variables). Similarity in composition (relative and absolute abundances of the 19 species belonging to the Rhyacophilidae, Perlodidae, and Chloroperlidae) declined significantly with distance. Streams that were most similar in predator composition were also most similar in physical factors related to disturbance, but were not more similar in prey abundance/composition or in environmental factors associated with productivity (chemistry, canopy cover, and riparian forest type). Similarity in the relative abundance of species within the Rhyacophilidae was linked to variation in the presence/abundance of brook trout. These results suggest that the invertebrate predator guilds of these small coastal streams are structured first and foremost by factors associated with the magnitude and variability of the flow regime, and second by response to top-down factors (predation by brook trout). There was no evidence that bottom-up effects altered the composition or abundance of the predator guild. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: Sonja Stendera     

Female distribution, genetic relatedness, and fostering behaviour in harbour seals, Phoca vitulina

Although harbour seals may not recognize their relatives, relatives could be chosen preferentially for fostering (i.e. kin selection) if harbour seals display natal philopatry coupled with breeding site fidelity, and thus kin are clustered within the colony. We used behavioural and genetic data to investigate population structure within the Sable Island breeding colony and to test whether harbour seals tend to foster related pups. Adult females on Sable Island showed a high level of breeding-colony site fidelity but low levels of within-colony site fidelity both within and between years. Similarly, although lactating females showed a clumped distribution, group composition was highly variable, suggesting that this study colony was not composed of groups of related animals. DNA fingerprint data supported the hypothesis that female distribution within the colony was not correlated with genetic relatedness. Furthermore, the mean DNA band sharing among foster dyads did not differ significantly from that for unrelated animals. These results indicate that among harbour seals, related pups are not usually chosen preferentially for fostering and hence, kin selection is not likely to be influencing the occurrence of this behaviour. Copyright 1999 The Association for the Study of Animal Behaviour.     

Tree diversity,composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest

Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent decades, however, tropical forest fires occur more frequently and at larger spatial scales than they used to. We studied forest structure, tree species diversity, tree species composition, and aboveground biomass during the first 7 years since fire in unburned, once burned and twice burned forest of eastern Borneo to determine the rate of recovery of these forests. We paid special attention to changes in the tree species composition during burned forest regeneration because we expect the long-term recovery of aboveground biomass and ecosystem functions in burned forests to largely depend on the successful regeneration of the pre-fire, heavy-wood, species composition. We found that forest structure (canopy openness, leaf area index, herb cover, and stem density) is strongly affected by fire but shows quick recovery. However, species composition shows no or limited recovery and aboveground biomass, which is greatly reduced by fire, continues to be low or decline up to 7 years after fire. Consequently, large amounts of the C released to the atmosphere by fire will not be recaptured by the burned forest ecosystem in the near future. We also observed that repeated fire, with an inter-fire interval of 15 years, does not necessarily lead to a huge deterioration in the regeneration potential of tropical forest. We conclude that burned forests are valuable and should be conserved and that long-term monitoring programs in secondary forests are necessary to determine their recovery rates, especially in relation to aboveground biomass accumulation.     

Seed coats: Structure,development, composition,and biotechnology

Summary Although seeds have been the subject of extensive studies for many years, their seed coats are just beginning to be examined from the perspective of molecular genetics and control of development. The seed coat, plays a vital role in the life cycle of plants by controlling the development of the embryo and determining seed dormancy and germination. Within the seed coat are a number of unique tissues that undergo differentiation to serve specific functions in the seed. A large number of genes are known to be specifically expressed within the seed coat tissues; however, very few of them are understood functionally. The seed coat synthesizes a wide range of novel compounds that may serve the plant in diverse ways, including defense and control of development. Many of the compounds are sources of industrial products and are components of food and feeds. The use of seed coat biotechnology to enhance seed quality and yield, or to generate novel components has not been exploited, largely because of lack of knowledge of the genetic systems that govern seed coat development and composition. In this review, we will examine the recent advances in seed coat, biology from the perspective of structure, composition and molecular genetics. We will consider the diverse avenues that are possible for seed coat biotechnology in the future. This review will focus principally on the seed coats of the Brassicaceae and Fabaceae as they allow us to merge the areas of molecular biology, physiology and structure to gain a perspective on the possibilities for seed coat modifications in the future. The authors have contributed equally and are considered first authors.     

Variability of seedling recruitment under dominant, moss, and litter removal over four years

In a four-year removal experiment we investigated the effect of removing a dominant species (Nardus stricta), the litter layer and moss layer on species composition of established vegetation and on numbers and species composition of seedlings. The experiment was conducted in an oligotrophic wet meadow (Molinion with some features ofViolion caninae according to phytosociological classification). After four years of the experiment, the redundancy analysis (RDA) did not reveal any changes in the composition of the established plant community. Seedling numbers and their species composition, however, varied significantly both among treatments and over years. Whereas the differences between treatments were mainly in total seedling numbers, the years differed in both seedling numbers and relative representation of individual species. In particular,Myosotis nemorosa seedlings highly increased their abundance in a favourable year 1995 constituting one third of all the seedlings found, whereas in other years their abundance was between 4% and 10%. The effects of year and treatment were not additive (significant year × treatment interaction). This means that plots under different treatments are differently affected by climatic conditions of individual years. The greatest increase of seedling recruitment was observed in the plots with the moss layer removed. Microsites with high seedling recruitment persisted in the plots for no more than two years. Why the established vegetation composition does not differ among treatments even after four years, despite the relatively pronounced and immediate response of seedlings? The number of species with regular seedling recruitment is limited. They are mostly perennials, and consequently, it might take even longer than four years before recruitment limitation affects the population size of established plants.