Root responses to nutrient patches in grassland and forest

Differences between growth forms in root responses to experimentally created heterogeneity have been documented in many greenhouse and plot studies, but not in natural vegetation. Here we examined the response of roots to experimental nutrient patches in undisturbed grassland and forest at the northern edge of the North American Great Plains. Forest vegetation increases the spatial heterogeneity of soil resources, and we tested for differences between forest and grassland roots in response to patches. Ten minirhizotrons (clear tubes, 5 cm diameter, 180 cm long) were installed in both grassland and forest 3 years before the experiment. Minirhizotrons ran horizontally 10 cm beneath the soil surface. Patches of available nitrogen (N) were created over the tubes, using three concentrations (0, 3, 15 g N m⁻² yr⁻¹) and two patch sizes (1␣and 10 cm²). Root images were collected beneath patches over the course of a growing season. Root length was significantly greater in grassland than forest at the start and end of the growing season, but did not respond to N patches. Root production was also significantly greater in grassland than forest, and was significantly greater (about 20%) in high-N patches than in unfertilized patches. This increase, however, did not differ between vegetation types. Turnover did not vary with any treatment, and patch size had no effect on any response variable. Overall, differences caused by experimental patches were much smaller than differences between habitats, and did not vary between habitats. Realistic levels of experimentally imposed hetereogeneity in established vegetation may not be much greater than background levels, and field vegetation has extant root systems which respond to patches via uptake instead of growth. Both mechanisms should contribute to less root proliferation in field experiments than in greenhouse experiments.     

Microsatellite markers uncover cryptic species of Odontotermes (Termitoidae: Termitidae) from Peninsular Malaysia

Termites from the genus Odontotermes are known to contain numerous species complexes that are difficult to tell apart morphologically or with mitochondrial DNA sequences. We developed markers for one such cryptic species complex, that is, Odontotermes srinakarinensis sp. nov. from Maxwell Hill Forest Reserve (Perak, Malaysia), and characterised them using a sample of 41 termite workers from three voucher samples from the same area. We then genotyped 150 termite individuals from 23 voucher samples/colonies of this species complex from several sites in Peninsular Malaysia. We analysed their population by constructing dendograms from the proportion of shared-alleles between individuals and genetic distances between colonies; additionally, we examined the Bayesian clustering pattern of their genotype data. All methods of analysis indicated that there were two distinct clusters within our data set. After the morphologies of specimens from each cluster were reexamined, we were able to separate the two species morphologically and found that a single diagnostic character found on the mandibles of its soldiers could be used to separate the two species quite accurately. The additional species in the clade was identified as Odontotermes denticulatus after it was matched to type specimens at the NHM London and Cambridge Museum of Zoology.     

Random forests-based differential analysis of gene sets for gene expression data

In DNA microarray studies, gene-set analysis (GSA) has become the focus of gene expression data analysis. GSA utilizes the gene expression profiles of functionally related gene sets in Gene Ontology (GO) categories or priori-defined biological classes to assess the significance of gene sets associated with clinical outcomes or phenotypes. Many statistical approaches have been proposed to determine whether such functionally related gene sets express differentially (enrichment and/or deletion) in variations of phenotypes. However, little attention has been given to the discriminatory power of gene sets and classification of patients.     

Revision of the genus Evanos Laporte de Castelnau, 1840, with the description of a second species (Coleoptera: Scarabaeoidea: Rutelidae: Geniatini)

The monotypic genus Evanos (Coleoptera: Rutelidae: Geniatini) is revised and a new species, E. danieleae Grossi, n. sp., is described based on specimens collected from Minas Gerais, Brazil. A lectotype is designated for Evanos villatus. Diagnostic characters and comments about the taxonomic status of the genus are given, as well as a key for both species and a distribution map with the known locality records.     

Identification of Penicillin-binding proteins employing support vector machines and random forest

Penicillin-Binding Proteins are peptidases that play an important role in cell-wall biogenesis in bacteria and thus maintaining bacterial infections. A wide class of β-lactam drugs are known to act on these proteins and inhibit bacterial infections by disrupting the cell-wall biogenesis pathway. Penicillin-Binding proteins have recently gained importance with the increase in the number of multi-drug resistant bacteria. In this work, we have collected a dataset of over 700 Penicillin-Binding and non-Penicillin Binding Proteins and extracted various sequence-related features. We then created models to classify the proteins into Penicillin-Binding and non-binding using supervised machine learning algorithms such as Support Vector Machines and Random Forest. We obtain a good classification performance for both the models using both the methods.     

碳汇目标下农户森林经营最优决策及碳汇供给能力——基于浙江和江西两省调查

增加森林碳汇已成为应对气候变化的重要举措.基于浙江和江西两省农户调研数据,以杉木为案例树种,引用生长模型、修正的Faustmann模型碳密度和价格数据,对单一和碳汇木材复合经营目标下的杉木最佳轮伐期和林地期望值进行比较研究,并模拟了不同碳价格和利率水平下的变化,同时绘制了农户的碳汇供给曲线.可以发现,在碳汇林经营模式下,基于目前的杉木市场价格远高于碳价格的现实,农户的经营采伐决策并不会发生明显改变,从而导致在大范围的碳价格变动下碳汇的供给也没有显著增加,这也说明木材收益和碳收益的两个不同经营目标是协调的.同时,基于碳汇经营模式下的杉木林地期望值增长迅速,碳汇林地潜在投资价值巨大,也意味着森林碳汇对于土地利用改变可能会产生巨大影响.     

Negative Effects of Conspecific Floral Density on Fruit Set of Two Neotropical Understory Plants

Plant reproductive success is usually positively related to conspecific floral density, but neutral or negative effects of floral density on reproduction have also been reported. Differences in the relationship between reproduction and floral density largely originate from a trade‐off between increasing attractiveness versus increasing competition for pollinators at high floral densities. Although floral densities strongly vary in the understory of tropical forests, for instance, due to variation in light availability, little is known about the density dependence of reproduction in tropical understory plants. We used path analyses to disentangle direct and indirect effects of canopy openness and floral density on fruit set and analyzed the relationship between pollen load and floral density for two Neotropical understory plants, Heliconia metallica and Besleria melancholica. In both species, fruit set was not directly related to canopy openness, but decreased with increasing floral density. In H. metallica, canopy openness had an indirect negative effect on reproduction mediated by its effects on floral density. Effects of floral density on pollen loads were species‐specific. In B. melancholica, pollen loads linearly decreased with increasing floral density, indicating competition for pollinators at high densities. In H. metallica, pollen loads were reduced at both low and high densities, indicating an interplay of facilitative and competitive effects of floral density on pollen deposition. In contrast to other studies, we found negative density dependence of reproduction in both understory species. Negative effects of floral density on reproduction appear to be related to pollinator‐mediated effects on reproduction rather than to variation in abiotic conditions.     

The role of forest residues in the accounting for the global warming potential of bioenergy

Bioenergy makes up a significant portion of the global primary energy pie, and its production from modernized technology is foreseen to substantially increase. The climate neutrality of biogenic CO₂ emissions from bioenergy grown from sustainably managed biomass resource pools has recently been questioned. The temporary change caused in atmospheric CO₂ concentration from biogenic carbon fluxes was found to be largely dependent on the length of biomass rotation period. In this work, we also show the importance of accounting for the unutilized biomass that is left to decompose in the resource pool and how the characterization factor for the climate impact of biogenic CO₂ emissions changes whether residues are removed for bioenergy or not. With the case of Norwegian Spruce biomass grown in Norway, we found that significantly more biogenic CO₂ emissions should be accounted towards contributing to global warming potential when residues are left in the forest. For a 100‐year time horizon, the global warming potential bio factors suggest that between 44 and 62% of carbon‐flux, neutral biogenic CO₂ emissions at the energy conversion plant should be attributed to causing equivalent climate change potential as fossil‐based CO₂ emissions. For a given forest residue extraction scenario, the same factor should be applied to the combustion of any combination of stem and forest residues. Life cycle analysis practitioners should take these impacts into account and similar region/species specific factors should be developed.     

A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district,eastern Japan

To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and C_MH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate.     

A new Brazilian Passiflora leafminer: Spinivalva gaucha,gen. n., sp. n. (Lepidoptera,Gracillariidae, Gracillariinae), the first gracillariid without a sap-feeding instar

Male, female, pupa, larva and egg of a new genus and species of Gracillariidae (Gracillariinae), Spinivalva gaucha Moreira and Vargas from southern Brazil are described and illustrated with the aid of optical and scanning electron microscopy. A preliminary analysis of mitochondrial DNA sequences including members of related lineages is also provided. The immature stages are associated with Passiflora actinia, Passiflora misera and Passiflora suberosa (Passifloraceae), and build mines on the adaxial leaf surface. Initially the mines are serpentine in shape, but later in larval ontogeny become a blotch type. Although the larvae are hypermetamorphic as in other Gracillariidae, there is no sap-feeding instar in Spinivalva gaucha; the larva feeds on the palisade parenchyma, thus producing granular frass during all instars. Pupation occurs outside the mine; prior to pupating, the larva excretes numerous bubbles that are placed in rows on the lateral margins of the cocoon external surface. This is the second genus of gracillariid moth described for the Atlantic Rain Forest, and the second gracillariid species known to be associated with Passifloraceae.