Summary of Study ST000914

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000632. The data can be accessed directly via it's Project DOI: 10.21228/M8038Z This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study ID	ST000914
Study Title	Metabolomic adaptation of a deep sea Microbacterium sediminis to prolonged low temperature under high pressure
Study Summary	Low temperature is the most wide-spread “hostile” environmental factor on earth while at the same time the most common condition for marine organisms. However, the unique adaptive mechanisms that enable the survival of marine microorganisms under low temperature are unclear. Since low temperature is always accompanied by high pressure and other adverse conditions in marine environment, here we studied the metabolic adaptation of a marine strain to prolonged low temperature under high pressure. The strain studied is a psychrotolerant Microbacterium sediminis isolated from deep sea sediment. By using 1H nuclear magnetic resonance (NMR)-based metabolomics approach, we detected the spectral data of polar extracts of the strain M. sediminis, and applied multivariate statistical analysis methods together with univariate analysis to analyze metabolic profiles associated to different conditions. The metabolic profiles of the M. sediminis strain cultivated under high pressure at low temperature were distinctly different from those cultivated under high pressure at normal temperature. We identified the differential metabolites which were responsible for distinguishing the metabolic profiles and compared their relative intensities between groups. We also compared the different adaptive responses of the strain at different growth stages to the prolonged low temperature under high pressure. We proposed that the low-temperature adapting process of the M. sediminis strain involves, 1) the regulation of osmotic pressure using amino acids as possible alternative osmolytes, and, 2) the strengthen of glycolysis and the maintenance of TCA cycle via amino acids anaplerotic reaction. We put forward that the main difference of adaptation to low temperature for the strain at different growth stages was related to energy metabolism. Our findings improved the understanding of the low-temperature adaptive mechanisms for marine microorganisms under high pressure on the metabolic level.
Institute	Third Institute of Oceanography, State Oceanic Administration
Last Name	Xia
First Name	Jinmei
Address	184 Daxue Road, Xiamen 361005, PR China
Email	xiajinmei@tio.org.cn
Phone	86-13003995626
Submit Date	2017-12-15
Analysis Type Detail	NMR
Release Date	2020-01-06
Release Version	1

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Project:

Project ID:	PR000632
Project DOI:	doi: 10.21228/M8038Z
Project Title:	Metabolomic adaptation of a deep sea Microbacterium sediminis to prolonged low temperature under high pressure
Project Summary:	Low temperature is the most wide-spread “hostile” environmental factor on earth while at the same time the most common condition for marine organisms. However, the unique adaptive mechanisms that enable the survival of marine microorganisms under low temperature are unclear. Since low temperature is always accompanied by high pressure and other adverse conditions in marine environment, here we studied the metabolic adaptation of a marine strain to prolonged low temperature under high pressure. The strain studied is a psychrotolerant Microbacterium sediminis isolated from deep sea sediment. By using 1H nuclear magnetic resonance (NMR)-based metabolomics approach, we detected the spectral data of polar extracts of the strain M. sediminis, and applied multivariate statistical analysis methods together with univariate analysis to analyze metabolic profiles associated to different conditions. The metabolic profiles of the M. sediminis strain cultivated under high pressure at low temperature were distinctly different from those cultivated under high pressure at normal temperature. We identified the differential metabolites which were responsible for distinguishing the metabolic profiles and compared their relative intensities between groups. We also compared the different adaptive responses of the strain at different growth stages to the prolonged low temperature under high pressure. We proposed that the low-temperature adapting process of the M. sediminis strain involves, 1) the regulation of osmotic pressure using amino acids as possible alternative osmolytes, and, 2) the strengthen of glycolysis and the maintenance of TCA cycle via amino acids anaplerotic reaction. We put forward that the main difference of adaptation to low temperature for the strain at different growth stages was related to energy metabolism. Our findings improved the understanding of the low-temperature adaptive mechanisms for marine microorganisms under high pressure on the metabolic level.
Institute:	Third Institute of Oceanography, State Oceanic Administration
Last Name:	Xia
First Name:	Jinmei
Address:	184 Daxue Road, Xiamen 361005, PR China
Email:	xiajinmei@tio.org.cn
Phone:	86-13003995626

Subject:

Subject ID:	SU000952
Subject Type:	NMR based metabolomics of microbes
Subject Species:	Microbacterium sediminis
Taxonomy ID:	904291

Factors:

Subject type: NMR based metabolomics of microbes; Subject species: Microbacterium sediminis (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA053770	4D	LT-L
SA053771	4C	LT-L
SA053772	4E	LT-L
SA053773	4G	LT-L
SA053774	4H	LT-L
SA053775	4B	LT-L
SA053776	4F	LT-L
SA053777	4A	LT-L
SA053778	4K	LT-S
SA053779	4J	LT-S
SA053780	4I	LT-S
SA053781	4L	LT-S
SA053782	4M	LT-S
SA053783	4O	LT-S
SA053784	4P	LT-S
SA053785	4N	LT-S
SA053786	2D	NT-L
SA053787	2C	NT-L
SA053788	2B	NT-L
SA053789	2E	NT-L
SA053790	2F	NT-L
SA053791	2A	NT-L
SA053792	2H	NT-L
SA053793	2G	NT-L
SA053794	2M	NT-S
SA053795	2L	NT-S
SA053796	2K	NT-S
SA053797	2N	NT-S
SA053798	2P	NT-S
SA053799	2I	NT-S
SA053800	2J	NT-S
SA053801	2O	NT-S

Showing results 1 to 32 of 32

Showing results 1 to 32 of 32

Collection:

Collection ID:	CO000946
Collection Summary:	A psychrotolerant strain of Microbacterium sediminis numbered as YLB-01 isolated from deep sea sediment of the Indian Ocean was used in this study. The strain can grow at temperatures ranging from 4 °C to 50 °C with an optimal growth temperature of 28 °C (Yu et al. 2013). Tryptone soy broth (TSB) medium, which contains 15 g/L tryptone, 5 g/L soy peptone, and 5 g/L NaCl, was used to cultivate the strain. The strain was maintained in glycerol tubes under -80 °C in a refrigerator and was activated using streaking inoculation on agar plates before use. For metabolomics research, a single colony was first inoculated from an agar plate to 32 test tubes containing 5 mL of TSB medium each and cultivated using a shaker under 28 °C for 12 hours. These seed cultures were then transferred to 150 mL Erlenmeyer flasks containing 100 mL of TSB medium each. In order to obtain a sufficient amount of cells, these cells were cultivated under normal temperature (28 °C) and atmospheric pressure (0.1 MPa) until logarithmic or stationary phase before transferred to lower temperature. Specifically, half of these samples were cultivated using a shaker under 28 °C for 18 hours to reach mid logarithmic phase (assigned as scenario L) and the other half were cultivated for 24 hours to reach stationary phase (assigned as scenario S) under the same condition. All samples were then transferred into 100 mL normal saline bags and put into a water-filled high-pressure chamber with the pressure set at 30 MPa. For half of the samples from a certain scenario (L or S) the temperature of the chamber was set at 28 °C. For the other half of the samples the temperature of the chamber was set at 4 °C. All samples were harvested after 7 days. The samples were grouped as NT-L, LT-L, NT-S, and LT-S based on their different cultivation conditions and sampling time
Sample Type:	cells

Treatment:

Treatment ID:	TR000966
Treatment Summary:	half of these samples were cultivated using a shaker under 28 °C for 18 hours to reach mid logarithmic phase (assigned as scenario L) and the other half were cultivated for 24 hours to reach stationary phase (assigned as scenario S) under the same condition. All samples were then transferred into 100 mL normal saline bags and put into a water-filled high-pressure chamber with the pressure set at 30 MPa. For half of the samples from a certain scenario (L or S) the temperature of the chamber was set at 28 °C. For the other half of the samples the temperature of the chamber was set at 4 °C. All samples were harvested after 7 days. The samples were grouped as NT-L, LT-L, NT-S, and LT-S based on their different cultivation conditions and sampling time

Treatment ID:

TR000966

Treatment Summary:

half of these samples were cultivated using a shaker under 28 °C for 18 hours to reach mid logarithmic phase (assigned as scenario L) and the other half were cultivated for 24 hours to reach stationary phase (assigned as scenario S) under the same condition. All samples were then transferred into 100 mL normal saline bags and put into a water-filled high-pressure chamber with the pressure set at 30 MPa. For half of the samples from a certain scenario (L or S) the temperature of the chamber was set at 28 °C. For the other half of the samples the temperature of the chamber was set at 4 °C. All samples were harvested after 7 days. The samples were grouped as NT-L, LT-L, NT-S, and LT-S based on their different cultivation conditions and sampling time

Sample Preparation:

Sampleprep ID:	SP000959
Sampleprep Summary:	All 100 mL of the fermentation broth in a flask was harvested and poured into a 250 mL centrifuge bottle and centrifuged at 6000g and 4 °C for 5 min. The supernatant was discarded and the cell pellets were quenched using 100 mL of a buffer composed of 3:2 methanol/water and 0.85% (wt./vol.) NaCl at -40 °C. The resuspended mixture was again centrifuged at 6000g and 4 °C for 5 min. The cell pellets were then washed using cold PBS for 3 times. The mixture was resuspended and transferred into a 5 mL Eppendorf tube during the 3rd wash and then centrifuged at 6000g and 4 °C for 5 min. The cell pellets were kept under -80 °C until use. Intracellular metabolites were extracted using a procedure adopted from Ye et al. (Ye et al. 2012). The frozen samples were homogenized in 600 μL of cold 1:1 acetonitrile/water buffer. To destroy the bacterial cells, the samples were further sonicated on wet ice for 180 cycles with each cycle consisting of 2 s pulses and 3 s stops. The supernatant was collected by centrifugation at 12000 g for 10 min at 4 °C. The remaining solid residues were further extracted using the same extract solution and intensively homogenized via vortexing. The second supernatant was collected after centrifugation and pooled with the first one. The combined supernatants from the two extractions were lyophilized, and stored at -80 °C. Immediately before 1H NMR measurements were taken, the extract powder was redisclosed in 550 µL phosphate buffer (50 mM K2HPO4/NaH2PO4, 10% D2O, 1mM 3-(Trimethylsilyl) propionate-2,2,3,3-d4 acid sodium salt (TSP), pH7.4). Subsequently, all the samples were vortexed and centrifuged at 12000 g for 15 min at 4 °C to remove any insoluble components. Finally, aliquots of the supernatant were transferred into 5 mm NMR tubes (Beckonert et al. 2007).

Sampleprep ID:

SP000959

Sampleprep Summary:

All 100 mL of the fermentation broth in a flask was harvested and poured into a 250 mL centrifuge bottle and centrifuged at 6000g and 4 °C for 5 min. The supernatant was discarded and the cell pellets were quenched using 100 mL of a buffer composed of 3:2 methanol/water and 0.85% (wt./vol.) NaCl at -40 °C. The resuspended mixture was again centrifuged at 6000g and 4 °C for 5 min. The cell pellets were then washed using cold PBS for 3 times. The mixture was resuspended and transferred into a 5 mL Eppendorf tube during the 3rd wash and then centrifuged at 6000g and 4 °C for 5 min. The cell pellets were kept under -80 °C until use. Intracellular metabolites were extracted using a procedure adopted from Ye et al. (Ye et al. 2012). The frozen samples were homogenized in 600 μL of cold 1:1 acetonitrile/water buffer. To destroy the bacterial cells, the samples were further sonicated on wet ice for 180 cycles with each cycle consisting of 2 s pulses and 3 s stops. The supernatant was collected by centrifugation at 12000 g for 10 min at 4 °C. The remaining solid residues were further extracted using the same extract solution and intensively homogenized via vortexing. The second supernatant was collected after centrifugation and pooled with the first one. The combined supernatants from the two extractions were lyophilized, and stored at -80 °C. Immediately before 1H NMR measurements were taken, the extract powder was redisclosed in 550 µL phosphate buffer (50 mM K2HPO4/NaH2PO4, 10% D2O, 1mM 3-(Trimethylsilyl) propionate-2,2,3,3-d4 acid sodium salt (TSP), pH7.4). Subsequently, all the samples were vortexed and centrifuged at 12000 g for 15 min at 4 °C to remove any insoluble components. Finally, aliquots of the supernatant were transferred into 5 mm NMR tubes (Beckonert et al. 2007).

Analysis:

Analysis ID:	AN001484
Analysis Type:	NMR
Num Factors:	4

NMR:

NMR ID:	NM000115
Analysis ID:	AN001484
Instrument Name:	Bruker Avance III 600 MHz spectrometer
Instrument Type:	FT-NMR
NMR Experiment Type:	1D 1H
Spectrometer Frequency:	600 MHz