Phase Variation Mediates Reductions in Expression of Surface Proteins during Persistent Meningococcal Carriage

Asymptomatic and persistent colonization of the upper respiratory tract by Neisseria meningitidis occurs despite elicitation of adaptive immune responses against surface antigens. A putative mechanism for facilitating host persistence of this bacterial commensal and pathogen is alterations in expression of surface antigens by simple sequence repeat (SSR)-mediated phase variation. We investigated how often phase variation occurs during persistent carriage by analyzing the SSRs of eight loci in multiple isolates from 21 carriers representative of 1 to 6 months carriage. Alterations in repeat number were detected by a GeneScan analysis and occurred at 0.06 mutations/gene/month of carriage. The expression states were determined by Western blotting and two genes, fetA and nadA, exhibited trends toward low expression states. A critical finding from our unique examination of combinatorial expression states, “phasotypes,” was for significant reductions in expression of multiple phase-variable surface proteins during persistent carriage of some strains. The immune responses in these carriers were examined by measuring variant-specific PorA IgG antibodies, capsular group Y IgG antibodies and serum bactericidal activity in concomitant serum samples. Persistent carriage was associated with high levels of specific IgG antibodies and serum bactericidal activity while recent strain acquisition correlated with a significant induction of antibodies. We conclude that phase-variable genes are driven into lower expression states during long-term persistent meningococcal carriage, in part due to continuous exposure to antibody-mediated selection, suggesting localized hypermutation has evolved to facilitate host persistence.     

Perennial grasslands enhance biodiversity and multiple ecosystem services in bioenergy landscapes

Agriculture is being challenged to provide food, and increasingly fuel, for an expanding global population. Producing bioenergy crops on marginal lands—farmland suboptimal for food crops—could help meet energy goals while minimizing competition with food production. However, the ecological costs and benefits of growing bioenergy feedstocks—primarily annual grain crops—on marginal lands have been questioned. Here we show that perennial bioenergy crops provide an alternative to annual grains that increases biodiversity of multiple taxa and sustain a variety of ecosystem functions, promoting the creation of multifunctional agricultural landscapes. We found that switchgrass and prairie plantings harbored significantly greater plant, methanotrophic bacteria, arthropod, and bird diversity than maize. Although biomass production was greater in maize, all other ecosystem services, including methane consumption, pest suppression, pollination, and conservation of grassland birds, were higher in perennial grasslands. Moreover, we found that the linkage between biodiversity and ecosystem services is dependent not only on the choice of bioenergy crop but also on its location relative to other habitats, with local landscape context as important as crop choice in determining provision of some services. Our study suggests that bioenergy policy that supports coordinated land use can diversify agricultural landscapes and sustain multiple critical ecosystem services.In agricultural landscapes, balancing the provisioning of food and energy with maintenance of biodiversity and ecosystem functions is a global challenge. To avoid impacts on food production, attention is increasingly being focused on the potential for marginal lands to support bioenergy production (1). Marginal lands, those suboptimal for food production, may consist of relatively small areas within generally productive landscapes or larger regions where conditions generally limit crop productivity. However, there is increasing recognition that these lands are already performing a variety of useful functions, and their conversion to bioenergy cropping could reduce these services. For example, in the north central United States, rising commodity prices are predicted to bring marginal croplands—including Conservation Reserve Program lands—into annual crop production with negative impacts on wildlife habitat and water quality (2, 3). With 2013 corn plantings at recent record highs (4) and new reports of grassland and wetland conversion to cropland (5, 6), this may be occurring already.An alternative to annual cropping is conversion of marginal croplands to perennial, cellulosic crops for bioenergy. Although current US biofuel production centers on grain ethanol derived from annual monocultures of maize (Zea mays), this situation could change with full implementation of the 2007 US Energy Independence and Security Act (7), which calls for increased production of cellulosic biofuels. In the Midwest United States, perennial grasses and forbs grown on marginal lands could provide up to 25% of national targets for cellulosic biofuel, with substantial greenhouse gas (GHG) benefits (8). Moreover, increasing the area of perennial cover on the landscape is predicted to positively affect a diverse array of organisms and ecological functions (9–11), leading to important synergies that have not yet informed the ongoing bioenergy debate. Here we provide the most comprehensive empirical evaluation of this hypothesis to date, reporting data that elucidate the impacts of different bioenergy cropping systems on a wide variety of organisms and the ecosystem functions they perform.Previous studies have examined the ability of select bioenergy crops to support specific taxa (12) or individual services such as energy production (13) or GHG mitigation (14), without consideration of the tradeoffs or synergies that can arise when considering entire suites of organisms and ecosystem functions. We report on a unique multidisciplinary study of matched sets of organisms and ecosystem services and show that perennial grass energy crops (switchgrass, Panicum virgatum, and mixed prairie plantings) synergistically enhance diversity of a variety of organisms and levels of the services they provide. We further quantify the importance of landscape context on service provisioning, suggesting that policy supporting intentional design of bioenergy landscapes could increase sustainability of both food and energy production.     

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus

To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.