Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1^T, HCA1^T, HCE1^T and PS0^T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15–0.26 µm in diameter and 0.50–1.59 µm in length. Motility was not observed, although strain PS0^T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1^T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76^T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1^T, HCE1^T, and PS0^T. Strain PS0^T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B_1 (thiamine), B_2 (riboflavin), B_6 (pyridoxine), and B_(12) (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0–34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76^T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1^T (=ATCC TSD-97^T =NCIMB 15022^T), HCA1^T (=ATCC TSD-96^T), HCE1^T(=ATCC TSD-98^T), and PS0^T (=ATCC TSD-99^T) are type strains of the species Nitrosopumilus maritimus sp. nov., Nitrosopumilus cobalaminigenessp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1^T, HCA1^T, HCE1^T and PS0^T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15–0.26 µm in diameter and 0.50–1.59 µm in length. Motility was not observed, although strain PS0^T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1^T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76^T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1^T, HCE1^T, and PS0^T. Strain PS0^T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B_1 (thiamine), B_2 (riboflavin), B_6 (pyridoxine), and B_(12) (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0–34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76^T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1^T (=ATCC TSD-97^T =NCIMB 15022^T), HCA1^T (=ATCC TSD-96^T), HCE1^T(=ATCC TSD-98^T), and PS0^T (=ATCC TSD-99^T) are type strains of the species Nitrosopumilus maritimus sp. nov., Nitrosopumilus cobalaminigenessp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria

Methanosarcina acetivorans

Raw data files of Methanosarcina acetivorans<strong>Tilt Series Date:</strong> 2013-12-09</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> Methanosarcina acetivorans</p> <strong>Strain:</strong> </p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 130.0 eV/Ų, defocus: -10.0 μm, magnification: 18000x. </p> <strong>Microscope:</strong> 0</p> <strong>Acquisition Software:</strong> Undefined</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> Raptor</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2013-12-09-53</p>grid30021.mrc, Tilt Series (Pixel Size 0.63 nm), 3.2 GB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2013-12-09-53/rawdata/grid30021.mrc" > <i class="download icon"></i> Download </a></p> grid30021_full.rec, Reconstruction (Pixel Size 2.52 nm), 623.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2013-12-09-53/3dimage_35932/grid30021_full.rec" > <i class="download icon"></i> Download </a></p&gt

HeLa

Synchronized, looking for midbodies<strong>Tilt Series Date:</strong> 2014-01-05</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> HeLa cells</p> <strong>Strain:</strong> ATCC</p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Ų, defocus: -10.0 μm, magnification: 18000x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> UCSF tomo</p> <strong>Collaborators and Roles:</strong> With Doug Mckay and Katherine Ullman</p> <strong>Sample Preparation:</strong> HeLa cells+ siRNA NUP 153+ Thymidine 2mM. 14 hour after release</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-01-05-3</p>10003.mrc, Tilt Series (Pixel Size 0.6 nm), 861.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-01-05-3/rawdata/10003.mrc" > <i class="download icon"></i> Download </a></p> 10003_part121_58.rec, Reconstruction (Pixel Size 2.4 nm), 156.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-01-05-3/3dimage_50336/10003_part121_58.rec" > <i class="download icon"></i> Download </a></p&gt

Sulfolobus solfac.P2

Sulfolobus solfactaricus P2 cells- active culture fixed with 0.5% glutiraldehyde.<strong>Tilt Series Date:</strong> 2014-02-20</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> Sulfolobus solfataricus </p> <strong>Strain:</strong> P2</p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-50.0°, 50.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Ų, defocus: -10.0 μm, magnification: 22500x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> Raptor</p> <strong>Collaborators and Roles:</strong> with Jamie Snyder from Montana</p> <strong>Purification / Growth Conditions / Treatment:</strong> Active culture fixed</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-13</p>atlas20009.mrc, Tilt Series (Pixel Size 0.48 nm), 2.9 GB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-13/rawdata/atlas20009.mrc" > <i class="download icon"></i> Download </a></p> atlas20009_part101_44.rec, Reconstruction (Pixel Size 1.92 nm), 623.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-13/3dimage_39264/atlas20009_part101_44.rec" > <i class="download icon"></i> Download </a></p&gt

Sulfolobus cells synchronized fo

search for ESCRT in dividing cells<strong>Tilt Series Date:</strong> 2014-02-04</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p> <strong>Strain:</strong> </p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Ų, defocus: -8.0 μm, magnification: 27500x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> Raptor</p> <strong>Collaborators and Roles:</strong> Megan Dobro's samples gridbox 8.</p> <strong>Purification / Growth Conditions / Treatment:</strong> grown in Brock's Medium at 80C, synchronize with Baby Machine</p> <strong>Sample Preparation:</strong> frozen at Kay Grunewald's lab. Harrick plasma cleaner. Blotted on both sides, 5 sec, sponge for humidity</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-04-13</p>atlas30007.mrc, Tilt Series (Pixel Size 0.39 nm), 3.2 GB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-04-13/rawdata/atlas30007.mrc" > <i class="download icon"></i> Download </a></p> atlas30007_part111_6.rec, Reconstruction (Pixel Size 1.56 nm), 623.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-04-13/3dimage_38362/atlas30007_part111_6.rec" > <i class="download icon"></i> Download </a></p&gt

HeLa

Looking for midbodies<strong>Tilt Series Date:</strong> 2014-01-06</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> HeLa cells</p> <strong>Strain:</strong> ATCC</p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Ų, defocus: -10.0 μm, magnification: 18000x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> UCSF tomo</p> <strong>Collaborators and Roles:</strong> with Doug Mckay</p> <strong>Sample Preparation:</strong> HeLa cells+siRNA NUP153 + Thymidine. Freeze after 14 hours of thymidine release.</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-01-06-26</p>midbody10006.mrc, Tilt Series (Pixel Size 0.6 nm), 861.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-01-06-26/rawdata/midbody10006.mrc" > <i class="download icon"></i> Download </a></p> midbody10006_full.rec, Reconstruction (Pixel Size 2.4 nm), 156.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-01-06-26/3dimage_50433/midbody10006_full.rec" > <i class="download icon"></i> Download </a></p&gt

Sulfolobus solfac.P2

Sulfolobus solfactaricus P2 cells- active culture fixed with 0.5% glutiraldehyde.<strong>Tilt Series Date:</strong> 2014-02-20</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> Sulfolobus solfataricus </p> <strong>Strain:</strong> P2</p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-50.0°, 50.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Ų, defocus: -10.0 μm, magnification: 22500x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> Raptor</p> <strong>Collaborators and Roles:</strong> with Jamie Snyder from Montana</p> <strong>Purification / Growth Conditions / Treatment:</strong> Active culture fixed</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-23</p>atlas20019.mrc, Tilt Series (Pixel Size 0.48 nm), 2.9 GB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-23/rawdata/atlas20019.mrc" > <i class="download icon"></i> Download </a></p> atlas20019_full.rec, Reconstruction (Pixel Size 1.92 nm), 623.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-23/3dimage_39283/atlas20019_full.rec" > <i class="download icon"></i> Download </a></p&gt

HeLa cells

LOOKING FOR MIDBODIES<strong>Tilt Series Date:</strong> 2014-11-18</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> HeLa cells</p> <strong>Strain:</strong> ATCC</p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-55.0°, 55.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Ų, defocus: -10.0 μm, magnification: 18000x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> UCSF TOMO</p> <strong>Collaborators and Roles:</strong> cells and siRNA obtained from Doug Mackay/ Cathrine Ullman</p> <strong>Sample Preparation:</strong> HeLa cells+ siRNA NUP153+ Thymidine 2mM, 14 h post thymidine release</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-18-6</p>midbody60006.mrc, Tilt Series (Pixel Size 0.6 nm), 3.2 GB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-18-6/rawdata/midbody60006.mrc" > <i class="download icon"></i> Download </a></p> midbody60006_full.rec, Reconstruction (Pixel Size 2.4 nm), 623.6 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-18-6/3dimage_48171/midbody60006_full.rec" > <i class="download icon"></i> Download </a></p> midbody60006new_full.rec, Reconstruction (Pixel Size 0.0 nm), 266.7 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-18-6/3dimage_48302/midbody60006new_full.rec" > <i class="download icon"></i> Download </a></p&gt

nitrosopumilus maritimus

Looking for dividing cells<strong>Tilt Series Date:</strong> 2014-11-26</p> <strong>Data Taken By:</strong> Rasika Ramdasi</p> <strong>Species / Specimen:</strong> Nitrosopumilus maritimus</p> <strong>Strain:</strong> None</p> <strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Ų, defocus: -10.0 μm, magnification: 19000x. </p> <strong>Microscope:</strong> Caltech Polara</p> <strong>Acquisition Software:</strong> UCSFTomo</p> <strong>Upload Method:</strong> pipeline</p> <strong>Processing Software Used:</strong> UCSF tomo</p> <strong>Collaborators and Roles:</strong> With David Stahl</p> rra2014-11-26-1_slicer10607.jpg: Filament?Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-26-1</p>1-1-new-atlas-SA0001.mrc, Tilt Series (Pixel Size 0.56 nm), 3.3 GB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-26-1/rawdata/1-1-new-atlas-SA0001.mrc" > <i class="download icon"></i> Download </a></p> 1-1-new-atlas-SA0001_full.rec, Reconstruction (Pixel Size 2.24 nm), 602.8 MB <a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-11-26-1/3dimage_48350/1-1-new-atlas-SA0001_full.rec" > <i class="download icon"></i> Download </a></p&gt