Nitrogen deposition and temperature structure fungal communities associated with alpine moss-sedge heath in the UK

Funding Information: We are very grateful to Ruth Mitchell, Dave Riach, Julia Fisher and Hannah Urpeth for their help with fieldwork. Helaina Black is thanked for helpful discussion during the design of the project. Numerous conservation agency staff and landowners gave permission to carry out work on their land, without which this study would not have been possible. The study was financially supported by the Scottish Government Rural and Environment Science and Analytical Services Division (RESAS).Peer reviewe

Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal

Acknowledgements This work was funded by BBSRC research project BB/J00336/1. FS and a part of the proportion of the cost of the Illumina genotyping was funded by a Beachell-Borlag International Fellowship. The authors would like to acknowledge the help of Dr MK Sarmah in collecting seed samples of the landraces and improved cultivars from Assam used in this study and Dr. Ma. Elizabeth B. Naredo and Ms. Sheila Mae Q. Mercado for handling of IRGC accessions and preparation of DNAs for genotyping. All rice seeds used here were obtained with MTA agreements and seed and dry leaves imported into the UK under import licence IMP⁄SOIL⁄18⁄2009 issued by Science and Advice for Scottish Agriculture.Peer reviewedPublisher PD

Phytophthora austrocedri in Argentina and co-Inhabiting phytophthoras: roles of anthropogenic and abiotic factors in species distribution and diversity

This work reports the first survey of Phytophthora diversity in the forests soils of Andean Patagonia. It also discusses the role of anthropogenic impact on Phytophthora distribution inferred from the findings on Phytophthora diversity and on the distribution of Phytophthora austrocedri-diseased forests. Invasive pathogen species threatening ecosystems and human activities contribute to their entry and spread. Information on pathogens already established, and early detection of potential invasive ones, are crucial to disease management and prevention. Phytophthora austrocedri causes the most damaging forest disease in Patagonia, affecting the endemic species Austrocedrus chilensis (D. Don) Pic. Sern. and Bizzarri. However, the relationship between anthropogenic impacts and the disease distribution has not been analyzed enough. The aims of this work were: to evaluate Phytophthora diversity in soils of Andean Patagonia using a metabarcoding method, and analyze this information in relation to soil type and land use; to assess the distribution of Austrocedrus disease over time in relation to anthropogenic and abiotic gradients in an area of interest; and to discuss the role of human activities in Phytophthora spread. High throughput Illumina sequencing was used to detect Phytophthora DNA in soil samples. The distribution of Austrocedrus disease over time was assessed by satellite imagery interpretation. Twenty-three Phytophthora species, 12 of which were new records for Argentina, were detected. The most abundant species was P. austrocedri, followed by P. × cambivora, P. ramorum and P. kernoviae. The most frequent was P. × cambivora, followed by P. austrocedri and P. ramorum. Phytophthora richness and abundance, and Austrocedrus disease distribution, were influenced by land use, anthropogenic impact and soil drainage. Results showed several Phytophthoras, including well-known pathogenic species. The threat they could present to Patagonian ecosystems and their relations to human activities are discussed. This study evidenced the need of management measures to control the spread of P. austrocedri and other invasive Phytophthora species in Patagonia.EEA EsquelFil: Vélez, María Laura. Centro de Investigación y Extensión Forestal Andino Patagónico (CIEFAP); ArgentinaFil: Vélez, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vélez, María Laura. Universidad Nacional de la Patagonia San Juan Bosco; ArgentinaFil: La Manna, Ludmila. Universidad Nacional de la Patagonia San Juan Bosco. Facultad de Ingeniería. Centro de Estudios Ambientales Integrados; ArgentinaFil: La Manna, Ludmila. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Tarabini, Manuela. Universidad Nacional de la Patagonia San Juan Bosco. Facultad de Ingeniería. Centro de Estudios Ambientales Integrados; ArgentinaFil: Tarabini, Manuela. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gómez, Federico Antonio. Universidad Nacional de la Patagonia San Juan Bosco. Facultad de Ingeniería. Centro de Estudios Ambientales Integrados; ArgentinaFil: Gómez, Federico Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gómez, Federico Antonio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agroforestal Esquel; ArgentinaFil: Elliott, Matt. Forest Research; EscociaFil: Hedley, Pete. Instituto James Hutton, Cell and Molecular Sciences; Reino UnidoFil: Cock, Peter. Instituto James Hutton, Information and Computational Sciences; Reino UnidoFil: Greslebin, Alina. Centro de Investigación Esquel de Montaña y Estepa Patagónica; ArgentinaFil: Greslebin, Alina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Greslebin, Alina. Universidad Nacional de la Patagonia San Juan Bosco. Facultad de Ciencias Naturales y Ciencias de la Salud; Argentin

Single-feature polymorphism discovery in the barley transcriptome

A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes

Diversity of woody-host infecting Phytophthora species in public parks and botanic gardens as revealed by metabarcoding, and opportunities for mitigation through best practice

The diversity of Phytophthora species in soils collected from 14 highly disturbed sites in northern Britain, including botanic gardens, arboreta, public parks and other amenity woodland sites, was analysed using a molecular technique known as DNA metabarcoding. This technique enables the identification of multiple species present in a single environmental sample based on a DNA ‘barcode’ unique to each species. The genus Phytophthora was targeted in this study due to its increasing impact on Britain’s forests and woodlands over thelast 20 years. The introduction and spread of new Phytophthora species into Britain has been strongly associated with the movement of traded containerised plants, with a number of Phytophthora outbreaks reported on host trees located in public gardens and parks that had recently undergone planting or landscape regeneration schemes. This study was undertaken to assess the extent to which these highly disturbed sites with extensive planting regimes act as harbours for woody-host infecting Phytophthora species. A total of 23 Phytophthora species, the majority of which are known to be pathogens of woody hosts, were detected across the 14 sites sampled. These included four quarantine-regulated pathogens and four species notpreviously recorded in Britain. Also detected were three as-yet undescribed Phytophthora species and nine oomycete sequences with no clear match to any known genus. There was no effect of geographical location, elevation, underlying soil type, host family or host health status on the Phytophthora assemblages at each site, suggesting that the Phytophthora communities detected are likely to comprise introduced species associated with planting programmes. P. austrocedri and P. pseudosyringae were two of the most abundant Phytophthoraspecies detected, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain. The practical implications of the findings in terms of mitigating Phytophthora introduction, spread and impact at botanic gardens, arboreta and urban parks are discussed

Seagrass Canopy Photosynthetic Response Is a Function of Canopy Density and Light Environment: A Model for Amphibolis griffithii

A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments

Nitrogen deficiency in barley (<i>Hordeum vulgare)</i> seedlings induces molecular and metabolic adjustments that trigger aphid resistance

Agricultural N2O pollution resulting from the use of synthetic fertilisers represents a significant contribution to anthropogenic greenhouse gas emissions, providing a rationale for reduced use of nitrogen fertilisers. Nitrogen limitation results in extensive systems rebalancing that remodels metabolism and defence processes. To analyse the regulation underpinning these responses, barley (Horedeum vulgare) seedlings were grown for seven days under nitrogen-deficient conditions until net photosynthesis was 50% lower than in nitrogen-replete controls. Although shoot growth was decreased there was no evidence for the induction of oxidative stress despite lower total concentrations of nitrogen containing antioxidants. Nitrogen deficient barley leaves were rich in amino acids, sugars and tricarboxylic acid cycle intermediates. In contrast to N-replete leaves one day old nymphs of the green peach aphid (Myzus persicae) failed to reach adulthood when transferred to N-deficient barley leaves. Transcripts encoding cell, sugar and nutrient signalling, protein degradation and secondary metabolism were over-represented in nitrogen-deficient leaves while those associated with hormone metabolism were similar under both nutrient regimes with the exception of mRNAs encoding proteins involved in auxin metabolism and responses. Significant similarities were observed between the N-limited barley leaf transcriptome and that of aphid infested Arabidopsis leaves. These findings not only highlight significant similarities between biotic and abiotic stress signalling cascades but also identify potential targets for increasing aphid resistance with implications for the development of sustainable agriculture

Intercomparison of shallow water bathymetry, hydro-optics, and benthos mapping techniques in Australian and Caribbean coastal environments

Science, resource management, and defense need algorithms capable of using airborne or satellite imagery to accurately map bathymetry, water quality, and substrate composition in optically shallow waters. Although a variety of inversion algorithms are available, there has been limited assessment of performance and no work has been published comparing their accuracy and efficiency. This paper compares the absolute and relative accuracies and computational efficiencies of one empirical and five radiative-transfer-based published approaches applied to coastal sites at Lee Stocking Island in the Bahamas and Moreton Bay in eastern Australia. These sites have published airborne hyperspectral data and field data. The assessment showed that (1) radiative-transfer-based methods were more accurate than the empirical approach for bathymetric retrieval, and the accuracies and processing times were inversely related to the complexity of the models used; (2) all inversion methods provided moderately accurate retrievals of bathymetry, water column inherent optical properties, and benthic reflectance in waters less than 13 m deep with homogeneous to heterogeneous benthic/substrate covers; (3) slightly higher accuracy retrievals were obtained from locally parameterized methods; and (4) no method compared here can be considered optimal for all situations. The results provide a guide to the conditions where each approach may be used (available image and field data and processing capability). A re-analysis of these same or additional sites with satellite hyperspectral data with lower spatial and radiometric resolution, but higher temporal resolution would be instructive to establish guidelines for repeatable regional to global scale shallow water mapping approaches