Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity

Tom Verbeelen; Celia Alvarez Hernandez; Thanh Huy Nguyen; Surya Gupta; Raf Aarts; Kevin Tabury; Baptiste Leroy; Ruddy Wattiez; Siegfried  E. Vlaeminck; Natalie Leys; Ramon Ganigué; Felice Mastroleo

doi:10.1038/s41526-024-00345-z

Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity

Tom Verbeelen, Celia Alvarez Hernandez, Thanh Huy Nguyen, Surya Gupta, Raf Aarts, Kevin Tabury, Baptiste Leroy, Ruddy Wattiez, Siegfried E. Vlaeminck, Natalie Leys, Ramon Ganigué, Felice Mastroleo

Research output › peer-review

Abstract

Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.

Original language	English
Article number	3
Number of pages	19
Journal	npj Microgravity
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41526-024-00345-z
State	Published - Dec 2024

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology (miscellaneous)
Agricultural and Biological Sciences (miscellaneous)
Medicine (miscellaneous)
Space and Planetary Science
Materials Science (miscellaneous)
Physics and Astronomy (miscellaneous)

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Cite this

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title = "Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity",

abstract = "Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.",

keywords = "RNA extraction, RNA sequencing, Microgravity, MELiSSA",

author = "Tom Verbeelen and {Alvarez Hernandez}, Celia and Nguyen, {Thanh Huy} and Surya Gupta and Raf Aarts and Kevin Tabury and Baptiste Leroy and Ruddy Wattiez and Vlaeminck, {Siegfried E.} and Natalie Leys and Ramon Ganigu{\'e} and Felice Mastroleo",

note = "Score=10 Funding Information: This work was part of the URINIS-A project, funded by the Belgian Federal Science Policy Office (BELSPO; Contract # PEA 4000129030) and ESA via the PRODEX program. The URINIS-A project is part of the MELiSSA program of ESA, ESA{\textquoteright}s life support system development program ( www.melissafoundation.org ). RG was supported by the Special Research Fund of Ghent University [BOF19/STA/044]. The authors thank Dr. Mohamed Mysara for his valuable support on the RNA-Seq analysis, Dr. Rob Van Houdt for his resourceful advice on the qPCR workflow, and Sam Devolder for helping with the printing of the PL-70 cell culture bag holders. Publisher Copyright: {\textcopyright} 2024, The Author(s).",

year = "2024",

month = dec,

doi = "10.1038/s41526-024-00345-z",

language = "English",

volume = "10",

journal = "npj Microgravity",

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T1 - Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity

AU - Verbeelen, Tom

AU - Alvarez Hernandez, Celia

AU - Nguyen, Thanh Huy

AU - Gupta, Surya

AU - Aarts, Raf

AU - Tabury, Kevin

AU - Leroy, Baptiste

AU - Wattiez, Ruddy

AU - Vlaeminck, Siegfried E.

AU - Leys, Natalie

AU - Ganigué, Ramon

AU - Mastroleo, Felice

N1 - Score=10 Funding Information: This work was part of the URINIS-A project, funded by the Belgian Federal Science Policy Office (BELSPO; Contract # PEA 4000129030) and ESA via the PRODEX program. The URINIS-A project is part of the MELiSSA program of ESA, ESA’s life support system development program ( www.melissafoundation.org ). RG was supported by the Special Research Fund of Ghent University [BOF19/STA/044]. The authors thank Dr. Mohamed Mysara for his valuable support on the RNA-Seq analysis, Dr. Rob Van Houdt for his resourceful advice on the qPCR workflow, and Sam Devolder for helping with the printing of the PL-70 cell culture bag holders. Publisher Copyright: © 2024, The Author(s).

PY - 2024/12

Y1 - 2024/12

N2 - Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.

AB - Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.

KW - RNA extraction

KW - RNA sequencing

KW - Microgravity

KW - MELiSSA

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U2 - 10.1038/s41526-024-00345-z

DO - 10.1038/s41526-024-00345-z

M3 - Article

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VL - 10

JO - npj Microgravity

JF - npj Microgravity

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