Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium

Background: The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic ‘Candidatus Phytoplasma’, all characterized Spiroplasma species were found to be associated with eukaryotic hosts. While most of the Spiroplasma species appeared to be harmless commensals of insects, a small number of species have evolved pathogenicity toward various arthropods and plants. In this study, we isolated a novel strain of honeybee-associated S. melliferum and investigated its genetic composition and evolutionary history by whole-genome shotgun sequencing and comparative analysis with other Mollicutes genomes. Results: The whole-genome shotgun sequencing of S. melliferum IPMB4A produced a draft assembly that was ~1.1 Mb in size and covered ~80% of the chromosome. Similar to other Spiroplasma genomes that have been studied to date, we found that this genome contains abundant repetitive sequences that originated from plectrovirus insertions. These phage fragments represented a major obstacle in obtaining a complete genome sequence of Spiroplasma with the current sequencing technology. Comparative analysis of S. melliferum IPMB4A with other Spiroplasma genomes revealed that these phages may have facilitated extensive genome rearrangements in these bacteria and contributed to horizontal gene transfers that led to species-specific adaptation to different eukaryotic hosts. In addition, comparison of gene content with other Mollicutes suggested that the common ancestor of the SEM (Spiroplasma, Entomoplasma, and Mycoplasma) clade may have had a relatively large genome and flexible metabolic capacity; the extremely reduced genomes of present day Mycoplasma and ‘Candidatus Phytoplasma’ species are likely to be the result of independent gene losses in these lineages. Conclusions: The findings in this study highlighted the significance of phage insertions and horizontal gene transfer in the evolution of bacterial genomes and acquisition of pathogenicity. Furthermore, the inclusion of Spiroplasma in comparative analysis has improved our understanding of genome evolution in Mollicutes. Future improvements in the taxon sampling of available genome sequences in this group are required to provide further insights into the evolution of these important pathogens of humans, animals, and plants

Spiroplasmas: Evolution, Adaptation and Diversity

Since its designation as a separate genus some 30 years ago, Spiroplasmas have been well documented in a wide range of hosts and as the causative agent of several plant and insect diseases. One major area of research is the continued identification and taxonomical characterization of new Spiroplasma sp. combined with a determination of phylogenetic relationships among the various Spiroplasma sp. and between the Spiroplasmas and other members of the Mollicutes and Eubacteria. Although most phylogenetic analyses have been dependent on 16S rDNA sequence data, progress in two Spiroplasma sp. genome sequencing projects will provide new genomic regions for comparative focus. The co-evolution of Spiroplasmas with their arthropod hosts has provided an additional research focus to study host specificity and attachment. The diversity of symbiotic relationships between Spiroplasmas and their hosts has led to the study of commensal, mutualistic, and pathogenic relationships. Pathogenesis in insect hosts or in plants, transferred by insect hosts, is a major research focus, which requires attachment and invasion into insect tissues beyond the initial infection site, and successful movement to other tissues. The diversity and adaptations that have occurred during the evolution of the Spiroplasmas with their hosts will be the primary focus of this article

Integration of Ethics Across the Curriculum: From First Year Through Senior Seminar

The Fisher College of Science and Mathematics (FCSM) at Towson University (TU) has integrated authentic research experiences throughout the curriculum from first year STEM courses through advanced upper-level classes and independent research. Our observation is that training in both responsible conduct of research (RCR) and bioethics throughout the curriculum was an effective strategy to advance the cognitive and psychosocial development of the students. As students enter TU they generally lack the experience and tools to assess their own competence, to apply ethical debates, to investigate scientific topics from an ethical perspective, or to integrate ethics into final conclusions. Student behavior and development follow cognitive models such as described in the theories put forth by Piaget, Kohlberg, and Erikson, both for initial learning and for how concepts are understood and adopted. Three examples of this ethics training integration are described, including a cohort-based course for first year students in the STEM Residential Learning Community, a cohort-based course for community college students that are involved in an NIH-funded Bridges to the Baccalaureate program, and a senior seminar in Bioethics in the Molecular Biology, Biochemistry and Bioinformatics Program. All three focus on different aspects of RCR and bioethics training, providing opportunities for students to learn about the principles of effective decision-making, critical and analytical thinking, problem solving, and communication with increasing degrees of complexity as they move through the curriculum

Spiroplasma

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Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.)

Spiroplasma turonicum Tab4cT was isolated from a horse fly (Haematopota sp.; probably Haematopota pluvialis) collected at Champchevrier, Indre-et-Loire, Touraine, France, in 1991. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma spp

Found and Lost: The Fates of Horizontally Acquired Genes in Arthropod-Symbiotic Spiroplasma

Horizontal gene transfer (HGT) is an important mechanism that contributed to biological diversity, particularly in bacteria. Through acquisition of novel genes, the recipient cell may change its ecological preference and the process could promote speciation. In this study, we determined the complete genome sequence of two Spiroplasma species for comparative analyses and inferred the putative gene gains and losses. Although most Spiroplasma species are symbionts of terrestrial insects, Spiroplasma eriocheiris has evolved to be a lethal pathogen of freshwater crustaceans. We found that approximately 7% of the genes in this genome may have originated from HGT and these genes expanded the metabolic capacity of this organism. Through comparison with the closely related Spiroplasma atrichopogonis, as well as other more divergent lineages, our results indicated that these HGT events could be traced back to the most recent common ancestor of these two species. However, most of these horizontally acquired genes have been pseudogenized in S. atrichopogonis, suggesting that they did not contribute to the fitness of this lineage that maintained the association with terrestrial insects. Thus, accumulation of small deletions that disrupted these foreign genes was not countered by natural selection. On the other hand, the long-term survival of these horizontally acquired genes in the S. eriocheiris genome hinted that they might play a role in the ecological shift of this species. Finally, the implications of these findings and the conflicts among gene content, 16S rRNA gene sequencing, and serological typing, are discussed in light of defining bacterial species

The Importance of Terrestrial Dispersal for Connectivity Among Headwater Salamander Populations

Many organisms are primarily constrained to the channels of the upstream terminus of river networks with limited capacities for both in‐stream and overland dispersal. Dispersal is believed to contribute to gene flow and the demographic stability of headwater populations. While assumed, the importance of overland dispersal to gene flow is largely unexplored in headwater salamanders. Six microsatellite markers were used to assess patterns of genetic population structure for a headwater salamander, Desmognathus fuscus. Tissue samples were collected using a nested hierarchical study design, which specifically addressed the contribution of overland movements to the genetic connectivity of headwater populations. Genetic divergence was significant among all populations (Fst = 0.027–0.405) and at all hierarchical spatial scales. However, lower degrees of genetic population structure were observed among proximal streams that shared no downstream hydrologic connections. Mantel tests indicated a significant relationship between genetic divergence and overland distance, suggesting that D. fuscus populations conform to an isolation‐by‐distance model of gene flow. Estimated dispersal among headwater streams was limited, with an average of less than one effective migrant per generation moving between paired headwater streams. These results indicate that regional patterns of genetic population structure are influenced by overland dispersal and suggest the importance of terrestrial movements in maintaining population connectivity among D. fuscus populations

Complete Genome Sequence of Spiroplasma sp. NBRC 100390

Spiroplasma sp. NBRC 100390 was initially described as a duplicate of S. atrichopogonis GNAT3597T (ATCC BAA-520T) but later found to be different in the 16S rDNA sequences. Here, we report the complete genome sequence of this bacterium to establish its identity and to facilitate future investigation

Complete Genome Sequence of Spiroplasma sp. TU-14

Spiroplasma sp. TU-14 was isolated from a contaminated sample of Entomoplasma lucivorax PIPN-2T obtained from the International Organization for Mycoplasmology collection. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma spp