Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root) and habitat (epiphytes vs endophytes) structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024), while the reverse is true for the leaves (P = 0.032). Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001). The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.     

Assessment of river condition at a large spatial scale using predictive models

1. RIVPACS-type predictive models were developed at a relatively large spatial scale for the Australian state called New South Wales (NSW, 801 428 km²). Aquatic macroinvertebrate samples and physical and chemical data were collected from 250 reference sites (little affected by human activities) and 23 test sites (with known human impacts) throughout NSW in autumn and spring 1995 and identified mostly to family level. Reference sites were grouped based on their macroinvertebrate data using classification (UPGMA) and ordination techniques. Relationships between macroinvertebrate and environmental data were established using principal axis correlations and stepwise multiple discriminant function analysis. models for predicting invertebrate assemblages were developed separately for edge and riffle habitats for autumn and spring data sets and for combined autumn and spring data sets. 2. Sites in the lowland sections of the western flowing rivers were characterized by low taxonomic richness and were distinct from the sites in the eastern part of the state. Sites on the western slopes of the Great Dividing Range in southern and northern NSW mostly fell into separate groups. In eastern NSW, site groups did not represent a north, central and south division. Sites on highland streams, coastal fringe streams and large rivers mostly formed distinct groups, but most of the sites on east-flowing rivers fell into large site groups that did not have clear geographic boundaries. 3. Environmental variables that were strongly correlated with ordinations of macroinvertebrate presence/absence at sites were water temperature, altitude, longitude and maximum distance from source. The predictor variables determined by DFA for the six models created included alkalinity, altitude, location (longitude and/or latitude), stream size and substratum composition. These are generally in common with the variables determined for other large geographic areas in Australia and the United Kingdom. 4. Model outputs from reference sites suggest that, among the six models, the riffle model combining autumn and spring is likely to give the most reliable predictions. The combined edge model also performed well but refinements are needed for single season models to provide reliable outputs. 5. Combined season models both for riffles and for edges detected biological impairment at all but one of the test sites. Single season riffle models also detected impairment while single season edge models characterized sites as unimpaired despite other models’ indications of impaired fauna. Riffle models may be more sensitive than edge models but the sampling of riffles is often limited by flow. Edge habitats are available at most sites but there may be few riffles in floodplain rivers. Available resources, desired model sensitivity, and river type should be considered jointly to determine the most useful habitat to sample.     

Expression, purification and characterisation of soluble GlfT and the identification of a novel galactofuranosyltransferase Rv3782 involved in priming GlfT-mediated galactan polymerisation in Mycobacterium tuberculosis

The arabinogalactan (AG) component of the mycobacterial cell wall is an essential branched polysaccharide which tethers mycolic acids (m) to peptidoglycan (P), forming the mAGP complex. Much interest has been focused on the biosynthetic machinery involved in the production of this highly impermeable shield, which is the target for numerous anti-tuberculosis agents. The galactan domain of AG is synthesised via a bifunctional galactofuranosyltransferase (GlfT), which utilises UDP-Galf as its high-energy substrate. However, it has proven difficult to study the protein in its recombinant form due to difficulties in recovering pure soluble protein using standard expression systems. Herein, we describe the effects of glfT co-induction with a range of chaperone proteins, which resulted in an appreciable yield of soluble protein at 5 mg/L after a one-step purification procedure. We have shown that this purified enzyme transfers [¹⁴C]Galf to a range of both β(1 → 5) and β(1 → 6) linked digalactofuranosyl neoglycolipid acceptors with a distinct preference for the latter. Ligand binding studies using intrinsic tryptophan fluorescence have provided supporting evidence for the apparent preference of this enzyme to bind the β(1 → 6) disaccharide acceptor. However, we could not detect binding or galactofuranosyltransferase activity with an n-octyl β-d-Gal-(1 → 4)-α-l-Rha acceptor, which mimics the reducing terminus of galactan in the mycobacterial cell wall. Conversely, after an extensive bioinformatics analysis of the H37Rv genome, further cloning, expression and functional analysis of the Rv3792 open reading frame indicates that this protein affords galactofuranosyltransferase activity against such an acceptor and paves the way for a better understanding of galactan biosynthesis in Mycobacterium tuberculosis.     

Prognostic factors of 10-year radiographic outcome in early rheumatoid arthritis: a prospective study

Introduction  

The objectives of this study were to determine the predictive factors of long-term radiographic outcome of rheumatoid arthritis (RA) and to describe the relationship between joint damage and disability over the course of the disease.     

Proximity to forest edge does not affect crop production despite pollen limitation

A decline in pollination function has been linked to agriculture expansion and intensification. In northwest Argentina, pollinator visits to grapefruit, a self-compatible but pollinator-dependent crop, decline by approximately 50% at 1km from forest edges. We evaluated whether this decrease in visitation also reduces the pollination service in this crop. We analysed the quantity and quality of pollen deposited on stigmas, and associated limitation of fruit production at increasing distances (edge: 10, 100, 500 and 1000m) from the remnants of Yungas forest. We also examined the quantitative and qualitative efficiency of honeybees as pollen vectors. Pollen receipt and pollen tubes in styles decreased with increasing distance from forest edge; however, this decline did not affect fruit production. Supplementation of natural pollen with self- and cross-pollen revealed that both pollen quantity and quality limited fruit production. Despite pollen limitation, honeybees cannot raise fruit production because they often do not deposit sufficient high-quality pollen per visit to elicit fruit development. However, declines in visitation frequency well below seven visits during a flower's lifespan could decrease production beyond current yields. In this context, the preservation of forest remnants, which act as pollinator sources, could contribute to resilience in crop production. Like wild plants, pollen limitation of the yield among animal-pollinated crops may be common and indicative not only of pollinator scarcity, but also of poor pollination quality, whereby pollinator efficiency, rather than just abundance, can play a broader role than previously appreciated.     

The Decay of the Chromosomally Encoded ccdO157 Toxin–Antitoxin System in the Escherichia coli Species

The origin and the evolution of toxin–antitoxin (TA) systems remain to be uncovered. TA systems are abundant in bacterial chromosomes and are thought to be part of the flexible genome that originates from horizontal gene transfer. To gain insight into TA system evolution, we analyzed the distribution of the chromosomally encoded ccd_O157 system in 395 natural isolates of Escherichia coli. It was discovered in the E. coli O157:H7 strain in which it constitutes a genomic islet between two core genes (folA and apaH). Our study revealed that the folA–apaH intergenic region is plastic and subject to insertion of foreign DNA. It could be composed (i) of a repetitive extragenic palindromic (REP) sequence, (ii) of the ccd_O157 system or subtle variants of it, (iii) of a large DNA piece that contained a ccdA_O157 antitoxin remnant in association with ORFs of unknown function, or (iv) of a variant of it containing an insertion sequence in the ccdA_O157 remnant. Sequence analysis and functional tests of the ccd_O157 variants revealed that 69% of the variants were composed of an active toxin and antitoxin, 29% were composed of an active antitoxin and an inactive toxin, and in 2% of the cases both ORFs were inactive. Molecular evolution analysis showed that ccdB_O157 is under neutral evolution, suggesting that this system is devoid of any biological role in the E. coli species.