A robust procedure for comparing multiple means under heteroscedasticity in unbalanced designs.

Investigating differences between means of more than two groups or experimental conditions is a routine research question addressed in biology. In order to assess differences statistically, multiple comparison procedures are applied. The most prominent procedures of this type, the Dunnett and Tukey-Kramer test, control the probability of reporting at least one false positive result when the data are normally distributed and when the sample sizes and variances do not differ between groups. All three assumptions are non-realistic in biological research and any violation leads to an increased number of reported false positive results. Based on a general statistical framework for simultaneous inference and robust covariance estimators we propose a new statistical multiple comparison procedure for assessing multiple means. In contrast to the Dunnett or Tukey-Kramer tests, no assumptions regarding the distribution, sample sizes or variance homogeneity are necessary. The performance of the new procedure is assessed by means of its familywise error rate and power under different distributions. The practical merits are demonstrated by a reanalysis of fatty acid phenotypes of the bacterium Bacillus simplex from the "Evolution Canyons" I and II in Israel. The simulation results show that even under severely varying variances, the procedure controls the number of false positive findings very well. Thus, the here presented procedure works well under biologically realistic scenarios of unbalanced group sizes, non-normality and heteroscedasticity

Biologists meet statisticians: A workshop for young scientists to foster interdisciplinary team work

Life science and statistics have necessarily become essential partners. The need to plan complex, structured experiments, involving elaborated designs, and the need to analyse datasets in the era of systems biology and high throughput technologies has to build upon professional statistical expertise. On the other hand, conducting such analyses and also developing improved or new methods, also for novel kinds of data, has to build upon solid biological understanding and practise. However, the meeting of scientists of both fields is often hampered by a variety of communicative hurdles - which are based on field-specific working languages and cultural differences. As a step towards a better mutual understanding, we developed a workshop concept bringing together young experimental biologists and statisticians, to work as pairs and learn to value each others competences and practise interdisciplinary communication in a casual atmosphere. The first implementation of our concept was a cooperation of the German Region of the International Biometrical Society and the Leibnitz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (short: DSMZ), Braunschweig, Germany. We collected feedback in form of three questionnaires, oral comments, and gathered experiences for the improvement of this concept. The long-term challenge for both disciplines is the establishment of systematic schedules and strategic partnerships which use the proposed workshop concept to foster mutual understanding, to seed the necessary interdisciplinary cooperation network, and to start training the indispensable communication skills at the earliest possible phase of education

Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter

The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary trajectories of surface-associated marine bacteria can differ significantly from free-living marine bacteria or marine generalists

The multidimensionality of soil macroecology

The recent past has seen a tremendous surge in soil macroecological studies and new insights into the global drivers of one‐quarter of the biodiversity of the Earth. Building on these important developments, a recent paper in Global Ecology and Biogeography outlined promising methods and approaches to advance soil macroecology. Among other recommendations, White and colleagues introduced the concept of a spatial three‐dimensionality in soil macroecology by considering the different spheres of influence and scales, as soil organism size ranges vary from bacteria to macro‐ and megafauna. Here, we extend this concept by discussing three additional dimensions (biological, physical, and societal) that are crucial to steer soil macroecology from pattern description towards better mechanistic understanding. In our view, these are the requirements to establish it as a predictive science that can inform policy about relevant nature and management conservation actions. We highlight the need to explore temporal dynamics of soil biodiversity and functions across multiple temporal scales, integrating different facets of biodiversity (i.e., variability in body size, life‐history traits, species identities, and groups of taxa) and their relationships to multiple ecosystem functions, in addition to the feedback effects between humans and soil biodiversity. We also argue that future research needs to consider effective soil conservation policy and management in combination with higher awareness of the contributions of soil‐based nature's contributions to people. To verify causal relationships, soil macroecology should be paired with local and globally distributed experiments. The present paper expands the multidimensional perspective on soil macroecology to guide future research contents and funding. We recommend considering these multiple dimensions in projected global soil biodiversity monitoring initiatives

Characterization of JG024, a pseudomonas aeruginosa PB1-like broad host range phage under simulated infection conditions

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas aeruginosa </it>causes lung infections in patients suffering from the genetic disorder Cystic Fibrosis (CF). Once a chronic lung infection is established, <it>P. aeruginosa </it>cannot be eradicated by antibiotic treatment. Phage therapy is an alternative to treat these chronic <it>P. aeruginosa </it>infections. However, little is known about the factors which influence phage infection of <it>P. aeruginosa </it>under infection conditions and suitable broad host range phages.</p> <p>Results</p> <p>We isolated and characterized a phage, named JG024, which infects a broad range of clinical and environmental <it>P. aeruginosa </it>strains. Sequencing of the phage genome revealed that the phage JG024 is highly related to the ubiquitous and conserved PB1-like phages. The receptor of phage JG024 was determined as lipopolysaccharide. We used an artificial sputum medium to study phage infection under conditions similar to a chronic lung infection. Alginate production was identified as a factor reducing phage infectivity.</p> <p>Conclusions</p> <p>Phage JG024 is a suitable broad host range phage which could be used in phage therapy. Phage infection experiments under simulated chronic lung infection conditions showed that alginate production reduces phage infection efficiency.</p

Complete genome sequence of Meiothermus silvanus type strain (VI-R2).

Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. M. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biofouler. This is the second completed genome sequence of a member of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,721,669 bp long genome with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project

Complete genome sequence of Planctomyces limnophilus type strain (Mü 290).

Planctomyces limnophilus Hirsch and Müller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project