Studying beta diversity: ecological variation partitioning by multiple regression and canonical analysis

Aims Beta diversity is the variation in species composition among sites in a geographic region.Beta diversity is a key concept for understanding the functioning of ecosystems,for the conservation of biodiversity and for ecosystem management.The present report describes how to analyse beta diversity from community composition and associated environmental and spatial data tables.Methods Beta diversity can be studied by computing diversity indices for each site and testing hypotheses about the factors that may explain the variation among sites.Alternatively,one can carry out a direct analysis of the community composition data table over the study sites,as a function of sets of environmental and spatial variables.These analyses are carried out by the statistical method of partitioning the variation of the diversity indices or the community composition data table with respect to environmental and spatial variables.Variation partitioning is briefly described herein.Important findings Variation partitioning is a method of choice for the interpretation of beta diversity using tables of environmental and spatial variables.Beta diversity is an interesting‘currency’for ecologists to compare either different sampling areas or different ecological communities cooccurring in an area.Partitioning must be based upon unbiased estimates of the variation of the community composition data table that is explained by the various tables of explanatory variables.The adjusted coefficient of determination provides such an unbiased estimate in both multiple regression and canonical redundancy analysis.After partitioning,one can test the significance of the fractions of interest and plot maps of the fitted values corresponding to these fractions.

Transport Logistics in Pollen Tubes

Cellular organelles move within the cellular volume and the effect of the resulting drag forces on the liquid causes bulk movement in the cytosol. The movement of both organelles and cytosol leads to an overall motion pattern called cytoplasmic streaming or cyclosis. This streaming enables the active and passive transport of molecules and orga- nelles between cellular compartments. Furthermore, the fusion and budding of vesicles with and from the plasma mem- brane （exo/endocytosis） allow for transport of material between the inside and the outside of the cell. In the pollen tube, cytoplasmic streaming and exo/endocytosis are very active and fulfill several different functions. In this review, we focus on the logistics of intracellular motion and transport processes as well as their biophysical underpinnings. We discuss various modeling attempts that have been performed to understand both long-distance shuttling and short-distance targeting of organelles. We show how the combination of mechanical and mathematical modeling with cell biological approaches has contributed to our understanding of intracellular transport logistics.

SeSaMe:Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms

Arbuscular mycorrhizal fungi(AMF)are plant root symbionts that play key roles in plant growth and soil fertility.They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores.Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia,resulting in a metagenome when whole-genome sequencing(WGS)data are obtained from sequencing AMF cultivated in vivo.The metagenome contains not only the AMF sequences,but also those from associated microorganisms.In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes(SeSaMe),designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing.A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure.The program distinguishes between coding sequence(CDS)and non-CDS,and classifies a query sequence into a genus group out of 54 genera used as reference.The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria,68% and 73% for fungi(excluding AMF),and 49% and 72% for AMF(Rhizophagus irregularis),respectively.SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF.Therefore,it enables users to study the symbiotic roles of associated microorganisms.It can also be applicable to other microorganisms as well as soil metagenomes.SeSaMe is freely available at www.fungalsesame.org.

The effect of landscape complexity and microclimate on the thermal tolerance of a pest insect

Landscape changes are known to exacerbate the impacts of climate change. As such, understanding the combined effect of climate and landscape on agroecosystems is vital if we are to maintain the fimction of agroecosystems. This study aimed to elucidate the effects of agricultural landscape complexity on the microclimate and thermal tolerance of an aphid pest to better understand how landscape and climate may interact to affect the thermal tolerance of pest species within the context of global climate change. Meteo- rological data were measured at the landscape level, and cereal aphids （Sitobion avenae, Metopolophium dirhodum and Rhopalosiphum padi） sampled, from contrasting landscapes （simple and complex） in winter 2013/2014 and spring 2014 in cereal fields of Brittany, France. Aphids were returned to the laboratory and the effect of landscape of origin on aphid cold tolerance （as determined by CTmin） was investigated. Results revealed that local landscape complexity significantly affected microclimate, with simple homogenous landscapes being on average warmer, but with greater temperature variation. Landscape complexity was shown to impact aphid cold tolerance, with aphids from complex land- scapes being more cold tolerant than those from simple landscapes in both winter and spring, but with differences among species. This study highlights that future changes to land use could have implications for the thermal tolerance and adaptability of insects. Fur- thermore, not all insect species respond in a similar way to microhabitat and microclimate, which could disrupt important predator-prey relationships and the ecosystem service they provide.

SeSaMe PS Function:Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi

In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org.