Exploring the relationship between macrofungi diversity, abundance, and vascular plant diversity in semi-natural and managed forests in north-east Hungary

The diversity of easy-to-study organisms (e.g. vascular plants) is often used as a proxy for the diversity of other organisms whose investigation needs more effort, time and specialist knowledge. Some previous studies have found positive relationships between plant and macrofungal diversity and thus support this approach, while others question this practice. Our aim was to explore the possibility of using plant diversity as surrogate for macrofungal diversity in the forests of the Pannonian ecoregion. A total of 19 permanent plots in north-east Hungary were sampled for vascular plants and macrofungi. The effect on macrofungal abundance and diversity, as well as degradation level, of plant evenness and richness was tested using generalized linear models. Species richness of macrofungi assemblages proved to be independent of the diversity and naturalness of vascular plant communities; however, there was congruence in the composition of the two communities. In contrast to diversity, macrofungi abundance was significantly negatively correlated to plant species richness. There was a hump-backed relationship between the abundance of terricolous macrofungi and the degradation level estimated on the basis of the occurrence of vascular plants, although degradation did not influence the abundance of lignicolous macrofungi. Our results question the reliability of decisions on nature conservation actions based on a few groups of easy-to-observe organisms, and underline the necessity of studying as wide a range of taxonomic groups as possible.     

塔里木沙漠公路防护林土壤微生物生物量与土壤环境因子的关系

为探讨极端干旱区风沙土土壤微生物与土壤环境因子的作用规律,采用相关分析法研究了塔里木沙漠公路防护林地土壤微生物生物量与理化因子和酶活性的关系.结果表明：土壤容重和粒径减小（R<-0.84）、含水量和孔隙增大（R>0.85）时,防护林地中土壤微生物数量和生物量有增大趋势,由容重与微生物量的相关性主导;土壤养分含量与土壤微生物数量和生物量呈正相关,主要由速效养分和放线菌、微生物生物量C、P的相关性所致;土壤酶活性与土壤微生物数量和生物量的相关性差异较大,R在0.51～0.91,主要取决于蔗糖酶、磷酸酶与放线菌、微生物量C的相关;土壤盐分增加不利于土壤微生物生物量的积累(R<-0.71);土壤微生物数量与生物量呈较高正相关（R>0.63）.实践中应为干旱区林地土壤微生物营造良好的土体,促进土壤物质循环.     

Darwin's legacy: the forms,function and sexual diversity of flowers

Charles Darwin studied floral biology for over 40 years and wrote three major books on plant reproduction. These works have provided the conceptual foundation for understanding floral adaptations that promote cross-fertilization and the mechanisms responsible for evolutionary transitions in reproductive systems. Many of Darwin''s insights, gained from careful observations and experiments on diverse angiosperm species, remain remarkably durable today and have stimulated much current research on floral function and the evolution of mating systems. Here I review Darwin''s seminal contributions to reproductive biology and provide an overview of the current status of research on several of the main topics to which he devoted considerable effort, including the consequences to fitness of cross- versus self-fertilization, the evolution and function of stylar polymorphisms, the adaptive significance of heteranthery, the origins of dioecy and related gender polymorphisms, and the transition from animal pollination to wind pollination. Post-Darwinian perspectives on floral function now recognize the importance of pollen dispersal and male outcrossed siring success in shaping floral adaptation. This has helped to link work on pollination biology and mating systems, two subfields of reproductive biology that remained largely isolated during much of the twentieth century despite Darwin''s efforts towards integration.     

Growth responses of ciliate protozoa to the abundance of their bacterial prey

The growth rate or numerical response of five species of bactivorous ciliates to the abundance ofEnterobacter aerogenes was examined in monoxenic culture. The ciliatesColpidium campylum, C. colpoda, Glaucoma scintillons, G. frontata, andCyclidium glaucoma were isolated from a small pond. Four were grown in shaken cultures, while three were grown in cultures in which the bacteria were allowed to settle on the bottom of the culture vessel. Of the seven response curves generated, four had distinct thresholds, so that the Michaelis-Menten model usually fitted to ciliate numerical response curves was not appropriate. In shaken cultures, half-saturation prey densities ranged from 5.5 × 10⁶ to 42.9 × 10⁶ bacteria/ml. In unshaken cultures, half-saturation densities ranged from 0.057 × 10⁶ to 14.6 × 10⁶ bacteria/cm². Two species grown on both suspended and settled bacteria attained higher growth rates and had lower half-saturation prey densities feeding on settled bacteria.     

Viruses in soils: morphological diversity and abundance in the rhizosphere

Soil viruses are potentially of great importance as they may influence the ecology and evolution of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Despite this importance, the area of soil virology is understudied. Here, we report the isolation and preliminary characterisation of viruses from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod shaped, filamentous and bacilliform particles were detected in the soil samples. An apparent predominance of small spherical and filamentous bacteriophages was observed, whereas tailed bacteriophages were significantly less abundant. In this report, we also present observations and characterisation of viruses from different soil functional domains surrounding wheat roots: rhizosheath, rhizosphere and bulk soil. In spite of the differences in abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically, there were approximately 1.1–1.2 × 10⁹ virions g⁻¹ dry weight, implicating remarkable differences in virus-to-bacteria ratios in domains close to roots, rhizosphere and rhizosheath (approximately 0.27) and in bulk soil (approximately 4.68).     

Density and diversity of protozoa in some arid Australian soils

This is the first extensive study of soil protozoa of arid lands. Twenty-six samples from litters, soils, termitaria, and a cyanobacterial crust, collected from central and south Australian arid lands, were analyzed for numbers and species of gymnamoebae, ciliates, and testacea. Amoebae ranged from 1,000-5,000/g of material, and were two orders of magnitude more abundant than ciliates. Both groups increased in abundance and species richness from bare soils through spinifex to mulga to chenopod vegetations. Testacea ranged 900-5,000/g with similar species richness throughout vegetations, but reached 11,900/g with a doubling of species in a refugium in Kings Canyon. The most prevalent species of amoebae, ciliates, and testacea were taxa associated with ephemeral and disturbed habitats (r-selection). The cyanobacterial crust might be considered a micro-refugium because it contained a number of non-encysting protozoa, including Thecamoeba sp. and Nassula picta, feeding on cyanobacterial filaments. The numbers and species richness of protozoa under shrubs were greater than in bare soils, supporting the resource island hypothesis that desert plants create soil heterogeneity by localizing soil fertility under their canopies.     

Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico

Objectives

From an anthropological genetic perspective, little is known about the ethnogenesis of African descendants in Puerto Rico. Furthermore, historical interactions between Indigenous Caribbean and African descendant peoples that may be reflected in the ancestry of contemporary populations are understudied. Given this dearth of genetic research and the precedence for Afro-Indigenous interactions documented by historical, archeological, and other lines of evidence, we sought to assess the biogeographic origins of African descendant Puerto Ricans and to query the potential for Indigenous ancestry within this community.

Materials and Methods

Saliva samples were collected from 58 self-identified African descendant Puerto Ricans residing in Puerto Rico. We sequenced whole mitochondrial genomes and genotyped Y chromosome haplogroups for each male individual (n = 25). Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the sample and comparative populations.

Results

As indicated by mitochondrial haplogroups, 66% had African, 5% had European, and 29% had Indigenous American matrilines. Along the Y chromosome, 52% had African, 28% had Western European, 16% had Eurasian, and, notably, 4% had Indigenous American patrilines. Both mitochondrial and Y chromosome haplogroup frequencies were significantly different from several comparative populations.

Discussion

Biogeographic origins are consistent with historical accounts of African, Indigenous American, and European ancestry. However, this first report of Indigenous American paternal ancestry in Puerto Rico suggests distinctive features within African descendant communities on the island. Future studies expanding sampling and incorporating higher resolution genetic markers are necessary to more fully understand African descendant history in Puerto Rico.     

Exploring the diversity of plant proteome

The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.     

Distribution and diversity of soil protozoa in the McMurdo Dry Valleys of Antarctica

The polar desert soils of the McMurdo Dry Valley region support a limited water film community dominated by flagellates, amoebae, and nematodes. This study describes the protozoa and compares their distribution to nematodes. In 50 samples collected from 12 locations, rotifers and tardigrades were infrequent, and ciliates and testacea were rare. Soil protozoa occurred at all sites but the dominant nematode, Scottnema lindsayae (Timm 1971), did not, indicating soil habitat factors limiting nematode distribution are not limiting to protozoa. In contrast to the nematode species, which are all endemic to Antarctica, there were no endemic protozoan morphospecies found in our samples. The protozoan abundance was several orders of magnitude greater than that of the nematodes, and the species diversity was much greater. Most of the protozoa grew better at lower incubation temperatures. The ubiquitous distribution of protozoa suggests their importance in soil food webs and nutrient cycling in the dry valleys.     

Exploring the legacy effects of surface coal mining on stream chemistry

Surface coal mining results in dramatic alterations of the landscape in central Appalachia, leading to a myriad of environmental problems. In this study, we explore the long-term effects of surface coal mining on stream chemistry and endeavor to gain a better understanding of the efficacy of reclamation. We examined 30 sites in the Raccoon Creek watershed in southeastern Ohio, where the majority of surface mine sites are in various stages of reclamation. Our results show that conductivity (r = 0.862; P = 0.000), sulfate (r = 0.619; P = 0.000), and aluminum (r = 0.469; P = 0.009) levels increase linearly as a function of the areal extent of reclaimed mines in each subwatershed, suggesting limited success of reclamation to restore natural stream chemistry. In contrast, pH was not significantly linearly correlated with the areal extent of surface mines. This suggests that local acid mine drainage remediation projects are able to regulate acidity levels in the watershed but not conductivity and certain heavy metal concentrations. Many sites had conductivity levels high enough to impair aquatic biota via ionic and osmoregulatory stress. In sum, surface coal mining appears to have a strong legacy effect on stream chemistry in the Raccoon Creek watershed.     

Demographic trade-offs determine species abundance and diversity

Aims Much recent theory has focused on the role of neutral processes in assembling communities, but the basic assumption that all species are demographically identical has found little empirical support. Here, we show that the framework of the current neutral theory can easily be generalized to incorporate species differences so long as fitness equivalence among individuals is maintained through trade-offs between birth and death.Methods Our theory development is based on a careful reformulation of the Moran model of metacommunity dynamics in terms of a non-linear one-step stochastic process, which is described by a master equation.Important findings We demonstrate how fitness equalization through demographic trade-offs can generate significant macroecological diversity patterns, leading to a very different interpretation of the relation between Fisher's α and Hubbell's fundamental biodiversity number. Our model shows that equal fitness (not equal demographics) significantly promotes species diversity through strong selective sieving of community membership against high-mortality species, resulting in a positive association between species abundance and per capita death rate. An important implication of demographic trade-off is that it can partly explain the excessively high speciation rates predicted by the neutral theory of the stronger symmetry. Fitness equalization through demographic trade-offs generalizes neutral theory by considering heterospecific demographic difference, thus representing a significant step toward integrating the neutral and niche paradigms of biodiversity.     

Exploring the diversity of the microbial world

Yale's Microbial Diversity Institute (MDI) comprises scientists who seek to understand the largely unknown microbial world. In the first MDI symposium at Yale's West Campus in October 2010, four speakers discussed their research in diverse fields within the microbial sciences. The highlights of the symposium are presented here along with an outlook on the future of the MDI.     

Macrophyte architecture affects the abundance and diversity of littoral microfauna

We tested the hypothesis that structural complexity is an important factor influencing the abundance and taxon richness of microfauna (e.g., rotifers, copepods, cladocerans) in littoral habitats. Research on littoral microfauna has to date focused mainly on field observations, which commonly show microfauna have preference for some macrophytes over others. However, while such studies commonly conclude that macrophyte architecture is a major determinant of these variations, independent factors may also be responsible (e.g., differences in macrophyte ages, differences in macrophyte bed densities and the depth of the respective macrophyte beds sampled). We used artificial macrophytes with three levels of complexity to keep the surface area and mass of the substrate sampled constant, and to control for confounding factors not related to the complexity of the plants. Our results support the hypothesis that structural complexity is an important factor influencing abundance and taxon richness, independent of other potential confounding factors. Microfaunal (mainly rotifer) abundance and richness were generally greater on more complex artificial macrophytes, likely a result of more complex substrates (1) providing a greater variety of habitat, (2) supporting a greater concentration or variety of food and/or (3) affording greater protection against predators. Less mobile surface-associated (i.e., benthic/periphytic) taxa were found to discriminate among substrates, whereas the abundance and richness of planktonic species were not affected by complexity level. Relatively low abundances and taxon richness of microfauna recorded in control samples, which did not contain artificial macrophytes, supports the contention that vegetated areas sustain a higher abundance and variety of species than non-vegetated areas.     

Meta-analysis of tree diversity effects on the abundance,diversity and activity of herbivores' enemies

The natural enemies hypothesis predicts that the abundance and diversity of antagonists such as predators and parasitoids of herbivores increases with the diversity of plants, which can lead to more effective top-down control of insect herbivores. However, although the hypothesis has received large support in agricultural systems, fewer studies have been conducted in forest ecosystems and a comprehensive synthesis of previous research is still lacking.We conducted a meta-analysis of 65 publications comparing the diversity, abundance or activity of various groups of natural enemies (including birds, bats, spiders and insect parasitoids) in pure vs. mixed forest stands. We tested the effects of forest biome, natural enemy taxon and type of study (managed vs experimental forest).We found a significant positive effect of forest tree diversity on natural enemy abundance and diversity but not on their activity. The effect of tree diversity on natural enemies was stronger towards lower latitudes but was not contingent on the natural enemy taxon level.Overall, our study contributes toward a better understanding of the “natural enemies hypothesis” in forest systems and provides new insights about the mechanisms involved. Furthermore, we outline potential avenues for strengthening forest resistance to the growing threat of herbivorous insects.     

The impact of genetic diversity in protozoa on molecular diagnostics

Detection of intestinal parasitic protists, commonly referred to as 'intestinal protozoa,' by PCR is increasingly used not only for identification or confirmation but also as a first-line diagnostic tool. Apart from the ability to sample correctly and extract parasite DNA directly from faeces, primer and probe specificity and sensitivity affect predictive values and hence the utility of diagnostic assays. Molecular characterization of intestinal protists is necessary to design primers and probes because this is the basic material for current and future improved diagnostic PCRs for either detecting all genetic variants or specifically differentiating among such variants. As an example, this paper highlights the existence of interspecific and intraspecific genetic diversity among intestinal, unicellular parasites and its implications for nucleic acid-based diagnostic assays.     

Exploring the diversity of complex metabolic networks

MOTIVATION: Metabolism, the network of chemical reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochemical reaction from a given set of enzyme reaction rules that allows the de novo synthesis of metabolic pathways composed of these reactions, and the evaluation of these novel pathways with respect to their thermodynamic properties. RESULTS: We applied this framework to the analysis of the aromatic amino acid pathways and discovered almost 75,000 novel biochemical routes from chorismate to phenylalanine, more than 350,000 from chorismate to tyrosine, but only 13 from chorismate to tryptophan. Thermodynamic analysis of these pathways suggests that the native pathways are thermodynamically more favorable than the alternative possible pathways. The pathways generated involve compounds that exist in biological databases, as well as compounds that exist in chemical databases and novel compounds, suggesting novel biochemical routes for these compounds and the existence of biochemical compounds that remain to be discovered or synthesized through enzyme and pathway engineering. AVAILABILITY: Framework will be available via web interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). CONTACT: vassily@northwestern.edu or broadbelt@northwestern.edu SUPPLEMENTARY INFORMATION: http://systemsbiology.northwestern.edu/BNICE/publications.     

Tree diversity is key for promoting the diversity and abundance of forest-associated taxa in Europe

Plant diversity is an important driver of diversity at other trophic levels, suggesting that cascading extinctions could reduce overall biodiversity. Most evidence for positive effects of plant diversity comes from grasslands. Despite the fact that forests are hotspots of biodiversity, the importance of tree diversity, in particular its relative importance compared to other management related factors, in affecting forest-associated taxa is not well known. To address this, we used data from 183 plots, located in different forest types, from Mediterranean to Boreal, and established along a climatic gradient across six European countries (FunDivEUROPE project). We tested the influence of tree diversity, tree functional composition (i.e. functional trait values), forest structure, climate and soil on the diversity and abundance/activity of nine taxa (bats, birds, spiders, microorganisms, earthworms, ungulates, foliar fungal pathogens, defoliating insects and understorey plants) and on their overall diversity and abundance/activity (multidiversity, multiabundance/activity). Tree diversity was a key driver of taxon-level and overall forest-associated biodiversity, along with tree functional composition, forest structure, climate and soil. Both tree species richness and functional diversity (variation in functional trait values) were important. The effects of tree diversity on the abundance/activity of forest-associated taxa were less consistent. Nonetheless, spiders, ungulates and foliar fungal pathogens were all more abundant/active in diverse forests. Tree functional composition and structure were also important drivers of abundance/activity: conifer stands had lower overall multidiversity (although the effect was driven by defoliating insects), while stands with potentially tall trees had lower overall multiabundance/activity. We found more synergies than tradeoffs between diversity and abundance/activity of different taxa, suggesting that forest management can promote high diversity across taxa. Our results clearly show the high value of mixed forest stands for multiple forest-associated taxa and indicate that multiple dimensions of tree diversity (taxonomic and functional) are important.