Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M . W . B eijerinck

Luminous bacteria isolated by M artinus W . B eijerinck were sealed in glass ampoules in 1924 and 1925 and stored under the names P hotobacterium phosphoreum and ‘ P hotobacterium splendidum ’. To determine if the stored cultures were viable and to assess their evolutionary relationship with currently recognized bacteria, portions of the ampoule contents were inoculated into culture medium. Growth and luminescence were evident after 13 days of incubation, indicating the presence of viable cells after more than 80 years of storage. The B eijerinck strains are apparently the oldest bacterial cultures to be revived from storage. Multi‐locus sequence analysis, based on the 16S rRNA , gapA , gyrB , pyrH , recA , luxA , and luxB genes, revealed that the B eijerinck strains are distant from the type strains of P . phosphoreum , ATCC 11040 T , and V ibrio splendidus , ATCC 33125 T , and instead form an evolutionarily distinct clade of V ibrio . Newly isolated strains from coastal seawater in N orway, F rance, U ruguay, M exico, and J apan grouped with the B eijerinck strains, indicating a global distribution for this new clade, designated as the beijerinckii clade. Strains of the beijerinckii clade exhibited little sequence variation for the seven genes and approximately 6300 nucleotides examined despite the geographic distances and the more than 80 years separating their isolation. Gram‐negative bacteria therefore can survive for many decades in liquid storage, and in nature, they do not necessarily diverge rapidly over time.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/88047/1/fem1177.pd

Phylogenetic analysis of host–symbiont specificity and codivergence in bioluminescent symbioses

Several groups of marine fishes and squids form mutualistic bioluminescent symbioses with luminous bacteria. The dependence of the animal on its symbiont for light production, the animal's specialized anatomical adaptations for harboring bacteria and controlling light emission, and the host family bacterial species specificity characteristic of these associations suggest that bioluminescent symbioses are tightly coupled associations that might involve coevolutionary interactions. Consistent with this possibility, evidence of parallel cladogenesis has been reported for squid–bacterial associations. However, genetic adaptations in the bacteria necessary for and specific to symbiosis have not been identified, and unlike obligate endosymbiotic associations in which the bacteria are transferred vertically, bacterially bioluminescent hosts acquire their light-organ symbionts from the environment with each new host generation. These contrasting observations led us to test the hypotheses of species specificity and codivergence in bioluminescent symbioses, using an extensive sampling of naturally formed associations. Thirty-five species of fish in seven teleost families (Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae, Monocentridae, Acropomatidae, Leiognathidae) and their light-organ bacteria were examined. Phylogenetic analysis of a taxonomically broad sampling of associations was based on mitochondrial 16S rRNA and cytochrome oxidase I gene sequences for the fish and on recA , gyrB and luxA sequences for bacteria isolated from the light organs of these specimens. In a fine-scale test focused on Leiognathidae, phylogenetic analysis was based also on histone H3 subunit and 28S rRNA gene sequences for the fish and on gyrB , luxA , luxB , luxF and luxE sequences for the bacteria. Deep divergences were revealed among the fishes, and clear resolution was obtained between clades of the bacteria. In several associations, bacterial species identities contradicted strict host family bacterial species specificity. Furthermore, the fish and bacterial phylogenies exhibited no meaningful topological congruence; evolutionary divergence of host fishes was not matched by a similar pattern of diversification in the symbiotic bacteria. Re-analysis of data reported for squids and their luminous bacteria also revealed no convincing evidence of codivergence. These results refute the hypothesis of strict host family bacterial species specificity and the hypothesis of codivergence in bioluminescent symbioses. © The Willi Hennig Society 2007.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73754/1/j.1096-0031.2007.00157.x.pd

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology. 2013;14(11): R130.BACKGROUND: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. RESULTS: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. CONCLUSIONS: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host

Evolution in Squamata (Reptilia).

Evolution in Squamata (Reptilia) focuses primarily on the phylogenetics and evolution of Varanus, commonly known as monitor lizards. Mitochondrial DNA is used to test phylogenetic hypotheses of relationships among these lizards, and the evolution of other traits of Varanus is considered in light of this hypothesis. In addition, three phylogenetic hypotheses of Anguimorpha are tested, as are the relationships among squamates, and the evolutionary origin of snakes. Chapter I reviews the taxonomy and diversity of Lepidosauria, the group containing all of the taxa of interest. Chapter II presents a phylogenetic hypothesis for Varanoidea based on mitochondrial DNA data, addresses the chromosome evolution and taxonomy of Varanus, and refutes the hypothesis that heterogeneous rates of sequence evolution are necessarily problematic to cladistic analysis. The evolutionary conclusions of Chapter II are reconsidered in Chapter III, in which the phylogenetic hypothesis is tested with additional data. The evolution of several additional morphological traits of Varanus is evaluated, as is the biogeography of Varanus and clades within it. A new taxonomy for Varanus based on this phylogenetic hypotheses is proposed. Chapter IV tests Anguimorpha and the traditionally recognized groups within it, and refutes Anguioidea, Varanoidea, and Xenosauridae. Chapter V addresses the recent controversy concerning the origin of snakes, using morphological and mitochondrial DNA evidence from basal and derived snakes and most of the groups within Squamata. Analysis of the molecular data refutes a sister group relationship between snakes and Varanus, Varanidae, or Varanoidea. The hypothesis that snakes are sister to extinct marine varanoids (mosasaurs) is refuted by simultaneous analysis of morphological and molecular data, thereby casting doubt on the inference that snakes evolved in a marine environment.PhDBiological SciencesMolecular biologyZoologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/131189/2/3057888.pd

Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea Fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040(T), and the type strain of Photobacterium iliopiscarium, ATCC 51760(T). Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040(T). These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes

Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi

The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521 T , ATCC 25587, lequu .1.1 and lleuc .1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561 T and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561 T , ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE ), whereas ATCC 25521 T , ATCC 25587, lequu .1.1 and lleuc .1.1 lack this gene ( luxABE ). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561 T , ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521 T , ATCC 25587, lequu .1.1 and lleuc .1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521 T , ATCC 25587, lequu .1.1 and lleuc .1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561 T , ATCC 33981, PL-721, PL-741 and 554).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46133/1/203_2004_Article_663.pd

Observing the Scribe at Work Scribal Practice in the Ancient World

This volume collects contributions on scribal practice as it features on diverse media (including papyri, tablets, and inscriptions) in a range of ancient societies, from the Ancient Near East and Dynastic Egypt through the Graeco-Roman ..

Influence of Different Arm Positions in the Localizer Radiograph(s) on Patient Dose during Exposure-Controlled CT Examinations of the Neck to Pelvis

Our aim was to examine the impact of different arm positions during imaging of the localizer radiograph(s) on effective dose for exposure-controlled computed tomography (CT) (Siemens/Canon) scans of the neck to pelvis. An anthropomorphic whole-body phantom was scanned from the neck to pelvis with the arms positioned in three different ways during the acquisition of the localizer radiograph: (i) above the head, (ii) alongside the trunk, and (iii) along the trunk with the hands placed on the abdomen. In accordance with clinical routines, the arms were not included in the subsequent helical scans. Effective doses were computed to a standard-sized patient (male/female) using a dedicated system-specific Monte Carlo-based software. Effective doses for the Canon CT scanner for the different alternatives (male/female) were (a) 5.3/6.62 mSv, (b) 5.62/7.15 mSv and (c) 5.92/7.44 mSv. For the Siemens CT scanner, effective doses were (a) 4.47/5.59 mSv, (b) 5.4/6.69 mSv and (c) 5.7/6.99 mSv. Arms placed above the head during localizer radiograph imaging in the current CT procedures substantially reduced the total effective dose to the patient

Natural Merodiploidy of the lux-rib Operon of Photobacterium leiognathi from Coastal Waters of Honshu, Japan▿ †

Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib1 and lux-rib2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib1 and lux-rib2, whereas ATCC 25521T apparently carries only lux-rib1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib2 of lnuch.13.1, and the chromosomal location of lux-rib2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib1 and lux-rib2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib2 in P. leiognathi; lux-rib2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography