@article {RN2417,
	title = {Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys},
	journal = {Research Square},
	year = {2020},
	type = {Journal Article},
	doi = {10.21203/rs.3.rs-16462/v2},
	url = {https://app.dimensions.ai/details/publication/pub.1127583313 https://assets.researchsquare.com/files/rs-16462/v2.pdf},
	author = {Hou, Jialin and Sievert, Stefan M. and Wang, Yinzhao and Seewald, Jeff S. and Natarajan, Vengadesh Perumal and Wang, Fengping and Xiao, Xiang}
}
@article {RN2373,
	title = {Dissolved organic carbon in basalt-hosted deep subseafloor fluids of the Juan de Fuca Ridge flank},
	journal = {Earth and Planetary Science Letters},
	volume = {513},
	year = {2019},
	pages = {156-165},
	type = {Journal Article},
	issn = {0012-821X},
	doi = {10.1016/j.epsl.2019.02.008},
	author = {Lin, H. T. and Repeta, D. J. and Xu, L. and Rappe, M. S.}
}
@article {RN2376,
	title = {Diverse anaerobic methane- and multi-carbon alkane-metabolizing archaea coexist and show activity in Guaymas Basin hydrothermal sediment},
	journal = {Environmental Microbiology},
	volume = {21},
	number = {4},
	year = {2019},
	pages = {1344-1355},
	type = {Journal Article},
	issn = {1462-2912},
	doi = {10.1111/1462-2920.14568},
	author = {Wang, Y. Z. and Feng, X. Y. and Natarajan, V. P. and Xiao, X. and Wang, F. P.}
}
@article {RN2368,
	title = {Dimensions of Radiocarbon Variability within Sedimentary Organic Matter},
	journal = {Radiocarbon},
	volume = {60},
	number = {3},
	year = {2018},
	pages = {775-790},
	type = {Journal Article},
	issn = {0033-8222},
	doi = {10.1017/RDC.2018.22},
	author = {Bao, R. and McNichol, A. P. and McIntyre, C. P. and Xu, L. and Eglinton, T. I.}
}
@article {RN2360,
	title = {Dispersal of Hydrothermal Vent Larvae at East Pacific Rise 9-10 degrees N Segment},
	journal = {Journal of Geophysical Research-Oceans},
	volume = {123},
	number = {11},
	year = {2018},
	pages = {7877-7895},
	type = {Journal Article},
	issn = {2169-9275},
	doi = {10.1029/2018JC014290},
	author = {Xu, G. Y. and McGillicuddy, D. J. and Mills, S. W. and Mullineaux, L. S.}
}
@article {RN2358,
	title = {Observation and Modeling of Hydrothermal Response to the 2015 Eruption at Axial Seamount, Northeast Pacific},
	journal = {Geochemistry Geophysics Geosystems},
	volume = {19},
	number = {8},
	year = {2018},
	pages = {2780-2797},
	type = {Journal Article},
	issn = {1525-2027},
	doi = {10.1029/2018GC007607},
	author = {Xu, G. Y. and Chadwick, W. W. and Wilcock, W. S. D. and Bemis, K. G. and Delaney, J.}
}
@article {ISI:000358290000012,
	title = {{Characterization of a novel thermostable patatin-like protein from a Guaymas basin metagenomic library}},
	journal = {EXTREMOPHILES},
	volume = {19},
	number = {4},
	year = {2015},
	month = {jul},
	pages = {829{\textendash}840},
	type = {Article},
	abstract = {Deep-sea hydrothermal vents are a natural habitat for thermophiles, in which contain plenty of enzymes that can function at high temperatures. In this work, we constructed a fosmid library in Escherichia coli using metagenomic DNA isolated from a chimney sample collected in the hydrothermal vents in Guaymas Basin. The library was screened for lipolytic activity and positive clones were subjected to subcloning. A novel patatin-like protein (PLP) that exhibited less than 45 {\%} identity in amino acid sequence to known enzymes was obtained. Common features of the patatin-like proteins, such as four conserved blocks, were detected. Interestingly, there was an Ala at site 42 in PLP instead of the first Gly-residue in the consensus sequence Gly-X-Ser-X-Gly found in other PLP homologs. The active sites of PLP were Ser44 and Asp160. Spectrophotometric assays with different p-nitrophenyl esters demonstrated a preference for p-nitrophenyl butyrate (C4) and p-nitrophenyl decanoate (C10). Moreover, PLP demonstrated optimal activity at 70 A degrees C and at pH 9.0 (Tris-HCl). The activation energy from the linear Arrhenius plot was found to be 38.3 +/- A 0.9 kJ/mol. The K (m) and V (max) of PLP for C4 were 304 +/- A 38 mu M and 14 +/- A 0.38 mu mol min(-1) mg(-1), respectively. Gene-mining of the metagenome dataset that was generated by pyrosequencing the same chimney sample resulted in identification of 20 PLP homolog gene fragments, which could represent promising examples of this category of thermostable proteins.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1431-0651},
	doi = {10.1007/s00792-015-0758-x},
	author = {Fu, Ling and He, Ying and Xu, Fangdi and Ma, Qun and Wang, Fengping and Xu, Jun}
}
@article {ISI:000365379500011,
	title = {{Estimations of heat transfer from Grotto{\textquoteright}s North Tower: A NEPTUNE Observatory case study}},
	journal = {DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY},
	volume = {121},
	number = {SI},
	year = {2015},
	month = {nov},
	pages = {95{\textendash}111},
	type = {Article},
	abstract = {The overall heat transfer through an active hydrothermal sulfide edifice, in particular the North Tower of Grotto, has been estimated at 80 MW or greater based on the following in situ measurements and assumptions: (1) The heat transfer by diffuse flow is estimated at 33-380 MW based on extrapolating the acoustically mapped area to all sides of the North Tower ({\{}{\textquoteright}{\textquoteright}{\}}visible{\{}{\textquoteright}{\textquoteright}{\}} area=30 m(2); extrapolated area= 100 m(2)) and using the range of available spot measurements of temperature (6-23 degrees C) and vertical velocity (0.07-0.28 m/s). The lower number (33 MW) is more likely, but there is insufficient knowledge of the temporal and spatial variability of diffuse flow to be certain. (2) The heat transfer by focused flow is estimated at 30-70 MW based on summing the estimated individual rates of heat transfer for 4 out of 7 documented black smokers and flanges. (3) Conductive heat transfer out of the mound is unknown, but is likely to be much less than the advective heat transfer. Additionally, the plume transport of heat is estimated at 20-40 MW based on the direct measurement of temperature within the plume (at 5-25 m above the top of the edifice). Despite uncertainties, the lower estimate of plume versus smoker heat transfer suggests that heat transfer is dominantly by diffuse flow. Furthermore, not all plumes from individual smokers may merge even for so small an area as the North Tower of Grotto. (C) 2015 Elsevier Ltd. All rights reserved.},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {0967-0645},
	doi = {10.1016/j.dsr2.2015.05.010},
	author = {Rona, Peter A and Bemis, Karen G and Xu, Guangyu and Mitsuzawa, Kyohiko}
}
@article {Bemis2015,
	title = {{The path to COVIS: A review of acoustic imaging of hydrothermal flow regimes}},
	journal = {Deep-Sea Research Part II: Topical Studies in Oceanography},
	volume = {121},
	year = {2015},
	pages = {159{\textendash}176},
	abstract = {Acoustic imaging of hydrothermal flow regimes started with the incidental recognition of a plume on a routine sonar scan for obstacles in the path of the human-occupied submersible ALVIN. Developments in sonar engineering, acoustic data processing and scientific visualization have been combined to develop technology which can effectively capture the behavior of focused and diffuse hydrothermal discharge. This paper traces the development of these acoustic imaging techniques for hydrothermal flow regimes from their conception through to the development of the Cabled Observatory Vent Imaging Sonar (COVIS). COVIS has monitored such flow eight times a day for several years. Successful acoustic techniques for estimating plume entrainment, bending, vertical rise, volume flux, and heat flux are presented as is the state-of-the-art in diffuse flow detection.},
	keywords = {HOV Alvin (Human Occupied Vehicle), ROV Jason (Remotely Operated Vehicle)},
	doi = {10.1016/j.dsr2.2015.06.002},
	author = {Bemis, K G and Silver, D and Xu, G and Light, R and Jackson, D R and Jones, C D and Ozer, S and Liu, L}
}
@article {ISI:000331170400001,
	title = {{Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin}},
	journal = {FRONTIERS IN MICROBIOLOGY},
	volume = {4},
	year = {2013},
	month = {jun},
	type = {Article},
	abstract = {Deep-sea hydrothermal vent chimneys contain a high diversity of microorganisms, yet the metabolic activity and the ecological functions of the microbial communities remain largely unexplored. In this study, a metagenomic approach was applied to characterize the metabolic potential in a Guaymas hydrothermal vent chimney and to conduct comparative genomic analysis among a variety of environments with sequenced metagenomes. Complete clustering of functional gene categories with a comparative metagenomic approach showed that this Guaymas chimney metagenome was clustered most closely with a chimney metagenome from Juan de Fuca. All chimney samples were enriched with genes involved in recombination and repair, chemotaxis and flagellar assembly, highlighting their roles in coping with the fluctuating extreme deep-sea environments. A high proportion of transposases was observed in all the metagenomes from deep-sea chimneys, supporting the previous hypothesis that horizontal gene transfer may be common in the deep-sea vent chimney biosphere. In the Guaymas chimney metagenome, thermophilic sulfate reducing microorganisms including bacteria and archaea were found predominant, and genes coding for the degradation of refractory organic compounds such as cellulose, lipid, pullullan, as well as a few hydrocarbons including toluene, ethylbenzene and o-xylene were identified. Therefore, this oil-immersed chimney supported a thermophilic microbial community capable of oxidizing a range of hydrocarbons that served as electron donors for sulphate reduction under anaerobic conditions.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2013.00148},
	author = {He, Ying and Xiao, Xiang and Wang, Fengping}
}
@article {ISI:000308889800003,
	title = {{Deep sea hydrothermal plumes and their interaction with oscillatory flows}},
	journal = {GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS},
	volume = {13},
	year = {2012},
	month = {sep},
	type = {Article},
	abstract = {The acoustic scintillation method is applied to the investigation and monitoring of a vigorous hydrothermal plume from Dante within the Main Endeavour vent field (MEF) in the Endeavour Ridge segment. A 40 day time series of the plume{\textquoteright}s vertical velocity and temperature fluctuations provides a unique opportunity to study deep sea plume dynamics in a tidally varying horizontal cross flow. An integral plume model that takes into account ambient stratification and horizontal cross flows is established from the conservation equations of mass, momentum and density deficit. Using a linear additive entrainment velocity in the model ( E = alpha U-m + beta U-perpendicular to) that is a function of both the plume relative axial velocity (U-m) and the relative ambient flow perpendicular to the plume (U-perpendicular to) gives consistent results to the experimental data, suggesting entrainment coefficients alpha = 0.1 and beta = 0.6. Also from the integral model, the plume height in a horizontal cross flow ( U-a) is shown to scale as 1.8B(1/3)U(a)(-1/3)N(-2/3) for 0.01 {\textless}= U-a {\textless}= 0.1 m/s where B is the initial buoyancy transport and N is the ambient stratification, both of which are assumed constant.},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1525-2027},
	doi = {10.1029/2012GC004188},
	author = {Xu, Guangyu and Di Iorio, Daniela}
}
@article {ISI:000290021000005,
	title = {{Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries}},
	journal = {ISME JOURNAL},
	volume = {5},
	number = {3},
	year = {2011},
	month = {mar},
	pages = {414{\textendash}426},
	type = {Article},
	abstract = {Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production. The ISME Journal (2011) 5, 414-426; doi: 10.1038/ismej.2010.144; published online 7 October 2010},
	keywords = {HOV Alvin (Human Occupied Vehicle)},
	issn = {1751-7362},
	doi = {10.1038/ismej.2010.144},
	author = {Xie, Wei and Wang, Fengping and Guo, Lei and Chen, Zeling and Sievert, Stefan M and Meng, Jun and Huang, Guangrui and Li, Yuxin and Yan, Qingyu and Wu, Shan and Wang, Xin and Chen, Shangwu and He, Guangyuan and Xiao, Xiang and Xu, Anlong}
}
@article {ISI:000295799400034,
	title = {{The relative effects of particles and turbulence on acoustic scattering from deep-sea hydrothermal vent plumes}},
	journal = {JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA},
	volume = {130},
	number = {4, 1},
	year = {2011},
	month = {oct},
	pages = {1856{\textendash}1867},
	type = {Article},
	abstract = {Acoustic methods are applied to the investigation and monitoring of a vigorous hydrothermal plume within the Main Endeavor vent field at the Endeavor segment of the Juan de Fuca Ridge. Forward propagation and scattering from suspended particulates using Rayleigh scattering theory is shown to be negligible (log-amplitude variance sigma(2)(chi) similar to 10(-7)) compared to turbulence induced by temperature fluctuations (sigma(2)(chi) similar to 0.1). The backscattering from turbulence is then quantified using the forward scattering derived turbulence level, which gives a volume backscattering strength of s(V) = 6.5 x 10(-8) m(-1). The volume backscattering cross section from particulates can range from s(V) = 3.3 x 10(-6) to 7.2 x 10(-10) m(-1) depending on the particle size. These results show that forward scatter acoustic methods in hydrothermal vent applications can be used to quantify turbulence and its effect on backscatter measurements, which can be a dominant factor depending on the particle size and its location within the plume. (C) 2011 Acoustical Society of America. {\{}[{\}}DOI: 10.1121/1.3624816]},
	keywords = {ROV Jason (Remotely Operated Vehicle)},
	issn = {0001-4966},
	doi = {10.1121/1.3624816},
	author = {Xu, Guangyu and Di Iorio, Daniela}
}
@inbook {Xu1999,
	title = {{Automatic optical station keeping and navigation of an ROV; sea trial experiments}},
	booktitle = {Oceans {\textquoteright}99 MTS/IEEE: Riding the crest into the 21st century},
	volume = {1},
	year = {1999},
	pages = {71{\textendash}76},
	publisher = {IEEE},
	organization = {IEEE},
	address = {Piscataway, N.J.},
	isbn = {0-7803-5629-2},
	doi = {10.1109/OCEANS.1999.799709},
	url = {http://dx.doi.org/10.1109/OCEANS.1999.799709},
	author = {Xu, X and Negahdaripour, S}
}
