Putative lipoproteins identified by bioinformatic genome analysis of Leifsonia xyli ssp. xyli, the causative agent of sugarcane ratoon stunting disease

Leifsonia xyli ssp. x yli is the causative agent of ratoon stunting disease, a major cause of economic loss in sugarcane crops. Understanding of the biology of this pathogen has been hampered by its fastidious growth characteristics in vitro . However, the recent release of a genome sequence for this organism has allowed significant novel insights. Further to this, we have performed a bioinformatic analysis of the lipoproteins encoded in the L. xyli genome. These analyses suggest that lipoproteins represent c . 2.0% of the L. xyli predicted proteome. Functional analyses suggest that lipoproteins make an important contribution to the physiology of the pathogen and may influence its ability to cause disease in planta .     

The anatomical basis of sexual dichromatism in non-iridescent ultraviolet-blue structural coloration of feathers

Despite extensive research on the evolution of avian dichromatism, the anatomical bases for differences between the sexes in species with structurally coloured plumage remain largely unknown. Using full‐spectrum spectrometry and transmission electron microscopy, we compared the colour and morphology of rump feathers of male and female eastern bluebirds (Sialia sialis). The ultraviolet (UV)‐blue feather colour in this species is caused by coherent scattering of light within the medullary ‘spongy layer’ of feather barbs. This spongy layer lies beneath a keratin cortex and on top of a layer of melanin granules that surround a hollow central vacuole. Irregularly shaped electron‐dense regions are present within the cortex. Male and female S. sialis differed substantially in their plumage colour and feather structure. A backwards logistic regression predicted sex with 100% accuracy using the colour variables brightness, UV‐violet (UV‐V) chroma and spectral saturation. A second backwards logistical regression predicted sex with 100% accuracy using relative cortex area and size of air spaces. Thus, S. sialis are dimorphic both in colour and in the structures causing this colour. Multiple regression analyses using data pooled from both sexes indicated that multiple features of feather barb structure contributed to colour variation in complex ways. Brightness was negatively related to the relative surface area of cortex in barb cross‐sections. Hue was positively related and UV‐V chroma was negatively related to the distance between scattering elements (i.e. keratin rods and air spaces) in the spongy layer. In contrast, hue was negatively related and UV‐V chroma was positively related to the thickness of the spongy layer. UV‐V chroma was also negatively related to the relative area of electron‐dense regions in the cortex. Spectral saturation was negatively related to the distance between scatterers and the standard error of the size of air spaces. These results suggest that the dimensions of spongy‐layer elements are critical to colour production, but that UV‐blue coloration can also be modified by the cortex and the thickness of the spongy layer. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 259–271.     

Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence

Population genetics of the amphibian pathogen Batrachochytrium dendrobatidis ( Bd ) show that isolates are highly related and globally homogenous, data that are consistent with the recent epidemic spread of a previously endemic organism. Highly related isolates are predicted to be functionally similar due to low levels of heritable genetic diversity. To test this hypothesis, we took a global panel of Bd isolates and measured (i) the genetic relatedness among isolates, (ii) proteomic profiles of isolates, (iii) the susceptibility of isolates to the antifungal drug caspofungin, (iv) the variation among isolates in growth and phenotypic characteristics, and (v) the virulence of isolates against the European common toad Bufo bufo . Our results show (i) genotypic differentiation among isolates, (ii) proteomic differentiation among isolates, (iii) no significant differences in susceptibility to caspofungin, (iv) differentiation in growth and phenotypic/morphological characters, and (v) differential virulence in B. bufo . Specifically, our data show that Bd isolates can be profiled by their genotypic and proteomic characteristics, as well as by the size of their sporangia. Bd genotypic and phenotypic distance matrices are significantly correlated, showing that less-related isolates are more biologically unique. Mass spectrometry has identified a set of candidate genes associated with inter-isolate variation. Our data show that, despite its rapid global emergence, Bd isolates are not identical and differ in several important characters that are linked to virulence. We argue that future studies need to clarify the mechanism(s) and rate at which Bd is evolving, and the impact that such variation has on the host–pathogen dynamic.     

Endemic and introduced haplotypes of Batrachochytrium dendrobatidis in Japanese amphibians: sink or source?

The global emergence of the amphibian chytrid pathogen Batrachochytrium dendrobatidis (Bd) is one of the most compelling, and troubling, examples of a panzootic. Only discovered in 1998, Bd is now recognized as a proximate driver of global declines in amphibian diversity and is now widely acknowledged as a key threatening process for this ancient class of vertebrates. Moreover, Bd has become a member of a small group of highly virulent multihost pathogens that are known to have had effects on entire vertebrate communities and the ecosystem‐level effects of Bd‐driven amphibian declines are starting to emerge as a consequence of regional decreases in amphibian diversity. Despite the speed at which this species of aquatic chytrid has become a focus of research efforts, major questions still exist about where Bd originated, how it spreads, where it occurs and what are Bd’s effects on populations and species inhabiting different regions and biomes. In this issue, Goka et al. (2009 ) make an important contribution by publishing the first nationwide surveillance for Bd in Asia. Although previous data had suggested that amphibians in Asia are largely uninfected by Bd, these surveys were limited in their extent and few firm conclusions could be drawn about the true extent of infection. Goka et al. herein describe a systematic surveillance of Japan for both native and exotic species in the wild, as well as amphibians housed in captivity, using a Bd‐specific nested PCR reaction on a sample of over 2600 amphibians. Their results show that Bd is widely prevalent in native species across Japan in at least three of the islands that make up the archipelago, proving for the first time that Asia harbours Bd.     

Speciation in Passerina buntings: introgression patterns of sex-linked loci identify a candidate gene region for reproductive isolation

Sex-chromosomes are thought to play an important role in speciation, but few studies of non-model organisms have investigated the relative influence of multiple sex-linked markers on reproductive isolation. We collected 222 individuals along a geographical transect spanning the hybrid zone between Passerina amoena and P. cyanea (Aves: Cardinalidae). Using maximum-likelihood cline fitting methods, we estimated locus-specific introgression rates for 10 z-linked markers. Although the cline width estimates ranged from 2.8 to 584 km, eight of 10 loci had cline widths between 224 and 271 km. We also used coalescent-based estimates of locus-specific divergence times between P. amoena and P. cyanea to test a recently proposed hypothesis of an inverse relationship between divergence time and cline width but did not find a significant association. The narrow width (2.8 km) of the cline estimated from the VLDLR9 locus indicates strong selection retarding introgression of alleles at this locus across the hybrid zone. Interestingly, a mutation in the very low density lipoprotein receptor ( VLDLR ) gene, in which VLDLR9 is an intron, is known to reduce the egg-laying ability of some chickens, suggesting a possible link between this gene region and reproductive isolation between P. amoena and P. cyanea . These results underscore the importance of sampling multiple loci to investigate introgression patterns across a chromosome or genome and support previous findings of the importance of sex-linked genes in speciation.     

Unravelling complexities in benthic food webs using a dual stable isotope (hydrogen and carbon) approach

1. Stable carbon isotope studies have been an essential component of research regarding the contribution of methane (CH₄)-derived carbon to freshwater food webs and results have suggested that benthic macroinvertebrates in billabongs, streams and lakes may be partially, and in some instances, significantly 'fuelled' by methanotrophic biomass. However, the singular use of carbon isotopes can lead to ambiguous interpretations concerning the origin of carbon, especially in systems where phototrophs are likely to be using carbon respired sources and hence show more ¹³C-depleted values.
2. These uncertainties can be further resolved by the inclusion of additional isotopic data. Stable hydrogen isotopes are being increasingly used in food web studies with a marked advantage that sources may be isotopically distinct by one or two orders of magnitude greater than stable carbon or nitrogen, the isotopes most commonly used to delineate trophic interactions. By using hydrogen as a second biogeochemical tracer we provide further supportive evidence for the assimilation of methanotrophic microbial biomass by chironomid larvae.
3. Moreover, the hydrogen and carbon isotope values we found in chironomid tissues appear to reflect the original substrate used during methanogenesis; either acetate fermentation or carbonate reduction. Use of the former tends to result in relatively heavy carbon and light hydrogen isotope values due to kinetic isotope effects, whereas use of the latter results in relatively lighter carbon and heavier hydrogen isotope values.
4. We provide preliminary evidence to suggest that hydrogen and carbon isotope values in macroinvertebrates may be used to distinguish between CH₄ formation pathways and help to explain inter-depth and inter-specific differences between co-existing chironomid species found in the same lake.     

Regional water resource implications of bioethanol production in the Southeastern United States

The Energy Independence and Security Act (EISA) of 2007 mandates US production of 136 billion L of biofuel by 2022. This target implies an appropriation of regional primary production for dedicated feedstocks at scales that may dramatically affect water supply, exacerbate existing water quality challenges, and force undesirable environmental resource trade offs. Using a comparative life cycle approach, we assess energy balances and water resource implications for four dedicated ethanol feedstocks – corn, sugarcane, sweet sorghum, and southern pine – in two southeastern states, Florida and Georgia, which are a presumed epicenter for future biofuel production. Net energy benefit ratios for ethanol and coproducts range were 1.26 for corn, 1.94 for sweet sorghum, 2.51 for sugarcane, and 2.97 for southern pine. Corn also has high nitrogen (N) and water demand (11.2 kg GJ_net^?1 and 188 m³ GJ_net^?1, respectively) compared with other feedstocks, making it a poor choice for regional ethanol production. Southern pine, in contrast, has relatively low N demand (0.4 kg GJ_net^?1) and negligible irrigation needs. However, it has comparatively low gross productivity, which results in large land area per unit ethanol production (208 m² GJ_net^?1), and, by association, substantial indirect and incremental water use (51 m³ GJ_net^?1). Ultimately, all four feedstocks require substantial land (10.1, 3.1, 2.5, and 6.1 million ha for corn, sugarcane, sweet sorghum, and pine, respectively), annual N fertilization (3230, 574, 396, 109 million kg N) and annual total water (54 400, 20 840, 8840, and 14 970 million m³) resources when scaled up to meet EISA renewable fuel standards production goals. This production would, in turn, offset only 17.5% of regional gasoline consumption on a gross basis, and substantially less when evaluated on a net basis. Utilization of existing waste biomass sources may ameliorate these effects, but does not obviate the need for dedicated primary feedstock production. Careful scrutiny of environmental trade‐offs is necessary before embracing aggressive ethanol production mandates.     

Linking above- and belowground responses to global change at community and ecosystem scales

Cryptic belowground organisms are difficult to observe and their responses to global changes are not well understood. Nevertheless, there is reason to believe that interactions among above- and belowground communities may mediate ecosystem responses to global change. We used grassland mesocosms to manipulate the abundance of one important group of soil organisms, arbuscular mycorrhizal (AM) fungi, and to study community and ecosystem responses to CO₂ and N enrichment. Responses of plants, AM fungi, phospholipid fatty acids and community-level physiological profiles were measured after two growing seasons. Ecosystem responses were examined by measuring net primary production (NPP), evapotranspiration, total soil organic matter (SOM), and extractable mineral N. Structural equation modeling was used to examine the causal relationships among treatments and response variables. We found that while CO₂ and N tended to directly impact ecosystem functions (evapotranspiration and NPP, respectively), AM fungi indirectly impacted ecosystem functions by influencing the community composition of plants and other root fungi, soil fungi and soil bacteria. We found that the mycotrophic status of the dominant plant species in the mesocosms determined whether the presence of AM fungi increased or decreased NPP. Mycotrophic grasses dominated the mesocosm communities during the first growing season, and the mycorrhizal treatments had the highest NPP. In contrast, nonmycotrophic forbs were dominant during the second growing season and the mycorrhizal treatments had the lowest NPP. The composition of the plant community strongly influenced soil N, and the community composition of soil organisms strongly influenced SOM accumulation in the mesocosms. These results show how linkages between above- and belowground communities can determine ecosystem responses to global change.     

Habitat selection by the swamp wallaby (Wallabia bicolor) in relation to diel period,food and shelter

Patterns of resource selection by animals may be influenced by sex, and often change over a 24‐h period. We used a dry sclerophyll landscape managed for commercial timber production to investigate the effects of sex and diel period on habitat selection by the swamp wallaby (Wallabia bicolor). We predicted that selection would be (i) affected by both sex and diel period; and (ii) positively related to lateral cover during the day, but to food resources at night. Non‐metric multidimentional scaling indicated that some of the available habitats differed markedly with respect to visibility (an indicator of lateral cover), fern cover, forb cover, wallaby density and a forage quality index, providing the basis for non‐random habitat selection. At the landscape scale, wallabies showed strong selection for 5‐year‐old regenerating sites, selected against 10‐year‐old regenerating sites and unharvested forest, and avoided recently harvested (3–10 months post‐harvest) sites completely. At the scale of individual home ranges, a pooled male and female sample demonstrated selection for unharvested forest over recently harvested sites during both diurnal and nocturnal periods. A separate analysis showed that both sex and diel period influenced the selection of 5‐ and 10‐year‐old sites and the surrounding unharvested forest. Using a novel approach, we demonstrated that diurnal habitat selection by both sexes was negatively correlated with visibility, representing stronger selection for areas with more lateral cover. Nocturnal selection by females was positively correlated with values of a forage quality index, but this was not the case for males. We hypothesise that the observed patterns of selection were driven by the need to find food and avoid predators, but were also affected by the different reproductive strategies of males and females. Our results demonstrate the importance of incorporating factors such as sex and diel period into analyses of habitat selection.     

Differential Responses of Postmetamorphic Amphibians to Cattle Grazing in Wetlands

ABSTRACT Global amphibian declines have been linked to various anthropogenic land uses. Recent studies have documented negative impacts of cropland agriculture and deforestation on amphibians; however, few have examined potential impacts of cattle grazing in wetlands on resident amphibians. Therefore, we measured differences in number of captures and body size of postmetamorphic amphibians, egg mass abundance, and shoreline vegetation structure and composition between 4 wetlands with direct cattle access and 4 wetlands from which cattle were excluded on the Cumberland Plateau in Tennessee, USA. We captured amphibians at wetlands from March to August 2005 and 2006 using pitfall traps. Number of green frog (Rana clamitans) metamorphs captured at nonaccess wetlands was 2.5 times and 9.8 times greater than at wetlands with cattle access in 2005 and 2006, respectively. However, number of American toads (Bufo americanus) captured was 68 times and 76 times greater at cattle-access wetlands in 2005 and 2006, respectively. In general, metamorph body size was negatively correlated with species-specific capture rate. We detected no differences in egg mass abundance between cattle land-use types. Height, percent horizontal cover, and percent vertical cover of shoreline vegetation were 74%,25%, and 84% greater, respectively, in nonaccess wetlands in 2005; vegetation trends were similar in 2006. Our results suggest that cattle impact amphibian populations but effects vary by species. Differences in postmetamorphic capture rate may be related to less emergent vegetation at cattle-access wetlands. Although body size differed between land uses for metamorphs, these trends probably were short-lived, because we did not detect differences in juvenile and adult body size between land uses for most species. Based on our findings, we suggest that fencing cattle from wetlands may be a prudent conservation strategy for some amphibian species (e.g., ranids), whereas other species (e.g., bufonids) may benefit from controlled grazing.