SRX1364904 GB50-Bact SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1127126 Guay50-Archaea AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396239 GB37-ShortReads SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139772 SAMN04194116 GB 37 AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396240 GB37_bacteria SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139772 GB37_bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396244 E20-Archaea SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139775 SAMN04194117 E20-Bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396245 E20-Bacteria SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139775 E20-Bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396247 GF-Archaea SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139778 SAMN04194118 GF-Arch AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396250 GF-Bacteria SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139778 GF-Bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396252 AMV-Bacteria SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139781 AMV-Archaea AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396255 AMV-Archaea SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139781 AMV-Archaea AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396317 Black Sea Culture - ARCH SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139802 SAMN04194123 BS Culture Arch AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396398 Black Sea Culture - BACT SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139802 BS Culture Bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396422 Black Sea Mat - ARCH SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139814 SAMN04194122 BS Mat ARCH AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396425 Black Sea Mat - Bact SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139814 SAMN04194122 Black Sea Mat - Bact AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396428 MenezCaldera_Arch SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139818 SAMN04194120 MenezCaldera_Arch AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396430 MenezCaldera_Bact SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139818 SAMN04194120 MenezCaldera_Bact AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396433 GoM-ARCH SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139823 SAMN04194124 GoM-ARCH AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396436 GoM-Bact SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139823 GoM-Bact AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396592 HR Archaea SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs Arch20F/Arch958RV (Massana et al. 1997, Pires et al. 2012) for archaea. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139861 SAMN04194121 HR Archaea AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396593 HR Bacteria SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1139861 HR Bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+ SRX1396596 GB50_Bacteria SRP065102 DNA from AOM enrichments was extracted as described before (Zhou et al. 1996). The protocol encompassed three cycles of freezing and thawing, chemical lysis in a high-salt extraction buffer (1.5M NaCl) by heating of the suspension in the presence of sodium dodecyl sulfate and hexadecyltrimethyl-ammonium bromide, and treatment with proteinase K, followed by chloroform:isoamylalcohol extraction (24:1) and isopropanol based nucleic acid precipitation.To obtain an overview about the diversity of rare microbial phyla we performed massive parallel tag sequencing of ten long-term AOM enrichment cultures. In addition to the four enrichments presented in detail (E20, GB37, GB50 and GF) we also investigated six enrichment cultures that were inoculated with samples from Amon mud volcano, a Black Sea microbial reef, Black Sea sediments, Caldera mud volcano, the Gulf of Mexico and Hydrate Ridge. The latter six enrichment cultures were used for comparison, but are not focus of this study. From DNA that was extracted as described above, we amplified 16S rRNA genes using the primer pairs GM3/907RM (Muyzer et al. 1995, Muyzer et al. 1998) for bacteria. The amplicon libraries were prepared, and the V3-V5 region of these amplicons was sequenced on a 454 Genome Sequencer GS FLX+ (Roche, Basel, Switzerland) at the Max Planck Genome Centre (Cologne, Germany). The raw read data was processed based on a standard operating procedure (Schloss Patrick D et al. 2011) using mothur (release 1.33, 02/2014; (Schloss P. D. et al. 2009). Reads were denoised based on PyroNoise (Quince et al. 2009), trimmed, preclustered ((Huse et al. 2010)) and chimeras removed ((Edgar et al. 2011) SRS1127126 GB50_Bacteria AMPLICON METAGENOMIC PCR 0 0 Technical Read Adapter 1 1 Application Read Forward 5 454 GS FLX+