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Статті в журналах з теми "Alvinella"

Автор: Grafiati

Опубліковано: 26 жовтня 2023

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1

Tunnicliffe, Verena, Daniel Desbruyères, Didier Jollivet, and Lucien Laubier. "Systematic and ecological characteristics of Paralvinella sulfincola Desbruyères and Laubier, a new polychaete (family Alvinellidae) from northeast Pacific hydrothermal vents." Canadian Journal of Zoology 71, no. 2 (February 1, 1993): 286–97. http://dx.doi.org/10.1139/z93-041.

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Polychaetes of the family Alvinellidae (Terrebellida) are endemic to hydrothermal vent communities. A new species from the Juan de Fuca and Gorda ridges in the Northeast Pacific is described; aspects of its buccal appendages, segment number, and uncini placement are unique. Because of initial confusion with a sympatric species, Paralvinella palmiformis Desbruyères and Laubier, protein mobilities were examined to differentiate the species electrophoretically with reference to a third alvinellid, Alvinella pompejana. Among the 17 loci scored, fewer than a quarter of the alleles were present in the two Paralvinella species; Paralvinella sulfincola n.sp. has several diagnostic allozymes. This new species inhabits tubes on the sides of active smoker chimneys and migrates upward as the chimney grows. Individuals are recorded within 1 cm of hydrothermal fluids at temperatures in excess of 300 °C; the species appears to have several molecular adaptations to high ambient temperatures. The Alvinellidae form a fascinating group within which to study phylogenetic and selective processes.

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2

Alayse-Danet, A. M., F. Gaill, and D. Desbruyeres. "In situ Bicarbonate Uptake by Bacteria-Alvinella Associations." Marine Ecology 7, no. 3 (September 1986): 233–40. http://dx.doi.org/10.1111/j.1439-0485.1986.tb00160.x.

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3

Jeanthon, Christian, and Daniel Prieur. "Susceptibility to Heavy Metals and Characterization of Heterotrophic Bacteria Isolated from Two Hydrothermal Vent Polychaete Annelids, Alvinella pompejana and Alvinella caudata." Applied and Environmental Microbiology 56, no. 11 (1990): 3308–14. http://dx.doi.org/10.1128/aem.56.11.3308-3314.1990.

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4

Lee, Charles K., S. Craig Cary, Alison E. Murray, and Roy M. Daniel. "Enzymic Approach to Eurythermalism of Alvinella pompejana and Its Episymbionts." Applied and Environmental Microbiology 74, no. 3 (December 14, 2007): 774–82. http://dx.doi.org/10.1128/aem.01960-07.

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ABSTRACT The equilibrium model, which describes the influence of temperature on enzyme activity, has been established as a valid and useful tool for characterizing enzyme eurythermalism and thermophily. By introducing K eq, a temperature-dependent equilibrium constant for the interconversion between Eact, the active form of enzyme, and Einact, a reversibly inactive form of enzyme, the equilibrium model currently provides the most complete description of the enzyme-temperature relationship; its derived parameters are intrinsic and apparently universal and, being derived under reaction conditions, potentially have physiological significance. One of these parameters, T eq, correlates with host growth temperature better than enzyme stability does. The vent-dwelling annelid Alvinella pompejana has been reported as an extremely eurythermal organism, and the symbiotic complex microbial community associated with its dorsal surface is likely to experience similar environmental thermal conditions. The A. pompejana episymbiont community, predominantly composed of epsilonproteobacteria, has been analyzed metagenomically, enabling direct retrieval of genes coding for enzymes suitable for equilibrium model applications. Two such genes, coding for isopropylmalate dehydrogenase and glutamate dehydrogenase, have been isolated from the A. pompejana episymbionts, heterologously expressed, and shown by reverse transcription-quantitative PCR to be actively expressed. The equilibrium model parameters of characterized expression products suggested that enzyme eurythermalism constitutes part of the thermal adaptation strategy employed by the episymbionts. Moreover, the enzymes' thermal characteristics correspond to their predicted physiological roles and the abundance and expression of the corresponding genes. This paper demonstrates the use of the equilibrium model as part of a top-down metagenomic approach to studying temperature adaptation of uncultured organisms.

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5

Wijckmans, Eveline, Mieke Nys, Sarah Debaveye, Marijke Brams, Els Pardon, Katrien Willegems, Daniel Bertrand, Jan Steyaert, Rouslan Efremov, and Chris Ulens. "Functional and Biochemical Characterization of Alvinella pompejana Cys-Loop Receptor Homologues." PLOS ONE 11, no. 3 (March 21, 2016): e0151183. http://dx.doi.org/10.1371/journal.pone.0151183.

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6

Wijckmans, Eveline, Mieke Nys, Sarah Debaveye, Marijke Brams, Els Pardon, Daniel Bertrand, Jan Steyaert, and Chris Ulens. "Functional and Biochemical Characterization of Alvinella Pompejana Cys-Loop Receptor Homologues." Biophysical Journal 110, no. 3 (February 2016): 602a—603a. http://dx.doi.org/10.1016/j.bpj.2015.11.3218.

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7

Mary, Jean, Hélène Rogniaux, Jean-François Rees, and Franck Zal. "Response of Alvinella pompejana to variable oxygen stress: A proteomic approach." PROTEOMICS 10, no. 12 (April 7, 2010): 2250–58. http://dx.doi.org/10.1002/pmic.200900394.

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8

Taylor, Craig D., Carl O. Wirsen, and Françoise Gaill. "Rapid Microbial Production of Filamentous Sulfur Mats at Hydrothermal Vents." Applied and Environmental Microbiology 65, no. 5 (May 1, 1999): 2253–55. http://dx.doi.org/10.1128/aem.65.5.2253-2255.1999.

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ABSTRACT During recent oceanographic cruises to Pacific hydrothermal vent sites (9°N and the Guaymas Basin), the rapid microbial formation of filamentous sulfur mats by a new chemoautotrophic, hydrogen sulfide-oxidizing bacterium was documented in both in situ and shipboard experiments. Observations suggest that formation of these sulfur mats may be a factor in the initial colonization of hydrothermal surfaces by macrofaunal Alvinella worms. This novel metabolic capability, previously shown to be carried out by a coastal strain in H2S continuous-flow reactors, may be an important, heretofore unconsidered, source of microbial organic matter production at deep-sea hydrothermal vents.

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9

Le Bris, N., and F. Gaill. "How does the annelid Alvinella pompejana deal with an extreme hydrothermal environment?" Reviews in Environmental Science and Bio/Technology 6, no. 1-3 (November 25, 2006): 197–221. http://dx.doi.org/10.1007/s11157-006-9112-1.

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10

Gaill, F., and Y. Bouligand. "Supercoil of collagen fibrils in the integument of Alvinella, an abyssal annelid." Tissue and Cell 19, no. 5 (January 1987): 625–42. http://dx.doi.org/10.1016/0040-8166(87)90070-x.

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11

Jollivet, D., L. R. J. Dixon, D. Desbruyeres, and D. R. Dixon. "Ribosomal (rDNA) Variation in a Deep Sea Hydrothermal Vent Polychaete, Alvinella Pompejana, From 13°N on the East Pacific Rise." Journal of the Marine Biological Association of the United Kingdom 78, no. 1 (February 1998): 113–30. http://dx.doi.org/10.1017/s0025315400039989.

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The rDNA repeat-unit of the vent polychaete Alvinella pompejana was investigated using restriction analysis. Mapping revealed evidence of rDNA polymorphism within and between individuals which was due to individual restriction site variation and sequence rearrangements involving spacer regions. The size of the repeat unit was 10.5 kb with virtually no evidence of length variation. Sequence inversions indicated the presence of two spatially-distinct subfamilies of repeats, probably on different chromosome pairs. Animals from contrasting vent habitats with respect to age and chemical emissions (young vs old chimneys and white vs black smokers) from within the 13°N/EPR (East Pacific Rise) vent sector were analysed for evidence of population differentiation. Based on individual restriction site variation, average FST estimates across neighbouring populations were in the region of ~0.05 and differed significantly from zero. This level of genetic differentiation is comparable to values reported previously for allozymes. Spatial and temporal allelic frequency variances estimated from pairwise combinations (i.e. s2S and s2T) strongly suggested that differences in allelic frequency were the result of repeated extinction/recolonization events associated with the vent instability. Estimates of the effective population size derived from standardized temporal allelic frequency variances Fks were very low compared to actual population size indicating great temporal fluctuations in the former. Theoretically, such an effective population size is not sufficient to maintain the observed level of polymorphism within the 13N/EPR vent sector. Results are therefore consistent with a ‘propagule’ colonization-type model in which extinction/recolonization rates are high. In Alvinella, planktonic larval dispersal appears sufficient to overcome any genetic differentiation resulting from drift, but these findings also indicate that propagules may only be capable of dispersing a few tens of kilometres per generation.

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12

Hunt, Stephen. "Crystalline sulphur deposits on the tube of the hydrothermal vent worm Alvinella pompejana." Comparative Biochemistry and Physiology Part A: Physiology 102, no. 1 (May 1992): 71–77. http://dx.doi.org/10.1016/0300-9629(92)90014-h.

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13

Jouan, Ludovic, Sergio Marco, and Jean-Christophe Taveau. "Revisiting the structure of Alvinella pompejana hemoglobin at 20Å resolution by cryoelectron microscopy." Journal of Structural Biology 143, no. 1 (July 2003): 33–44. http://dx.doi.org/10.1016/s1047-8477(03)00115-1.

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14

Desbruyères, Daniel, and Lucien Laubier. "Les Alvinellidae, une famille nouvelle d'annélides polychètes inféodées aux sources hydrothermales sous-marines: systématique, biologie et écologie." Canadian Journal of Zoology 64, no. 10 (October 1, 1986): 2227–45. http://dx.doi.org/10.1139/z86-337.

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Examination of all the specimens collected from deep hydrothermal vents in the eastern Pacific allowed us to describe two new species and one new subspecies belonging to the genus Paralvinella Desbruyères and Laubier, 1982: P. pandorae sp.n., P. palmiformis sp. n., and P. pandorae irlandei ssp. n. Alvinella pompejana is split into two species, A. pompejana and A. caudata sp.n., based on to morphological and biochemical data. The six species and subspecies of Alvinellinae (Polychaeta: Ampharetidae) are well separated from all other terebellomorph species by the absence of differentiation between thorax and abdomen. We propose here the erection of a new family, Alvinellidae, which seems to be primitive within the order Terebellida. All known alvinellids are strictly associated with deep hydrothermal vent phenomena.

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15

Genard, B., B. Marie, E. Loumaye, B. Knoops, P. Legendre, F. Zal, and JF Rees. "Living in a hot redox soup: antioxidant defences of the hydrothermal worm Alvinella pompejana." Aquatic Biology 18, no. 3 (May 16, 2013): 217–28. http://dx.doi.org/10.3354/ab00498.

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16

Campbell, Barbara J., and S. Craig Cary. "Characterization of a Novel Spirochete Associated with the Hydrothermal Vent Polychaete Annelid, Alvinella pompejana." Applied and Environmental Microbiology 67, no. 1 (January 1, 2001): 110–17. http://dx.doi.org/10.1128/aem.67.1.110-117.2001.

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ABSTRACT A highly integrated, morphologically diverse bacterial community is associated with the dorsal surface of Alvinella pompejana, a polychaetous annelid that inhabits active high-temperature deep-sea hydrothermal vent sites along the East Pacific Rise (EPR). Analysis of a previously prepared bacterial 16S ribosomal DNA (rDNA) library identified a spirochete most closely related to an endosymbiont of the oligochete Olavius loisae. This spirochete phylotype (spirochete A) comprised only 2.2% of the 16S rDNA clone library but appeared to be much more dominant when the same sample was analyzed by denaturing gradient gel electrophoresis (DGGE) and the terminal restriction fragment length polymorphism procedure (12 to 18%). PCR amplification of the community with spirochete-specific primers used in conjunction with DGGE analysis identified two spirochete phylotypes. The first spirochete was identical to spirochete A but was present in only one A. pompejana specimen. The second spirochete (spirochete B) was 84.5% similar to spirochete A and, more interestingly, was present in the epibiont communities of all of theA. pompejana specimens sampled throughout the geographic range of the worm (13°N to 32°S along the EPR). The sequence variation of the spirochete B phylotype was less than 3% for the range of A. pompejana specimens tested, suggesting that a single spirochete species was present in the A. pompejanaepibiotic community. Additional analysis of the environments surrounding the worm revealed that spirochetes are a ubiquitous component of high-temperature vents and may play an important role in this unique ecosystem.

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17

Haddad, A., F. Camacho, P. Durand, and S. C. Cary. "Phylogenetic characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana." Applied and environmental microbiology 61, no. 5 (1995): 1679–87. http://dx.doi.org/10.1128/aem.61.5.1679-1687.1995.

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18

Gaill, F., and S. Hunt. "Tubes of deep sea hydrothermal vent worms Riftia pachyptila (Vestimentifera) and Alvinella pompejana (Annelida)." Marine Ecology Progress Series 34 (1986): 267–74. http://dx.doi.org/10.3354/meps034267.

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19

Pradillon, F. "Influence of environmental conditions on early development of the hydrothermal vent polychaete Alvinella pompejana." Journal of Experimental Biology 208, no. 8 (April 15, 2005): 1551–61. http://dx.doi.org/10.1242/jeb.01567.

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20

Saulnier-Michel, C., F. Gaill, A. Hily, P. Alberic, and M. A. Cosson-Mannevy. "Structure and functions of the digestive tract of Alvinella pompejana, a hydrothermal vent polychaete." Canadian Journal of Zoology 68, no. 4 (April 1, 1990): 722–32. http://dx.doi.org/10.1139/z90-105.

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The different parts of the digestive tract of Alvinella pompejana are described. The buccal apparatus presents a ventral pharyngeal organ, which is thought to be protrusible, and a dorsal anterior oesophageal gland. Unusual racks are observed in this part, a fact that confirms the deposit feeding behaviour of the worm which has been hypothetized. The serous cells of the oesophageal gland may be the origin of the proteolytic activity detected in the lumen. Intracellular enzymatic activities are detected in the stomach cells. These cells are characterized by numerous iron concretions and polyphagosomes. Comparative elemental analysis of these concretions lead us to think that this digestive segment is a homeostatic organ. The intestine is composed of an absorbant epithelium including enterocytic cells, myocytes, and cells containing zymogenic granules. As much as 90% of ingested protein matter occurs in a water-soluble state (half of it free amino acids, principally glycine) immediately on passing through the anterior part of the gut lumen. In the hindgut, solid faeces are mostly composed of elemental sulfur and are glycine depleted, making them good candidates to form the bulk of the suspended particles found in the waters closely surrounding the worm colonies. The whole gut content contains a high concentration of elemental sulfur. The digestive process of the worm is discussed.

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21

Maginn, Ellis J., Crispin T. S. Little, Richard J. Herrington, and Rachel A. Mills. "Sulphide mineralisation in the deep sea hydrothermal vent polychaete, Alvinella pompejana: implications for fossil preservation." Marine Geology 181, no. 4 (March 2002): 337–56. http://dx.doi.org/10.1016/s0025-3227(01)00196-7.

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22

Henscheid, Kristy L., David S. Shin, S. Craig Cary, and J. Andrew Berglund. "The splicing factor U2AF65 is functionally conserved in the thermotolerant deep-sea worm Alvinella pompejana." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1727, no. 3 (March 2005): 197–207. http://dx.doi.org/10.1016/j.bbaexp.2005.01.008.

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23

Campbell, Barbara J., Jeffrey L. Stein, and S. Craig Cary. "Evidence of Chemolithoautotrophy in the Bacterial Community Associated with Alvinella pompejana, a Hydrothermal Vent Polychaete." Applied and Environmental Microbiology 69, no. 9 (September 2003): 5070–78. http://dx.doi.org/10.1128/aem.69.9.5070-5078.2003.

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ABSTRACT The deep-sea polychaete Alvinella pompejana colonizes tubes on the sides of black smoker chimneys along the East Pacific Rise. A diverse, yet phylogenetically constrained episymbiotic community is obligately associated with its dorsal surface. The morphologically and phylogenetically distinct dominant episymbionts have not yet been cultured, and there are no clearly defined roles for these bacteria in this symbiosis. A large insert fosmid library was screened for the presence of the two dominant phylotypes. Two fosmids, 35.2 and 38 kb, containing phylotype-specific 16S ribosmal DNA sequences were fully sequenced. Each fosmid had a gene encoding ATP citrate lyase, a key enzyme in the reverse tricarboxylic acid (rTCA) cycle, a CO2 fixation pathway. A selection of episymbiont communities from various geographic locations and vent sites were screened for the presence, diversity, and expression (via reverse transcription-PCR) of the ATP citrate lyase gene. Our results indicate that the ATP citrate lyase gene is not only a consistent presence in these episymbiont communities but is also expressed. Phylogenetically distinct forms of ATP citrate lyase were also found associated with and expressed by bacteria extracted from the tubes of A. pompejana. Utilizing PCR with degenerate primers based on a second key enzyme in the rTCA cycle, 2-oxoglutarate:acceptor oxidoreductase, we also demonstrated the persistent presence and expression of this gene in the episymbiont community. Our results suggest that members of both the episymbiont and the surrounding free-living communities display a chemolithoautotrophic form of growth and therefore contribute fixed carbon to other organisms in the vent community.

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24

Hourdez, Stéphane, François H. Lallier, Marie‐Cécile De Cian, Brian N. Green, Roy E. Weber, and André Toulmond. "Gas Transfer System in Alvinella pompejana (Annelida Polychaeta, Terebellida): Functional Properties of Intracellular and Extracellular Hemoglobins." Physiological and Biochemical Zoology 73, no. 3 (May 2000): 365–73. http://dx.doi.org/10.1086/316755.

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25

Piccino, P., F. Viard, P. Sarradin, N. Le Bris, D. Le Guen, and D. Jollivet. "Thermal selection of PGM allozymes in newly founded populations of the thermotolerant vent polychaete Alvinella pompejana." Proceedings of the Royal Society of London. Series B: Biological Sciences 271, no. 1555 (November 22, 2004): 2351–59. http://dx.doi.org/10.1098/rspb.2004.2852.

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26

Faure, B., P. Chevaldonné, F. Pradillon, E. Thiébaut, and D. Jollivet. "Spatial and temporal dynamics of reproduction and settlement in the Pompeii worm Alvinella pompejana (Polychaeta: Alvinellidae)." Marine Ecology Progress Series 348 (October 25, 2007): 197–211. http://dx.doi.org/10.3354/meps07021.

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27

Di Meo-Savoie, Carol A., George W. Luther, and S. Craig Cary. "Physicochemical characterization of the microhabitat of the epibionts associated with Alvinella pompejana, a hydrothermal vent annelid." Geochimica et Cosmochimica Acta 68, no. 9 (May 2004): 2055–66. http://dx.doi.org/10.1016/j.gca.2003.10.039.

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28

Cary, S. C., M. T. Cottrell, J. L. Stein, F. Camacho, and D. Desbruyeres. "Molecular Identification and Localization of Filamentous Symbiotic Bacteria Associated with the Hydrothermal Vent Annelid Alvinella pompejana." Applied and environmental microbiology 63, no. 3 (1997): 1124–30. http://dx.doi.org/10.1128/aem.63.3.1124-1130.1997.

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29

Tasiemski, Aurélie, Sascha Jung, Céline Boidin-Wichlacz, Didier Jollivet, Virginie Cuvillier-Hot, Florence Pradillon, Costantino Vetriani, et al. "Characterization and Function of the First Antibiotic Isolated from a Vent Organism: The Extremophile Metazoan Alvinella pompejana." PLoS ONE 9, no. 4 (April 28, 2014): e95737. http://dx.doi.org/10.1371/journal.pone.0095737.

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30

Phleger, Charles F., Matthew M. Nelson, Ami K. Groce, S. Craig Cary, Kathryn Coyne, John A. E. Gibson, and Peter D. Nichols. "Lipid biomarkers of deep-sea hydrothermal vent polychaetes—Alvinella pompejana, A. caudata, Paralvinella grasslei and Hesiolyra bergii." Deep Sea Research Part I: Oceanographic Research Papers 52, no. 12 (December 2005): 2333–52. http://dx.doi.org/10.1016/j.dsr.2005.08.001.

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31

Shin, David S., Michael DiDonato, David P. Barondeau, Greg L. Hura, Chiharu Hitomi, J. Andrew Berglund, Elizabeth D. Getzoff, S. Craig Cary, and John A. Tainer. "Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis." Journal of Molecular Biology 385, no. 5 (February 2009): 1534–55. http://dx.doi.org/10.1016/j.jmb.2008.11.031.

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32

Jeanthon, Christian, and Daniel Prieur. "Resistance to heavy metals of heterotrophic bacteria isolated from the deep-sea hydrothermal vent polychaete, Alvinella pompejana." Progress in Oceanography 24, no. 1-4 (January 1990): 81–88. http://dx.doi.org/10.1016/0079-6611(90)90021-s.

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33

Talmont, Franck, and Bernard Fournet. "Isolation and characterization of methylated sugars from the tube of the hydrothermal vent tubiculous annelid worm Alvinella pompejana." FEBS Letters 281, no. 1-2 (April 9, 1991): 55–58. http://dx.doi.org/10.1016/0014-5793(91)80357-9.

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34

Pradillon, F., M. Zbinden, LS Mullineaux, and F. Gaill. "Colonisation of newly-opened habitat by a pioneer species, Alvinella pompejana (Polychaeta: Alvinellidae), at East Pacific Rise vent sites." Marine Ecology Progress Series 302 (2005): 147–57. http://dx.doi.org/10.3354/meps302147.

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35

Cottrell, Matthew T., and S. Craig Cary. "Diversity of Dissimilatory Bisulfite Reductase Genes of Bacteria Associated with the Deep-Sea Hydrothermal Vent Polychaete Annelid Alvinella pompejana." Applied and Environmental Microbiology 65, no. 3 (March 1, 1999): 1127–32. http://dx.doi.org/10.1128/aem.65.3.1127-1132.1999.

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ABSTRACT A unique community of bacteria colonizes the dorsal integument of the polychaete annelid Alvinella pompejana, which inhabits the high-temperature environments of active deep-sea hydrothermal vents along the East Pacific Rise. The composition of this bacterial community was characterized in previous studies by using a 16S rRNA gene clone library and in situ hybridization with oligonucleotide probes. In the present study, a pair of PCR primers (P94-F and P93-R) were used to amplify a segment of the dissimilatory bisulfite reductase gene from DNA isolated from the community of bacteria associated withA. pompejana. The goal was to assess the presence and diversity of bacteria with the capacity to use sulfate as a terminal electron acceptor. A clone library of bisulfite reductase gene PCR products was constructed and characterized by restriction fragment and sequence analysis. Eleven clone families were identified. Two of the 11 clone families, SR1 and SR6, contained 82% of the clones. DNA sequence analysis of a clone from each family indicated that they are dissimilatory bisulfite reductase genes most similar to the dissimilatory bisulfite reductase genes of Desulfovibrio vulgaris, Desulfovibrio gigas, Desulfobacterium autotrophicum, and Desulfobacter latus. Similarities to the dissimilatory bisulfite reductases ofThermodesulfovibrio yellowstonii, the sulfide oxidizerChromatium vinosum, the sulfur reducerPyrobaculum islandicum, and the archaeal sulfate reducerArchaeoglobus fulgidus were lower. Phylogenetic analysis separated the clone families into groups that probably represent two genera of previously uncharacterized sulfate-reducing bacteria. The presence of dissimilatory bisulfite reductase genes is consistent with recent temperature and chemical measurements that documented a lack of dissolved oxygen in dwelling tubes of the worm. The diversity of dissimilatory bisulfite reductase genes in the bacterial community on the back of the worm suggests a prominent role for anaerobic sulfate-reducing bacteria in the ecology of A. pompejana.

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36

Bioy, Alexis, Anne-Sophie Le Port, Emeline Sabourin, Marie Verheye, Patrice Piccino, Baptiste Faure, Stéphane Hourdez, Jean Mary, and Didier Jollivet. "Balanced Polymorphism at the Pgm-1 Locus of the Pompeii Worm Alvinella pompejana and Its Variant Adaptability Is Only Governed by Two QE Mutations at Linked Sites." Genes 13, no. 2 (January 24, 2022): 206. http://dx.doi.org/10.3390/genes13020206.

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The polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal chimneys along the East Pacific Rise (EPR), and displays specific adaptations to withstand the high temperatures and hypoxia associated with this highly variable habitat. Previous studies have revealed the existence of a balanced polymorphism on the enzyme phosphoglucomutase associated with thermal variations, where allozymes 90 and 100 exhibit different optimal activities and thermostabilities. Exploration of the mutational landscape of phosphoglucomutase 1 revealed the maintenance of four highly divergent allelic lineages encoding the three most frequent electromorphs over the geographic range of A. pompejana. This polymorphism is only governed by two linked amino acid replacements, located in exon 3 (E155Q and E190Q). A two-niche model of selection, including ‘cold’ and ‘hot’ conditions, represents the most likely scenario for the long-term persistence of these isoforms. Using directed mutagenesis and the expression of the three recombinant variants allowed us to test the additive effect of these two mutations on the biochemical properties of this enzyme. Our results are coherent with those previously obtained from native proteins, and reveal a thermodynamic trade-off between protein thermostability and catalysis, which is likely to have maintained these functional phenotypes prior to the geographic separation of populations across the Equator about 1.2 million years ago.

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37

Georgieva, Magdalena N., Crispin T. S. Little, Russell J. Bailey, Alexander D. Ball, and Adrian G. Glover. "Microbial-tubeworm associations in a 440 million year old hydrothermal vent community." Proceedings of the Royal Society B: Biological Sciences 285, no. 1891 (November 14, 2018): 20182004. http://dx.doi.org/10.1098/rspb.2018.2004.

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Microorganisms are the chief primary producers within present-day deep-sea hydrothermal vent ecosystems, and play a fundamental role in shaping the ecology of these environments. However, very little is known about the microbes that occurred within, and structured, ancient vent communities. The evolutionary history, diversity and the nature of interactions between ancient vent microorganisms and hydrothermal vent animals are largely undetermined. The oldest known hydrothermal vent community that includes metazoans is preserved within the Ordovician to early Silurian Yaman Kasy massive sulfide deposit, Ural Mountains, Russia. This deposit contains two types of tube fossil attributed to annelid worms. A re-examination of these fossils using a range of microscopy, chemical analysis and nano-tomography techniques reveals the preservation of filamentous microorganisms intimately associated with the tubes. The microfossils bear a strong resemblance to modern hydrothermal vent microbial filaments, including those preserved within the mineralized tubes of the extant vent polychaete genus Alvinella . The Yaman Kasy fossil filaments represent the oldest animal–microbial associations preserved within an ancient hydrothermal vent environment. They allude to a diverse microbial community, and also demonstrate that remarkable fine-scale microbial preservation can also be observed in ancient vent deposits, suggesting the possible existence of similar exceptionally preserved microfossils in even older vent environments.

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38

Raguenes, G., R. Christen, J. Guezennec, P. Pignet, and G. Barbier. "Vibrio diabolicus sp. nov., a New Polysaccharide-Secreting Organism Isolated from a Deep-Sea Hydrothermal Vent Polychaete Annelid, Alvinella pompejana." International Journal of Systematic Bacteriology 47, no. 4 (October 1, 1997): 989–95. http://dx.doi.org/10.1099/00207713-47-4-989.

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39

Vincent, P., P. Pignet, F. Talmont, L. Bozzi, B. Fournet, J. Guezennec, C. Jeanthon, and D. Prieur. "Production and Characterization of an Exopolysaccharide Excreted by a Deep-Sea Hydrothermal Vent Bacterium Isolated from the Polychaete Annelid Alvinella pompejana†." Applied and Environmental Microbiology 60, no. 11 (1994): 4134–41. http://dx.doi.org/10.1128/aem.60.11.4134-4141.1994.

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40

Tsuchida, Shinji, Yohey Suzuki, Yoshihiro Fujiwara, Masaru Kawato, Katsuyuki Uematsu, Toshiro Yamanaka, Chitoshi Mizota, and Hiroyuki Yamamoto. "Epibiotic association between filamentous bacteria and the vent-associated galatheid crab,Shinkaia crosnieri(Decapoda: Anomura)." Journal of the Marine Biological Association of the United Kingdom 91, no. 1 (November 24, 2010): 23–32. http://dx.doi.org/10.1017/s0025315410001827.

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The galatheid crabShinkaia crosnieri, is the sole member of the subfamily Shinkaiinae. It is abundant and forms dense beds around active hydrothermal vents in the Okinawa Trough. Thousands of filamentous bacteria attached to the plumose setae on the ventral surface of this crab were observed using field-emission scanning electron microscopy and transmission electron microscopy. Nucleic acids were extracted from the filamentous bacteria, and the phylotypes of 16S rRNA genes were identified from 81 clones. These phylotypes were divided into three groups: Epsilonproteobacteria (74%); Gammaproteobacteria (20%); and Bacteroidetes (6%). Gamma- and major phylotypes of Epsilonproteobacteria were also detected using fluorescencein situhybridization analysis. These Epsilon- and Gammaproteobacteria were closely related to cultured and uncultured bacteria from hydrothermal vent fields including episymbionts of vent-associated invertebrates such asRimicaris exoculata, Alvinella pompejana, the scaly-foot snail,Kiwa hirsutaetc. The carbon isotopic compositions of the muscle ofS. crosnieriand in filamentous bacteria were similar. The muscle ofS. crosniericontained monounsaturated C16and C18fatty acids, which are known to be characteristic of sulphur-oxidizing bacteria in H2S-rich marine habitats. Through the video images transmitted by a submersible and a remotely operated vehicle,S. crosnieriwas observed to comb out its ventral setae using the third maxilliped and appeared to consume the contents. These evidences suggest the epibiotic association betweenS. crosnieriand the filamentous bacteria attached to the ventral setae of the crab, but the details of role and function are still unclear at the present study.

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41

KAPLAREVIC, MIHAILO, ALISON E. MURRAY, STEPHEN C. CARY, and GUANG R. GAO. "EnGenIUS — ENVIRONMENTAL GENOME INFORMATIONAL UTILITY SYSTEM." Journal of Bioinformatics and Computational Biology 06, no. 06 (December 2008): 1193–211. http://dx.doi.org/10.1142/s0219720008003850.

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Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (> 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset.

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42

Plouviez, Sophie, Dominique Le Guen, Odile Lecompte, François H. Lallier, and Didier Jollivet. "Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana." BMC Evolutionary Biology 10, no. 1 (2010): 220. http://dx.doi.org/10.1186/1471-2148-10-220.

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43

Robertson, J. D. "Physiological constraints upon marine organisms." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 80, no. 3-4 (1989): 225–34. http://dx.doi.org/10.1017/s0263593300028662.

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ABSTRACTWhen compared with sea water, most marine invertebrates are isosmotic but show varying degrees of ionic regulation, from accumulation of potassium and calcium to reductions of magnesium and sulphate. A reduction of sulphate in pelagic animals such as jellyfish and salps, and an accumulation of ammonium ions in arrow-worms (Sagitta) contribute to their near-neutral buoyancy. Marked reductions in salinity exclude mahy marine invertebrates. In the Baltic, polychaetes, bivalve molluscs and decapod crustaceans are reduced from 193, ninety-two and sixty-four species in the Belt Sea (salinity S 10-30‰) to three, four and two in the Gulf of Finland (salinity S 5-9‰). The chelicerate Limulus can stand a wide range in salinity, a few insect larvae can tolerate concentrations of 200% sea water, while the branchiopod shrimp Artemia can stand crystallising brine (36-37% NaCl). Very few species can tolerate temperatures of 40°C. One such species is the polychaete Alvinella pompejana, a hydrothermal vent animal at East Pacific Ridge (to the W of S America). The harpacticid copepod Tigriopus living in evaporating rockpools has a lethal temperature of 42°C at a salinity of S 90‰, but at S 8‰ that temperature is 34°C. Lack of oxygen and presence of hydrogen sulphide limit the distribution of animals in certain areas. Most active animals have respiratory pigments in their principal body fluid. Burrowing invertebrates such as Arenicola and Lingula have respectively haemoglobin in the blood and haemerythrin in the coelomic fluid, with mean oxygen capacities of 6 ml O2 per 100 ml in each case, compared to 0·6 and 0·5 ml in sea water at 10° and 20°C.

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44

Pérez-Rodríguez, Ileana, Ashley Grosche, Lynnicia Massenburg, Valentin Starovoytov, Richard A. Lutz, and Costantino Vetriani. "Phorcysia thermohydrogeniphila gen. nov., sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent." International Journal of Systematic and Evolutionary Microbiology 62, Pt_10 (October 1, 2012): 2388–94. http://dx.doi.org/10.1099/ijs.0.035642-0.

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A novel hyperthermophilic, anaerobic, chemolithoautotrophic bacterium, designated strain HB-8T, was isolated from the tube of Alvinella pompejana tubeworms collected from the wall of an actively venting sulfide structure on the East Pacific Rise at 13° N. The cells were Gram-negative rods, approximately 1.0–1.5 µm long and 0.5 µm wide. Strain HB-8T grew between 65 and 80 °C (optimum 75 °C), 15 and 35 g NaCl l−1 (optimum 30 g l−1) and pH 4.5 and 8.5 (optimum pH 6.0). Generation time under optimal conditions was 26 min. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Nitrate and sulfur were used as electron acceptors, with concomitant formation of ammonium or hydrogen sulfide, respectively. The presence of lactate, formate, acetate or tryptone in the culture medium inhibited growth. The G+C content of the genomic DNA was 47.8 mol%. Phylogenetic analysis of the 16S rRNA gene and of the alpha subunit of the ATP citrate lyase of strain HB-8T indicated that this organism formed a novel lineage within the class Aquificae , equally distant from the type strains of the type species of the three genera that represent the family Desulfurobacteriaceae : Thermovibrio ruber ED11/3LLK8T, Balnearium lithotrophicum 17ST and Desulfurobacterium thermolithotrophum BSAT. The polar lipids of strain HB-8T differed substantially from those of other members of the Desulfurobacteriaceae , and this bacterium produced novel quinones. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, it is proposed that the organism represents a novel genus and species within the family Desulfurobacteriaceae , Phorcysia thermohydrogeniphila gen. nov., sp. nov. The type strain of Phorcysia thermohydrogeniphila is HB-8T ( = DSM 24425T = JCM 17384T).

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45

Bruneaux, Matthieu, Jean Mary, Marie Verheye, Odile Lecompte, Olivier Poch, Didier Jollivet, and Arnaud Tanguy. "Detection and Characterisation of Mutations Responsible for Allele-Specific Protein Thermostabilities at the Mn-Superoxide Dismutase Gene in the Deep-Sea Hydrothermal Vent Polychaete Alvinella pompejana." Journal of Molecular Evolution 76, no. 5 (April 23, 2013): 295–310. http://dx.doi.org/10.1007/s00239-013-9559-y.

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46

Desbruyères, D., P. Chevaldonné, A. M. Alayse, D. Jollivet, F. H. Lallier, C. Jouin-Toulmond, F. Zal, et al. "Biology and ecology of the “Pompeii worm” (Alvinella pompejana Desbruyères and Laubier), a normal dweller of an extreme deep-sea environment: A synthesis of current knowledge and recent developments." Deep Sea Research Part II: Topical Studies in Oceanography 45, no. 1-3 (January 1998): 383–422. http://dx.doi.org/10.1016/s0967-0645(97)00083-0.

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47

Shillito, Bruce, Nadine Le Bris, Françoise Gaill, Jean-François Rees, and Franck Zal. "First access to live alvinellas." High Pressure Research 24, no. 1 (January 2004): 169–72. http://dx.doi.org/10.1080/08957950310001635774.

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48

Madrid, Vanessa M., Gordon T. Taylor, Mary I. Scranton, and Andrei Y. Chistoserdov. "Phylogenetic Diversity of Bacterial and Archaeal Communities in the Anoxic Zone of the Cariaco Basin." Applied and Environmental Microbiology 67, no. 4 (April 1, 2001): 1663–74. http://dx.doi.org/10.1128/aem.67.4.1663-1674.2001.

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ABSTRACT Microbial community samples were collected from the anoxic zone of the Cariaco Basin at depths of 320, 500, and 1,310 m on a November 1996 cruise and were used to construct 16S ribosomal DNA libraries. Of 60 nonchimeric sequences in the 320-m library, 56 belonged to the ɛ subdivision of the Proteobacteria(ɛ-Proteobacteria) and 53 were closely related to ectosymbionts of Rimicaris exoculata and Alvinella pompejana, which are referred to here as epsilon symbiont relatives (ESR). The 500-m library contained sequences affiliated with the fibrobacteria, the Flexibacter-Cytophaga-Bacteroidesdivision, the division Verrucomicrobia, the divisionProteobacteria, and the OP3 candidate division. The Proteobacteria included members of the γ, δ, ɛ and new candidate subdivisions, and γ-proteobacterial sequences were dominant (25.6%) among the proteobacterial sequences. As in the 320-m library, the majority of the ɛ-proteobacteria belonged to the ESR group. The genusFibrobacter and its relatives were the second largest group in the library (23.6%), followed by the δ-proteobacteria and the ɛ-proteobacteria. The 1,310-m library had the greatest diversity; 59 nonchimeric clones in the library contained 30 unique sequences belonging to the planctomycetes, the fibrobacteria, theFlexibacter-Cytophaga-Bacteroides division, theProteobacteria, and the OP3 and OP8 candidate divisions. The proteobacteria included members of new candidate subdivisions and the β, γ, δ, and ɛ-subdivisions. ESR sequences were still present in the 1,310-m library but in a much lower proportion (8.5%). One archaeal sequence was present in the 500-m library (2% of all microorganisms in the library), and eight archaeal sequences were present in the 1,310-m library (13.6%). All archaeal sequences fell into two groups; two clones in the 1,310-m library belonged to the kingdom Crenarchaeota and the remaining sequences in both libraries belonged to the kingdom Euryarchaeota. The latter group appears to be related to the Eel-TA1f2 sequence, which belongs to an archaeon suggested to be able to oxidize methane anaerobically. Based on phylogenetic inferences and measurements of dark CO2 fixation, we hypothesized that (i) the ESR are autotrophic anaerobic sulfide oxidizers, (ii) sulfate reduction and fermentative metabolism may be carried out by a large number of bacteria in the 500- and 1,310-m libraries, and (iii) members of theEuryarchaeota found in relatively large numbers in the 1,310-m library may be involved in anaerobic methane oxidation. Overall, the composition of microbial communities from the Cariaco Basin resembles the compositions of communities from several anaerobic sediments, supporting the hypothesis that the Cariaco Basin water column is similar to anaerobic sediments.

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Matabos, Marjolaine, Nadine Le Bris, Sophie Pendlebury, and Eric Thiébaut. "Role of physico-chemical environment on gastropod assemblages at hydrothermal vents on the East Pacific Rise (13°N/EPR)." Journal of the Marine Biological Association of the United Kingdom 88, no. 5 (June 24, 2008): 995–1008. http://dx.doi.org/10.1017/s002531540800163x.

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Deep-sea hydrothermal vents display extreme and highly variable environmental conditions that are expected to be among the most important factors structuring associated benthic populations and communities. We tested this assumption, focusing on the distribution of gastropods, as well as on the demographic population structure and reproductive biology of one dominant gastropod species in zones characterized by alvinellid polychaetes and vestimentiferan tubeworms. A total of 14 biological samples from both types of habitats were collected at three sites on the East Pacific Rise 13°N vent field in May 2002. At all vents except one, the physico-chemical environment was described in two steps: (1) pH, total sulphide and reduced iron concentrations have been measuredin situinAlvinellahabitats and correlations to temperature were assessed at the scale of each sampled vent; and (2) assuming the consistency of these relationships within a single edifice, ranges of physico-chemical factors were estimated for each biological sample from the corresponding fine scale temperature measurements. A total of 11 gastropod species were identified from all samples and 2 main faunal assemblages were distinguished: one dominated byLepetodrilus elevatusin the alvinellid zone as well as in the vestimentiferan zone, and one dominated by the peltospiridsNodopelta heminoda, N. subnodaandPeltospira operculataconfined to the alvinellid zone. Peltospirid gastropods were dominant over lepetodrilid gastropods in the more acidic, sulphide-richer, and hotter environments. Although this pattern could be related to specific physiological tolerances to temperature and sulphide toxicity, the weak correlation between community structure and physico-chemical variables suggests that additional factors are also involved. Particularly, the low species richness and the overwhelming dominance ofL. elevatusin one faunal assemblage suggest that this species may outcompete peltospirids and greatly affect community structure. This hypothesis is supported by large differences in the demographic structure and reproductive biology ofL. elevatusbetween the 2 faunal assemblages.

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50

Martineu, Pascale, S. Kim Juniper, Charles R. Fisher, and Gary J. Massoth. "Sulfide Binding in the Body Fluids of Hydrothermal Vent Alvinellid Polychaetes." Physiological Zoology 70, no. 5 (September 1997): 578–88. http://dx.doi.org/10.1086/515864.

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