Früh-Green, G. L., Orcutt, B. N., Green, S. L., Cotterill, C., Morgan, S., Akizawa, N., Bayrakci, G., Behrmann, J.-H., Boschi, C., Brazelton, W. J.,
Cannat, M., Dunkel, K. G., Escartin, J., Harris, M., Herrero-Bervera, E.,
Hesse, K., John, B. E., Lang, S. Q., Lilley, M. D., Liu, H.-Q., Mayhew, L. E., McCaig, A. M., Menez, B., Morono, Y., Quéméneur, M., Rouméjon, S., Sandaruwan Ratnayake, A., Schrenk, M. O., Schwarzenbach, E. M., Twing, K. I., Weis, D., Whattam, S. A., Williams, M., and Zhao, R.: Expedition 357 summary, in: Proceedings of the International Ocean Discovery Program Volume 357, edited by: Früh-Green, G. L., Orcutt, B. N., Green, S. L., Cotterill, C., and the Expedition 357 Scientists, International Ocean Discovery Program Publications, College Station, TX, USA,
https://doi.org/10.14379/iodp.proc.357.101.2017, 2017a.
Früh-Green, G. L., Orcutt, B. N., Green, S. L., Cotterill, C., Morgan, S.,
Akizawa, N., Bayrakci, G., Behrmann, J.-H., Boschi, C., Brazelton, W. J.,
Cannat, M., Dunkel, K. G., Escartin, J., Harris, M., Herrero-Bervera, E.,
Hesse, K., John, B. E., Lang, S. Q., Lilley, M. D., Liu, H.-Q., Mayhew, L. E.,
McCaig, A. M., Menez, B., Morono, Y., Quéméneur, M., Rouméjon,
S., Sandaruwan Ratnayake, A., Schrenk, M. O., Schwarzenbach, E. M., Twing,
K. I., Weis, D., Whattam, S. A., Williams, M., and Zhao, R.: Expedition
357 methods, in: Proceedings of the International
Ocean Discovery Program, 357, edited by: Früh-Green, G. L., Orcutt, B. N., Green, S. L., Cotterill,
C., and the Expedition 357 Scientists,
International Ocean Discovery Program
Publications, College Station, TX, USA,
https://doi.org/10.14379/iodp.proc.357.102.2017, 2017b.
Hickok, K. A., Nguyen, T. B., and Lang, S. Q.: Assessment of apolar lipids in
subseafloor rocks and potential contaminants from the Atlantis Massif (IODP
Expedition 357), Org. Geochem., 122, 68–77, https://doi.org/10.1016/j.orggeochem.2018.05.003, 2018.
Kallmeyer, J.: Contamination Control for Scientific Drilling Operations, Adv. Appl. Microbiol., 98, 61–91, https://doi.org/10.1016/bs.aambs.2016.09.003, 2017.
Kallmeyer, J., Mangelsdorf, K., Cragg, B., and Horsfield, B.: Techniques for
Contamination Assessment During Drilling for Terrestrial Subsurface
Sediments, Geomicrobiol. J., 23, 227–239, https://doi.org/10.1080/01490450600724258, 2006.
Knights, D., Kuczynski, J., Charlson, E. S., Zaneveld, J., Mozer, M. C.,
Collman, R. G., Bushman, F. D., Knight, R., and Kelley, S. T.: Bayesian
community-wid
e culture-independent microbial source tracking, Nat.
Methods, 8, 761–763, https://doi.org/10.1038/nmeth.1650, 2011.
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., and
Schloss, P. D.: Development of a Dual-Index Sequencing Strategy and Curation
Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina
Sequencing Platform, Appl. Environ. Microbiol., 79, 5112–5120,
https://doi.org/10.1128/AEM.01043-13, 2013.
Lang, S. Q. and Brazelton, W. J.: Habitability of the marine serpentinite
subsurface: a case study of the Lost City hydrothermal field, Philos.
T. R. Soc. A, 378, 20180429, https://doi.org/10.1098/rsta.2018.0429,
2020.
Lever, M. A., Alperin, M., Engelen, B., Inagaki, F., Nakagawa, S., Steinsbu,
B. O., and Teske, A.: Trends in Basalt and Sediment Core Contamination During
IODP Expedition 301, Geomicrobiol. J., 23, 517–530,
https://doi.org/10.1080/01490450600897245, 2006.
Motamedi, S., Orcutt, B. N., Früh-Green, G. L., Twing, K. I., Pendleton,
H. L., and Brazelton, W. J.: Microbial Residents of the Atlantis Massif's
Shallow Serpentinite Subsurface, Appl. Environ. Microbiol., 86, e00356-20,
https://doi.org/10.1128/AEM.00356-20, 2020.
Orcutt, B. N., Bergenthal, M., Freudenthal, T., Smith, D., Lilley, M. D., Schnieders, L., Green, S., and Früh-Green, G. L.: Contamination tracer testing with seabed drills: IODP Expedition 357, Sci. Dril., 23, 39–46, https://doi.org/10.5194/sd-23-39-2017, 2017.
Pauli, U., Liniger, M., and Zimmermann, A.: Detection of DNA in soybean oil, Z. Lebensm. Unters. Forsch., 207, 264–267, https://doi.org/10.1007/s002170050330, 1998.
Pruesse, E., Peplies, J., and Glöckner, F. O.: SINA: Accurate
high-throughput multiple sequence alignment of ribosomal RNA genes,
Bioinformatics, 28, 1823–1829, https://doi.org/10.1093/bioinformatics/bts252, 2012.
Rognes, T., Flouri, T., Nichols, B., Quince, C., and Mahé, F.: VSEARCH: a
versatile open source tool for metagenomics, PeerJ, 4, e2584, https://doi.org/10.7717/peerj.2584, 2016.
Rohland, N. and Reich, D.: Cost-effective,
high-throughput DNA sequencing libraries for multiplexed target capture,
Genome Res., 22, 939–946, https://doi.org/10.1101/gr.128124.111, 2012.
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O.,
Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., and Walker, A. W.:
Reagent and laboratory contamination can critically impact sequence-based
microbiome analyses, BMC Biol., 12, 87, https://doi.org/10.1186/s12915-014-0087-z, 2014.
Santelli, C. M., Banerjee, N., Bach, W.,
and Edwards, K. J.: Tapping the Subsurface Ocean Crust Biosphere: Low
Biomass and Drilling-Related Contamination Calls for Improved Quality
Controls, Geomicrobiol. J., 27, 158–169, https://doi.org/10.1080/01490450903456780, 2010.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M.,
Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson,
C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Horn, D. J. V., and Weber,
C. F.: Introducing mothur: Open-Source, Platform-Independent,
Community-Supported Software for Describing and Comparing Microbial
Communities, Appl. Environ. Microbiol., 75, 7537–7541, https://doi.org/10.1128/AEM.01541-09, 2009.
Schloss, P. D., Gevers, D., and Westcott, S. L.: Reducing the Effects of PCR
Amplification and Sequencing Artifacts on 16S rRNA-Based Studies, PLOS ONE,
6, e27310, https://doi.org/10.1371/journal.pone.0027310, 2011.
Sheik, C. S., Reese, B. K., Twing, K. I., Sylvan, J. B., Grim, S. L.,
Schrenk, M. O., Sogin, M. L., and Colwell, F. S.: Identification and Removal
of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the
Census of Deep Life, Front. Microbiol., 9, 840, https://doi.org/10.3389/fmicb.2018.00840, 2018.
Smith, D. C., Spivack, A. J., Fisk, M. R., Haveman, S. A., Staudigel, H., and the Leg 185 Shipboard Scientific Party: Methods for quantifying potential microbial contamination during deep ocean coring, ODP Tech. Note, Ocean Drilling Program, 28, https://doi.org/10.2973/odp.tn.28.2000, 2000a.
Smith, D. C., Staudigel, H., Spivack, A. J., Fisk, M. R., and Haveman, S. A.:
Tracer-Based Estimates of Drilling-Induced Microbial Contamination of Deep
Sea Crust, Geomicrobiol. J., 17, 207–219, https://doi.org/10.1080/01490450050121170, 2000b.
Testolin, R. and Lain, O.: DNA Extraction from Olive Oil and PCR
Amplification of Microsatellite Markers, J. Food Sci., 70,
108–112, https://doi.org/10.1111/j.1365-2621.2005.tb09011.x, 2005.
Wilkins, M. J., Daly, R., Mouser, P. J., Trexler, R., Wrighton, K. C.,
Sharma, S., Cole, D. R., Biddle, J. F., Denis, E., Fredrickson, J. K.,
Kieft, T. L., Onstott, T. C., Petersen, L., Pfiffner, S. M., Phelps, T. J.,
and Schrenk, M. O.: Trends and Future Challenges in Sampling the Deep
Terrestrial Biosphere, Front. Microbiol., 5, 481, https://doi.org/10.3389/fmicb.2014.00481, 2014.
Yanagawa, K., Nunoura, T., McAllister, S., Hirai, M., Breuker, A., Brandt,
L., House, C., Moyer, C. L., Birrien, J.-L., Aoike, K., Sunamura, M., Urabe,
T., Mottl, M., and Takai, K.: The first microbiological contamination
assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya
North hydrothermal field in the Mid-Okinawa Trough (IODP Expedition 331),
Front. Microbiol., 4, 327, https://doi.org/10.3389/fmicb.2013.00327, 2013.
