@article {ISI:000360368300003,
	title = {{Molecular study of bacterial diversity within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae}},
	journal = {MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE},
	volume = {36},
	number = {1, SI},
	year = {2015},
	month = {aug},
	pages = {35{\textendash}44},
	type = {Article},
	abstract = {A large proportion of the faunal biomass in hydrothermal vent ecosystems relies on symbiotic relationships, with bacteria as a source of nutrition. Whereas multiple symbioses have been observed in diverse vent hosts, siboglinid tubeworms have been thought to harbour a single endosymbiont phylotype affiliated to the Gammaproteobacteria. In the case of the Northeast Pacific vestimentiferan Ridgeia piscesae, two previous studies suggested the presence of more than one symbiont. The possibility of multiple, and possibly habitat-specific, symbionts in R. piscesae provided a potential explanation for the tube-worm{\textquoteright}s broad ecological niche, compared with other hydrothermal vent siboglinids. This study further explored the diversity of trophosome bacteria in R. piscesae using two methodological approaches not yet applied to this symbiosis. We carried out 454-pyrosequencing on trophosome samples from 46 individual worms and used catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) to verify the presence of the major groups detected in the pyrotag data. Both methods yielded inconsistent and sometimes contradictory results between sampling sites, and neither provided irrefutable evidence for the presence of symbionts other than the expected Gammaproteobacteria. We therefore conclude that the other adaptive mechanisms must be considered to explain the broad physico-chemical niche occupied by the different growth forms of R. piscesae.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0173-9565},
	doi = {10.1111/maec.12169},
	author = {Forget, Nathalie L and Perez, Maeva and Juniper, S Kim}
}
@article {ISI:000345292900023,
	title = {{Diversity and abundance of Bacteria and nirS-encoding denitrifiers associated with the Juan de Fuca Ridge hydrothermal system}},
	journal = {ANNALS OF MICROBIOLOGY},
	volume = {64},
	number = {4},
	year = {2014},
	month = {dec},
	pages = {1691{\textendash}1705},
	type = {Article},
	abstract = {Denitrification, which results in the loss of bioavailable nitrogen-an essential macronutrient for all living organisms-may potentially affect chemosynthetic primary production in hydrothermal vent ecosystems where sub-oxic conditions favorable to denitrification are common. Here we describe the diversity and abundance of denitrifying bacteria in the subsurface biosphere at Axial Volcano and the Endeavour Segment on the Juan de Fuca Ridge using a combination of quantitative polymerase chain reaction assays, and small subunit ribosomal RNA (SSU or 16S rRNA) pyrotag and nitrite reductase (nirS) clone library sequencing methods. Bacterial communities were diverse and dominated by members of the epsilon- and gamma-proteobacteria, including taxonomic groups containing known denitrifiers. Assemblages of denitrifiers that could be evaluated by nirS gene sequence comparisons showed low diversity. The single nirS sequence shared by the two locations, affiliated with a gamma-proteobacteria isolated from estuarine sediments (Pseudomonas sp. BA2), represented more than half of all sequences recovered when clustered at 97 {\%} identity. All other nirS sequences clustered into different taxonomic groups, indicating important differences in denitrifier community membership between the two sites. Total nirS gene abundance was at least two orders of magnitude lower than 16S rRNA abundance. Overall, our results demonstrate that the diversity and abundance of the nirS gene-containing bacterial community are rather low, as might be expected under the extreme conditions encountered in the subsurface biosphere of hydrothermal vent systems, and do not correlate clearly with any environmental variables investigated (i.e., pH, temperature, and H2S, NO3-, NH4+ concentrations).},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {1590-4261},
	doi = {10.1007/s13213-014-0813-3},
	author = {Bourbonnais, Annie and Juniper, S Kim and Butterfield, David A and Anderson, Rika E and Lehmann, Moritz F}
}
@article {ISI:000326430500019,
	title = {{Activity and positioning of eurythermal hydrothermal vent sulphide worms in a variable thermal environment}},
	journal = {JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY},
	volume = {448},
	year = {2013},
	month = {oct},
	pages = {149{\textendash}155},
	type = {Article},
	abstract = {Here we investigate behavioral responses to fine-scale spatial and temporal temperature gradients in a heat tolerant hydrothermal vent worm (Paralvinella sulfincola). While this species has been a model organism for understanding physiological adaptations to extreme environments, lacking are corroborative in situ experiments and characterization of temperature-related behaviors representing the lower thermal tolerance range of this species. To address this knowledge gap, we first quantified the upper thermal limit for this species using a rapid heating protocol executed remotely on the seafloor. Second, we used a combination of in situ observations and shipboard experiments to test for temperature-dependent patterns in activity and behavior. We confirm that P. sulfincola is remarkably eurythermal and demonstrates a thermal niche breadth exceeding 45 degrees C. We further show that the activity and positioning of worms relate to temperatures within its lower preferred range (i.e., between 4 and 20 degrees C). Worms tended to remain closer to their tube openings and held their branchial crown in a consistent location when fluids were relatively warm. By contrast, when fluids were cooler, both the distance worms were observed from their tubes and positioning of their branchial crown were more variable. A Bayesian hidden Markov model classified each worm at each time interval as being in a high or low activity state according to the magnitude of change in their orientation and how far they moved between successive time lapse images. We found that the transition between active and inactive states at any time period is related to fluid temperature. Our observations indicate that the behavior of the worms is temperature-dependent, which may in turn reflect temperature-related variables such as the delivery of food particles, dissolved oxygen concentration, or relative environmental variability. Our findings demonstrate that this species can respond behaviorally to very fine-scale environmental variability in a manner not simply predicted by models of increasing activity with temperature. (C) 2013 Elsevier B.V. All rights reserved.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {0022-0981},
	doi = {10.1016/j.jembe.2013.06.015},
	author = {Bates, Amanda E and Bird, Tomas J and Robert, Katleen and Onthank, Kirt L and Quinn, Gerry P and Juniper, S Kim and Lee, Raymond W}
}
@article {ISI:000299990700001,
	title = {{Subseafloor nitrogen transformations in diffuse hydrothermal vent fluids of the Juan de Fuca Ridge evidenced by the isotopic composition of nitrate and ammonium}},
	journal = {GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS},
	volume = {13},
	year = {2012},
	month = {feb},
	type = {Article},
	abstract = {Little is known about dissolved inorganic nitrogen (DIN) transformations in hydrothermal vent (HV) fluids. Here, we present the first isotopic measurements of nitrate (delta N-15 and delta O-18) and ammonium (delta N-15) from three HV fields on the Juan de Fuca ridge (NE-Pacific). The dominant process that drives DIN concentration variations in low-T diffuse fluids is water mass mixing below the seafloor, with no effect on the DIN isotope ratios. Strong inter-site variations in the concentration and delta N-15 of NH4+ in high-T fluids suggest different subsurface nitrogen (N) sources (deep-sea nitrate versus organic sediments) for hydrothermally discharged ammonium. Low NH4+ community N isotope effects ({\textless}3 parts per thousand) for net NH4+ consumption suggest an important contribution from gross ammonium regeneration in low-T fluids. Elevation of HV nitrate N-15/N-14 and O-18/O-16 over deep-sea mean isotope values at some sites, concomitant with decreased nitrate concentrations, indicate assimilatory or dissimilatory nitrate consumption by bacteria in the subsurface, with relatively low community N isotope effects ((15)epsilon(k) {\textless} 3 parts per thousand). The low N isotope effects suggest that nitrate assimilation or denitrification occur in bacterial mats, and/or in situ production of low delta N-15 nitrate. A significantly stronger relative increase for nitrate delta O-18 than for delta N-15 was observed at many sites, resulting in marked deviations from the 1:1 relationship for nitrate delta N-15 versus delta O-18 that is expected for nitrate reduction in marine settings. Simple box-model calculation show that the observed un-coupling of N and O nitrate isotope ratios is consistent with nitrate regeneration by either nitrite reoxidation and/or partial nitrification of hydrothermal ammonium (possibly originating from N-2 fixation). Our isotope data confirm the role of subsurface microbial communities in modulating hydrothermal fluxes to the deep ocean.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	issn = {1525-2027},
	doi = {10.1029/2011GC003863},
	author = {Bourbonnais, Annie and Lehmann, Moritz F and Butterfield, David A and Juniper, S Kim}
}
