The viability of spermatozoa is a crucial parameter to appreciate semen quality and insemination potential of males both in natural mating and instrumental insemination. Here, we conducted a step-by-step investigation to address the questions why and at which step(s) the viability loss is occurring in spermatozoa of honeybees during natural mating and preparation for instrumental insemination. We detected the viability of spermatozoa in semen samples obtained from seminal vesicles and partly and fully everted endophalli of drones and in ejaculates collected into syringe tips, as well as the viability of spermatozoa in lateral oviducts of queens returning from the mating flight. A great diminish of spermatozoa viability (~10 %) was found in lateral oviducts of queens returning from mating flight (88.7 %) in comparison to viable spermatozoa in intact seminal vesicles of drones (98.1 %). Our results demonstrated that the decrease in spermatozoa viability occurs during the second stage of eversion of endophallus (viability loss, 3.3 %), and during injection of semen into the lateral oviducts of queens (viability loss, 6.1 %). The acting factor decreasing the viability of spermatozoa was the increased pressure occurring during the process of natural and instrumental insemination.

This study assessed the response of Apis mellifera to brood deliberately infested with Tropilaelaps mercedesae. The reproductive success of T. mercedesae in mite-inoculated and naturally infested brood was also compared. The presence of T. mercedesae inside brood cells significantly affected brood removal. Thai A. mellifera removed 52.6 ± 8.2 % of the brood inoculated with T. mercedesae as compared to 17.2 ± 1.8 and 5.7 ± 1.1 % removal rates for the groups of brood with their cell cappings opened and closed without mite inoculation and the control brood (undisturbed, no mite inoculation), respectively. Brood removal peaked during the second and third days post inoculation when test brood was at the prepupal stage. Overall, non-reproduction (NR) of foundress T. mercedesae was high. However, when NR was measured based on the criteria used for Varroa, the naturally infested pupae (NIP) supported the highest NR (92.8 %). Newly sealed larvae inoculated with Tropilaelaps collected from newly sealed larvae (NSL) had 78.2 % NR and those inoculated with Tropilaelaps collected from tan-bodied pupae (TBP) had 76.8 % NR. Since Tropilaelaps is known to have a short development period and nearly all progeny reach adulthood by the time of host emergence, we also used two Tropilaelaps-specific criteria to determine NR. Foundresses that did not produce progeny and those that produced only one progeny were considered NR. Using these two criteria, NR decreased tremendously but showed similar trends with means of 65, 40 and 33 % for NIP, NSL and TBP, respectively. High NR in the NIP group may indicate increased hygienic behavior in Thai A. mellifera colonies. The removal of infested prepupae or tan-bodied pupae will likely decrease the reproductive potential of Tropilaelaps. Our study suggests that brood removal may be one of the resistance mechanisms towards T. mercedesae by naturally adapted Thai A. mellifera.

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.

Despite >130 years of microbial cultivation studies, many microorganisms remain resistant to traditional cultivation approaches, including numerous candidate phyla of bacteria and archaea. Unraveling the mysteries of these candidate phyla is a grand challenge in microbiology and is especially important in habitats where they are abundant, including some extreme environments and low-energy ecosystems. Over the past decade, parallel advances in DNA amplification, DNA sequencing and computing have enabled rapid progress on this problem, particularly through metagenomics and single-cell genomics. Although each approach suffers limitations, metagenomics and single-cell genomics are particularly powerful when combined synergistically. Studies focused on extreme environments have revealed the first substantial genomic information for several candidate phyla, encompassing putative acidophiles (Parvarchaeota), halophiles (Nanohaloarchaeota), thermophiles (Acetothermia, Aigarchaeota, Atribacteria, Calescamantes, Korarchaeota, and Fervidibacteria), and piezophiles (Gracilibacteria). These data have enabled insights into the biology of these organisms, including catabolic and anabolic potential, molecular adaptations to life in extreme environments, unique genomic features such as stop codon reassignments, and predictions about cell ultrastructure. In addition, the rapid expansion of genomic coverage enabled by these studies continues to yield insights into the early diversification of microbial lineages and the relationships within and between the phyla of Bacteria and Archaea. In the next 5 years, the genomic foliage within the tree of life will continue to grow and the study of yet-uncultivated candidate phyla will firmly transition into the post-genomic era.

Background

Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced.

Results

Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host.

Conclusions

The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.

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.

The nesting sites of open- and cavity-nesting honeybees are reviewed in terms of nest sites, space and honeybee density. Space comprises building space for new combs and living space for clustering bees. In a container of a fixed volume, a strong colony constructs more than a colony with a smaller population; but, the amount of comb constructed per bee decreases with increased density and increases in colony size. The quality aspects of space as a stimulus for comb-building include illumination and air movement. Volume, space and density will only operate on wax production when the colony has reached some critical, if yet indefinable, threshold. Wax bees move throughout the nest so there is a close synchrony between the ‘needs’ of specific comb-building areas and the presence of bees producing wax scales. During comb-building there are concomitant changes in population size, population density, nectar and pollen influx, all of which affect honeybee/comb interactions.

The phylum Thermotogae is comprised of anaerobic, thermophilic, as well as mesophilic bacteria that are surrounded by an outer sheathlike envelope referred to as a “toga.” The species from this deep-branching group exhibit Gram-negative staining, but due to the absence of an archetypal outer cell membrane, they are considered monoderm (or atypical diderm) bacteria. This phylum presently contains 10 genera harboring 41 validated species which are all part of a single family, Thermotogaceae, within the order Thermotogales. Comparative analyses of genome sequences have led to the discovery of numerous conserved signature indels (CSIs), in proteins, which are specific for different monophyletic clades of Thermotogae. These molecular markers provide reliable means for demarcation of different clades of the Thermotogae and for the taxonomical organization of this phylum. Based upon their phylogenetic branching and the discovered molecular markers, it has been proposed that the class Thermotogae be divided into three orders. These include an emended order Thermotogales containing the families Thermotogaceae (emended) and Fervidobacteriaceae fam. nov. and two new orders, Petrotogales and Kosmotogales. The identified CSIs also suggest that although the Thermotogae species have undergone gene exchanges with other prokaryotes, particularly with thermophilic organisms, the extent of such gene transfers is limited and they do not significantly affect the monophyly or distinctness of species from this phylum. Thermotogae species, due to their ability to efficiently metabolize numerous organic substrates, producing H₂ gas as a by-product, in conjunction with the thermostability of their enzymes, have also become an important focal point for different biotechnological applications.

Regularities of the appearance of family in the bee superfamily have been analyzed. It is shown that conversion in highly organized eusocial bee species into the biological unit is coupled to perfection of instincts of care of offspring of the female-founderer, an increase of its lifespan, with strengthening of various forms of domination. The concept is substantiated that development of offspring of dominating females under similar conditions ruling out the intranest competition as well as strengthening of interconnection and interdependence between members of the family have led to the appearance of family selection.

Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope (¹³C)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.