Opinion

In this Opinion article, James Prosser considers the conceptual limitations of metagenomics and metatranscriptomics in contributing to our understanding of soil microbial ecology, and also explores potential opportunities for using these techniques to address specific ecological questions.

Chemical dispersants are routinely applied during oil spills in marine ecosystems, yet little is known about how they affect microbial communities. Here, Joye and colleagues explore how dispersants affect the composition and activity of microbial communities and discuss crucial knowledge gaps that should guide future research efforts.

Mignot and colleagues present an evolutionary scenario to explain the emergence of the two distinct machines — the Agl–Glt and Agl–Nfs complexes — that are involved in motility and assembly of the spore coat inMyxococcus xanthus. They argue that elucidation of the composition and mechanism of action of these complexes will improve our understanding of the evolution of macromolecular complexes.

Antibiotic resistance constitutes a threat to human and animal health worldwide. Here, Manaia and colleagues report the main findings of the European COST (Cooperation in Science and Technology) Action DARE (Detecting Evolutionary Hotspots of Antibiotic Resistance in Europe) and discuss the need for improved sampling of the environment and more comprehensive databases, as well as the policy and management options that should be considered as priorities to tackle antibiotic resistance in the environment.

In this Opinion article, Errington reviews the studies that describe the role of MreB in the determination and maintenance of rod cell shape in bacteria, and he presents a model to reconcile the conflicting data.

Polintons are large DNA transposons that are widespread in the genomes of eukaryotes. Here, Krupovic and Koonin propose that Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish elements.

In this Opinion article, Baquero and colleagues propose a hierarchical system for estimating the risks associated with genes present in environmental resistomes, by evaluating the likelihood of their introduction into human pathogens, and the consequences of such introduction events for the treatment of bacterial infections.

Recent studies have shown that submicroscopicPlasmodium falciparuminfections are an important, but often undetected, reservoir of malaria and are major contributors to transmission. In this Opinion article, Bousema and colleagues discuss the epidemiology of these infections and the prospects for intervention strategies, and they argue for the wider deployment of molecular diagnostic tools to understand and quantify infection dynamics.

In this Opinion article, Dan Barouch and Louis Picker discuss recent data regarding the clinical development of novel serotype adenovirus and cytomegalovirus vaccine vectors for use in HIV-1 vaccines.

Combination antiretroviral therapy (cART) has revolutionized the treatment of HIV-1 infection, but the mechanistic basis of successful treatment is poorly understood. In this Opinion article, Siliciano and Laskey present a model to assess the efficacy of antiretroviral drugs and argue that this is a more accurate metric to predict the success of cART than current metrics.

The extensive genome reduction that is observed in bacterial endosymbionts is expected for species with small effective population sizes; however, similar reduction is observed in some free-living marine cyanobacteria that have extremely large effective population sizes. In this Opinion article, the authors discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

It has recently emerged that pervasive transcription is widespread in bacteria and is caused by transcription from non-canonical promoters and terminator readthrough. However, whether the resultant transcripts have any functional role is unclear. In this Opinion article, Wade and Grainger argue that pervasive transcripts are likely to be important for the regulation of gene expression and genome evolution.

The development of a vaccine againstStaphylococcus aureusinfection has been the subject of an intensive research effort, but none of the vaccine trials has been successful so far. In this Opinion article, the authors suggest that an over-reliance on mouse models and a focus on targeting cell surface components have been major contributing factors to this failure.

McInerney and colleagues summarize the phylogenetic, cell biological, population biology, biochemical and paleontological evidence that cellular life consists of two primary, paraphyletic, prokaryotic groups and one secondary, monophyletic group that has symbiogenic origins — the eukaryotes.

Antivirulence drugs are a promising avenue to revitalize the antimicrobial drug-development pipeline, and it has been claimed that such compounds will generate much weaker selection for resistance than traditional antibiotics. Sam P. Brown and colleagues examine this claim and argue that, although resistance to antivirulence drugs may emerge, the crucial factor is whether or not this resistance will spread.

Protective immunity against tuberculosis is multifactorial, and correlates of protection — either during natural infection or after vaccination — are lacking. Here, Behar and colleagues discuss why it is time to look beyond interferon-γ for protective mechanisms againstMycobacterium tuberculosis.

David M. Whiley and colleagues discuss the problem of antimicrobial resistance (AMR) inNeisseria gonorrhoeae, particularly emerging resistance to the cephalosporin ceftriaxone, and propose the use of molecular approaches to enhance gonococcal AMR surveillance.

In this Opinion article, Kenneth Bayles describes our current knowledge of programmed cell death in bacteria and argues that the processes involved are functionally analogous to eukaryotic systems. On the basis of recent observations, a testable model to guide further investigations in the field is presented.

Antonio Cassone outlines why he thinks univalent subunit vaccines targetingCandida albicansare unlikely to succeed and argues that the development of a multivalent vaccine could be a better approach.

Richards and Talbot propose that in osmotrophic eukaryotic microorganisms, horizontal gene transfer has had a major role in reconfiguring osmotrophic functions, which involve the production and acquisition of public goods.