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Böhnke-Brandt, Stefanie; Perner, Mirjam (2021): Specific RubisCO activity of currently uncultured microorganisms inhabiting hydrothermal deep sea vents [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.931785

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Abstract:
In 2014 we described a new activity-based screen suited to seek active recombinant RubisCOs from the environment - independent of the native host's culturability. Within this study we aimed at seeking novel RubisCO active enzymes from the environment. For this purpose we screened six metagenomic fosmid libraries from hydrothermal vent environments, differing with respect to their (i) geographic origin (north or south Mid Atlantic Ridge) and their (ii) environmental characteristics (basalt vs. ultramafic hosted, temperature, and pH). Overall we screened roughly 12500 metagenomic fosmid clones and identified forty active RubisCOs. Additional sequence-based screening uncovered eight further RubisCOs, which could then also be detected by a modified version of the screen. Seven were active form III RubisCOs from yet uncultured Archaea. This indicates the potential of the activity-based screen to detect RubisCO enzymes even from organisms that would not be expected to be targeted.
Keyword(s):
activity-based screen; autotrophic CO2-fixation; functional metagenomic; HPLC; hydrothermal deep sea vents; specific RubisCO activities
Supplement to:
Böhnke, Stefanie; Perner, Mirjam (2019): Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments. The ISME Journal, 13(10), 2475-2488, https://doi.org/10.1038/s41396-019-0439-3
Project(s):
From Mantle to Ocean: Energy-, Material- and Life-cycles at Spreading Axes (DERIDGE)
Linkage between the distribution and biochemical properties of RuBisCO and CODH enzymes and abiotic properties in thermally and chemically distinct deep-sea hydrothermal vent systems (RuBisCO)
Funding:
German Research Foundation (DFG), grant/award no. 5471797: From Mantle to Ocean: Energy-, Material- and Life-cycles at Spreading Axes
German Research Foundation (DFG), grant/award no. PE1549/5 1: Linkage between the distribution and biochemical properties of RuBisCO and CODH enzymes and abiotic properties in thermally and chemically distinct deep-sea hydrothermal vent systems
Coverage:
Median Latitude: -0.844444 * Median Longitude: -19.737040 * South-bound Latitude: -8.300000 * West-bound Longitude: -44.966670 * North-bound Latitude: 14.750000 * East-bound Longitude: -12.366670
Date/Time Start: 2009-02-04T12:37:00 * Date/Time End: 2009-04-27T09:53:00
Minimum ELEVATION: -3047 m a.s.l. * Maximum ELEVATION: -2915 m a.s.l.
Event(s):
M78/2_274  * Latitude: -4.804000 * Longitude: -12.372333 * Date/Time: 2009-04-17T18:08:00 * Elevation: -2980.0 m * Campaign: M78/2 (MARSUED5) * Basis: Meteor (1986) * Method/Device: Remote operated vehicle (ROV)
M78/2_314  * Latitude: -8.297167 * Longitude: -13.508833 * Date/Time: 2009-04-27T10:01:00 * Elevation: -2886.0 m * Campaign: M78/2 (MARSUED5) * Basis: Meteor (1986) * Method/Device: Remote operated vehicle (ROV)
MSM10/3_300  * Latitude: 14.752500 * Longitude: -44.978000 * Date/Time: 2009-02-04T12:37:00 * Elevation: -3003.3 m * Location: South Atlantic Ocean * Campaign: MSM10/3 * Basis: Maria S. Merian * Method/Device: Remote operated vehicle (ROV)
Comment:
Samples were collected within the DFG-SPP 1144 priority program “From Mantle to Ocean: Energy-, Material-, and Life-cycles at Spreading Axes".
Specific enzyme activity measurements were performed within the scope of the DFG Project PE1549/5 1 "Linkage between the distribution and biochemical properties of RubisCO and CODH enzymes and abiotic properties in thermally and chemically distinct deep-sea hydrothermal vent systems".
For anoxic activity measurements crude extractes were produced aerobically and allowed to become anoxic by placing them under N2/H2 atmosphere (95%/5%; v/v) at 4°C over night. The assay was then performed in an anaerobic chamber under the same atmosphere using anoxic buffer A (100 mM Tris-HCl (pH 7.8), 10 mM MgCl2, 1 mM EDTA, 25 mM NaHCO3 and 1 mM DTT) and anoxic ribulose-1,5-bisphosphate substrate.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1 Event labelEventBöhnke-Brandt, Stefanie
2 Sample code/labelSample labelBöhnke-Brandt, Stefanie
3 Sample typeSamp typeBöhnke-Brandt, Stefanie
4 IdentificationIDBöhnke-Brandt, Stefaniefosmid clone designation
5 SiteSiteBöhnke-Brandt, Stefaniesampling site
6 Area/localityAreaBöhnke-Brandt, Stefanie
7 DATE/TIMEDate/TimeBöhnke-Brandt, StefanieGeocode
8 LATITUDELatitudeBöhnke-Brandt, StefanieGeocode
9 LONGITUDELongitudeBöhnke-Brandt, StefanieGeocode
10 ELEVATIONElevationm a.s.l.Böhnke-Brandt, StefanieGeocode
11 Temperature, technicalT tech°CBöhnke-Brandt, Stefanieheat blockenzyme assay temperature
12 TreatmentTreatBöhnke-Brandt, StefaniePresence of oxygen during assay (oxic/anoxic)
13 Specific ribulose-1,5-bisphosphate carboxylase/oxygenase activitySpec RubisCO actnmol/mg/minBöhnke-Brandt, StefanieHigh Performance Liquid Chromatography (HPLC)
14 Specific ribulose-1,5-bisphosphate carboxylase/oxygenase activity, standard deviationSpec RubisCO act std dev±Böhnke-Brandt, StefanieGaussian propagation of error
15 Accession number, geneticsAccess no genBöhnke-Brandt, StefanieSanger Sequencing modified after Sanger et al. (1977); PacBio Sequencing according to Rhoads and Au (2015)nt sequences have been deposited in the NCBI (National Center for Biotechnology Information)
16 Accession number, geneticsAccess no genBöhnke-Brandt, StefanieSanger Sequencing modified after Sanger et al. (1977); PacBio Sequencing according to Rhoads and Au (2015)nt sequences have been deposited in the NCBI (National Center for Biotechnology Information)
17 Accession number, geneticsAccess no genBöhnke-Brandt, StefanieSanger Sequencing modified after Sanger et al. (1977); PacBio Sequencing according to Rhoads and Au (2015)nt sequences have been deposited in the NCBI (National Center for Biotechnology Information)
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
279 data points

Data

Download dataset as tab-delimited text — use the following character encoding:

1 
Event		2 
Sample label		3 
Samp type		4 
ID
(fosmid clone designation)		5 
Site
(sampling site)		6 
Area		7 
Date/Time		8 
Latitude		9 
Longitude		10 
Elevation [m a.s.l.]		11 
T tech [°C]
(enzyme assay temperature, hea...)		12 
Treat
(Presence of oxygen during ass...)		13 
Spec RubisCO act [nmol/mg/min]
(High Performance Liquid Chrom...)		14 
Spec RubisCO act std dev [±]
(Gaussian propagation of error)		15 
Access no gen
(nt sequences have been deposi...)		16 
Access no gen
(nt sequences have been deposi...)		17 
Access no gen
(nt sequences have been deposi...)
M78/2_274 MAR-SUEDV/274ROV1Bchimney sampleSP52C8Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0oxic3.221.67insdc:MK564616
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP88G2Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0oxic8.003.36insdc:MK564617
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP92E10Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0oxic5.822.63insdc:MK564618
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP96F12Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0oxic2.400.77insdc:MK564619
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP119A5Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0oxic1.811.39insdc:MK564620
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP133E7Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0oxic6.724.79insdc:MK564621
MSM10/3_313ROV-12 MSM10-3/313ROV1chimney sampleSB29A9SiteBLogatchev hydrothermal vent field2009-02-08T15:3514.75000-44.96667-304725.0oxic32.534.62insdc:MK204372insdc:MK204373insdc:MK204374
M78/2_314 MAR-SUEDV/314 ROV 7-9fluid sampleD71C2DrachenschlundNibelungen hydrothermal vent field2009-04-27T09:53-8.30000-13.50000-291525.0oxic481.408.16insdc:KJ639815
MSM10/3_300 MSM10-3/300 ROV 19-21fluid sampleIrIIF9IrinaIILogatchev hydrothermal vent field2009-02-04T12:3714.75000-44.96667-300325.0oxic699.2829.24insdc:MK204370insdc:MK204371
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP52C8Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0anoxic9.488.68insdc:MK564616
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP88G2Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0anoxic5.886.69insdc:MK564617
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP92E10Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0anoxic24.759.52insdc:MK564618
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP96F12Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0anoxic53.8813.75insdc:MK564619
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP119A5Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0anoxic38.7518.67insdc:MK564620
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP133E7Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298225.0anoxic19.645.03insdc:MK564621
MSM10/3_313ROV-12MSM10-3/313ROV1chimney sampleSB29A9SiteBLogatchev hydrothermal vent field2009-02-08T15:3514.75000-44.96667-304725.0anoxic11.515.80insdc:MK204372insdc:MK204373insdc:MK204374
M78/2_314MAR-SUEDV/314 ROV 7-9fluid sampleD71C2DrachenschlundNibelungen hydrothermal vent field2009-04-27T09:53-8.30000-13.50000-291525.0anoxic437.3439.04insdc:KJ639815
MSM10/3_300MSM10-3/300 ROV 19-21fluid sampleIrIIF9IrinaIILogatchev hydrothermal vent field2009-02-04T12:3714.75000-44.96667-300325.0anoxic583.3814.15insdc:MK204370insdc:MK204371
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP52C8Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298255.0anoxic22.7710.72insdc:MK564616
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP88G2Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298255.0anoxic18.327.46insdc:MK564617
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP92E10Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298255.0anoxic29.566.37insdc:MK564618
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP96F12Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298255.0anoxic18.437.28insdc:MK564619
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP119A5Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298255.0anoxic28.075.07insdc:MK564620
M78/2_274MAR-SUEDV/274ROV1Bchimney sampleSP133E7Sisters PeakComfortless Cove hydrothermal vent field)2009-04-17T16:32-4.80000-12.36667-298255.0anoxic32.786.41insdc:MK564621
MSM10/3_313ROV-12MSM10-3/313ROV1chimney sampleSB29A9SiteBLogatchev hydrothermal vent field2009-02-08T15:3514.75000-44.96667-304755.0anoxic65.069.89insdc:MK204372insdc:MK204373insdc:MK204374
M78/2_314MAR-SUEDV/314 ROV 7-9fluid sampleD71C2DrachenschlundNibelungen hydrothermal vent field2009-04-27T09:53-8.30000-13.50000-291555.0anoxic259.9934.78insdc:KJ639815
MSM10/3_300MSM10-3/300 ROV 19-21fluid sampleIrIIF9IrinaIILogatchev hydrothermal vent field2009-02-04T12:3714.75000-44.96667-300355.0anoxic462.6841.71insdc:MK204370insdc:MK204371