Bacteria Are Smartphones and Mobile Genes Are Apps

Bacterial core and accessory genome components are analogous to the operating system and applications of smartphones. The core genome provides stable taxonomy and species lists, but phenotypes reflect the mobile pool of accessory genes. This suggests changes to the ways we define bacterial species and describe bacterial communities

Orientation-sensitivity to facial features explains the Thatcher illusion

The Thatcher illusion provides a compelling example of the perceptual cost of face inversion. The Thatcher illusion is often thought to result from a disruption to the processing of spatial relations between face features. Here, we show the limitations of this account and instead demonstrate that the effect of inversion in the Thatcher illusion is better explained by a disruption to the processing of purely local facial features. Using a matching task, we found that participants were able to discriminate normal and Thatcherized versions of the same face when they were presented in an upright orientation, but not when the images were inverted. Next, we showed that the effect of inversion was also apparent when only the eye region or only the mouth region was visible. These results demonstrate that a key component of the Thatcher illusion is to be found in orientation-specific encoding of the expressive features (eyes and mouth) of the face

Slipins: ancient origin, duplication and diversification of the stomatin protein family

<p>Abstract</p> <p>Background</p> <p>Stomatin is a membrane protein that was first isolated from human red blood cells. Since then, a number of stomatin-like proteins have been identified in all three domains of life. The conservation among these proteins is remarkable, with bacterial and human homologs sharing 50 % identity. Despite being associated with a variety of diseases such as cancer, kidney failure and anaemia, precise functions of these proteins remain unclear.</p> <p>Results</p> <p>We have constructed a comprehensive phylogeny of all 'stomatin-like' sequences that share a 150 amino acid domain. We show these proteins comprise an ancient family that arose early in prokaryotic evolution, and we propose a new nomenclature that reflects their phylogeny, based on the name "slipin" (stomatin-like protein). Within prokaryotes there are two distinct subfamilies that account for the two different origins of the eight eukaryotic stomatin subfamilies, one of which gave rise to eukaryotic SLP-2, renamed here "paraslipin". This was apparently acquired through the mitochondrial endosymbiosis and is widely distributed amongst the major kingdoms. The other prokaryotic subfamily gave rise to the ancestor of the remaining seven eukaryotic subfamilies. The highly diverged "alloslipin" subfamily is represented only by fungal, viral and ciliate sequences. The remaining six subfamilies, collectively termed "slipins", are confined to metazoa. Protostome stomatin, as well as a newly reported arthropod subfamily slipin-4, are restricted to invertebrate groups, whilst slipin-1 (previously SLP-1) is present in nematodes and higher metazoa. In vertebrates, the stomatin family expanded considerably, with at least two duplication events giving rise to podocin and slipin-3 subfamilies (previously SLP-3), with the retained ancestral sequence giving rise to vertebrate stomatin.</p> <p>Conclusion</p> <p>Stomatin-like proteins have their origin in an ancient duplication event that occurred early on in the evolution of prokaryotes. By constructing a phylogeny of this family, we have identified and named a number of orthologous groups: these can now be used to infer function of stomatin subfamilies in a meaningful way.</p

Multilocus sequence analysis reveals multiple symbiovars within Mesorhizobium species

The genus Mesorhizobium includes species nodulating several legumes, such as chickpea, which has a high agronomic importance. Chickpea rhizobia were originally described as either Mesorhizobium ciceri or M. mediterraneum. However, rhizobia able to nodulate chickpea have been shown to belong to several different species within the genus Mesorhizobium. The present study used a multilocus sequence analysis approach to infer a high resolution phylogeny of the genus Mesorhizobium and to confirm the existence of a new chickpea nodulating genospecies. The phylogenetic structure of the Mesorhizobium clade was evaluated by sequence analysis of the 16S rRNA gene, ITS region and the five core genes atpD, dnaJ, glnA, gyrB, and recA. Phylogenies obtained with the different genes are in overall good agreement and a well-supported, almost fully resolved, phylogenetic tree was obtained using the combined data. Our phylogenetic analyses of core genes sequences and their comparison with the symbiosis gene nodC, corroborate the existence of one new chickpea Mesorhizobium genospecies and one new symbiovar, M. opportunistum sv. ciceri. Furthermore, our results show that symbiovar ciceri spreads over six species of mesorhizobia. To our knowledge this study shows the most complete Mesorhizobium multilocus phylogeny to date and contributes to the understanding of how a symbiovar may be present in different species. (c) 2012 Elsevier GmbH. All rights reserved

Effects of carbon dioxide on the searching behaviour of the root-feeding clover weevil <i>Sitona lepidus</i> (Coleoptera: Curculionidae)

The respiratory emission of CO2 from roots is frequently proposed as an attractant that allows soil-dwelling insects to locate host plant roots, but this role has recently become less certain. CO2 is emitted from many sources other than roots, so does not necessarily indicate the presence of host plants, and because of the high density of roots in the upper soil layers, spatial gradients may not always be perceptible by soil-dwelling insects. The role of CO2 in host location was investigated using the clover root weevil Sitona lepidus Gyllenhall and its host plant white clover (Trifolium repens L.) as a model system. Rhizochamber experiments showed that CO2 concentrations were approximately 1000 ppm around the roots of white clover, but significantly decreased with increasing distance from roots. In behavioural experiments, no evidence was found for any attraction by S. lepidus larvae to point emissions of CO2, regardless of emission rates. Fewer than 15% of larvae were attracted to point emissions of CO2, compared with a control response of 17%. However, fractal analysis of movement paths in constant CO2 concentrations demonstrated that searching by S. lepidus larvae significantly intensified when they experienced CO2 concentrations similar to those found around the roots of white clover (i.e. 1000 ppm). It is suggested that respiratory emissions of CO2 may act as a ‘search trigger’ for S. lepidus, whereby it induces larvae to search a smaller area more intensively, in order to detect location cues that are more specific to their host plant.<br/

Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron

BACKGROUND: The specific associations between plant roots and the soil microbial community are key to understanding nutrient cycling in grasslands, but grass roots can be difficult to identify using morphology alone. A molecular technique to identify plant species from root DNA would greatly facilitate investigations of the root rhizosphere. RESULTS: We show that trnL PCR product length heterogeneity and a maximum of two restriction digests can separate 14 common grassland species. The RFLP key was used to identify root fragments at least to genus level in a field study of upland grassland community diversity. Roots which could not be matched to known types were putatively identified by comparison of the nuclear ribosomal ITS sequence to the GenBank database. Ten taxa were identified among almost 600 root fragments. Additionally, we have employed capillary electrophoresis of fluorescent trnL PCR products (fluorescent fragment length polymorphism, FFLP) to discriminate all taxa identified at the field site. CONCLUSION: We have developed a molecular database for the identification of some common grassland species based on PCR-RFLP of the plastid transfer RNA leucine (trnL) UAA gene intron. This technique will allow fine-scale studies of the rhizosphere, where root identification by morphology is unrealistic and high throughput is desirable

Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules

Rhizobial strains isolated from effective root nodules of field-grown lentil (Lens culinaris) from different parts of Bangladesh were previously analysed using sequences of the 16S rRNA gene, three housekeeping genes (recA, atpD and glnll) and three nodulation genes (nodA, nodC and nodD), DNA fingerprinting and phenotypic characterization. Analysis of housekeeping gene sequences and DNA fingerprints indicated that the strains belonged to three novel clades in the genus Rhizobium. In present study, a representative strain from each clade was further characterized by determination of cellular fatty acid compositions, carbon substrate utilization patterns and DNA DNA hybridization and average nucleotide identity (ANI) analyses from whole-genome sequences. DNA DNA hybridization showed 50-62 % relatedness to their closest relatives (the type strains of Rhizobium etli and Rhizobium phaseoh) and 50-60 % relatedness to each other. These results were further supported by ANI values, based on genome sequencing, which were 87-92 % with their close relatives and 88-89 % with each other. On the basis of these results, three novel species, Rhizobium lentis sp. nov. (type strain BLR27(T)=LMG 28441(T)=DSM 29286(T)), Rhizobium bangladeshense sp. nov. (type strain BLR175(T)=LMG 28442(T)=DSM 29287(T)) and Rhizobium binae sp. nov. (type strain BLR195(T)=LMG 28443(T)=DSM 29288(T)), are proposed. These species share common nodulation genes (nodA, nodC and nodD) that are similar to those of the symbiovar viciae

Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations

Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution and genetic conservation of the IS found in the genome of Rhizobium etli CFN42 in a collection of 87 Rhizobium strains belonging to populations with different geographical origins. We used PCR to generate presence/absence profiles of the 39 IS found in R. etli CFN42 and evaluated whether the IS were located in consistent genomic contexts. We found that the IS from the symbiotic plasmid were frequently present in the analyzed strains, whereas the chromosomal IS were observed less frequently. We then examined the evolutionary dynamics of these strains based on a population genetic analysis of two chromosomal housekeeping genes (glyA and dnaB) and three symbiotic sequences (nodC and the two IS elements). Our results indicate that the IS contained within the symbiotic plasmid have a higher degree of genomic context conservation, lower nucleotide diversity and genetic differentiation, and fewer recombination events than the chromosomal housekeeping genes. These results suggest that the R. etli populations diverged recently in Mexico, that the symbiotic plasmid also had a recent origin, and that the IS elements have undergone a process of cyclic infection and expansion