The complex social structure and male-biased sex ratio of honeybee mating systems are analysed, followed by detailed treatments of panmictic drone congregation areas and species-specific daily mating flight periods. This is followed by an account of queen polyandry and drone monogamy and competition. Mating on the wing is a finely tuned technical tour de force involving initial docking, establishing the internal connection of drone and queen, the deposition and transfer of sperm and, finally, decoupling of the pair and deposition of a mating sign. Subsequent to mating, the problems of the ultimate storage and utilisation of sperm are discussed. Finally, the matter of reproductive isolation is considered.

The bulbus is a part of the unique functional penis (endophallus) in the genus Apis and was studied in Apis mellifera drones. The bulbus consists of a thin cuticular membrane, covered by four different epithelia (dorsal epithelium, anterior epithelium, ventral epithelium I and ventral epithelium II). One day before eclosion, pupae have no sclerotised plates in the bulbus lumen. In emerging drones, however, the lumen contains tanned plate-like structures, the chitin plates, subjacent are small droplets. The chitin plates are connected to each other by a transparent matrix. They consist of globular sclerotized structures which are connected by a network of fibrils. In young adult drones, the dorsal and lateral epithelia consist of highly columnar gland cells which decrease in thickness from the age of 6–12 days from 140 to 20 μm. The ultrastructural analysis combined with histochemistry shows that the gland cells secrete proteinaceous droplets towards the lumen which pass through the cuticle and the pores of the chitin plates and accumulate in the matrix. In sexually mature drones, all secretions have merged to a rigid connective substance, which extends laterally as a thin tapering membrane. The ventral epithelia I and II have no secretory function. The ventral epithelium II has a mucus-like content and several invaginations towards the lumen of the bulbus which enables widening of the bulbus orifice to discharge the bulbus secretions filled with viscous mucus via the cervix into the queen during the mating process.

Aerobic methanotrophs are metabolically unique bacteria that are able to utilize methane as a sole source of energy. They occur in a wide range of habitats where both methane and oxygen are available. Nearly all methanotrophic bacteria that are now isolated in pure cultures belong to the phylum Proteobacteria, while only a limited number of strains represent the Verrucomicrobia. Proteobacterial methanotrophs affiliate with the classes Gammaproteobacteria (type I methanotrophs) and Alphaproteobacteria (type II methanotrophs) and belong to 23 genera and 56 species with validly published names. Several described methanotrophic representatives of the Gammaproteobacteria are not yet obtained in pure cultures and have a “Candidatus” status. Cultivation-independent studies indicate the existence of several further groups of methanotrophic bacteria that have not yet been obtained in culture. However, the currently cultivated strains cover a surprisingly broad range of methanotrophs detected in various environments by molecular approaches. This chapter offers an overview of the currently described methanotroph diversity and the major groups of methanotrophic bacteria that have so far eluded isolation efforts.

Planctomyces brasiliensis Schlesner 1990 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 consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448^T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the GenomicEncyclopedia ofBacteriaandArchaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.

Summary

Queens, homozygous for three marker genes, were inseminated with eight different types of semen, each carrying one combination of the markers. Intracolonial worker relationship (ř_c) was estimated by genotype frequencies in the offspring of the experimental queens. ř_c was larger than under random distribution of semen types in the spermatheca. Estimates of most quantitative genetical parameters will be more accurate using the presented estimator for intracolonial relationship. The insemination order affected genotype frequencies in the offspring, suggesting a weak ‘last male advantage’. There was, however, no evidence of intra spermathecal sperm competition.

Summary

A deterministic model is presented which shows that multiple mating reduces the conflict between workers and queen in the optimal investment ratio in each sex. The natural risk of the nuptual flights of honeybee queens fits well into the theoretically determined risk when queens tend to optimize the numbers of drones with which they mate.

Background

A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data.

Results

We present acdc, a tool specifically developed to aid the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows.

Conclusions

Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.

Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the GenomicEncyclopedia ofBacteria andArchaea project, we here describe the features of E. coli DSM 30083^T together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083^T in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.