RNA-seq analysis in simulated microgravity unveils down-regulation of the beta-rhizobial siderophore phymabactin

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Recent scientific and technological innovations such as the development of reusable rockets or the commercialization of advanced semiconductor integrated circuits brought us a great leap forward in space exploration. Agencies from all around the world are now looking toward the sky with renewed interest and are now aiming at the closest astronomical objects. The Moon, our next target, is now the center of interest for a new generation of settlers through the Artemis campaign in 2031.  Yet, space exploration is a complex and challenging effort, which involves several scientific and technological challenges. One of these challenges consists of providing fresh and vitamin-rich food to long-term extraterrestrial inhabitants. Therefore, the establishment of permanent outposts on the surface of the lunar or Martian soil will demand the development and implementation of space farming.  However, the conditions far from Earth are by definition extraordinarily hostile to Life. Among others, the high levels of radiation, the extreme temperature variations, the absence of atmosphere, and the reduced gravity make life impossible on the Moon’s surface as it is. Most of these issues can be solved by building robust and permanent dwellings with a temperature and gas regulation system where people will be able to live. However, these accommodations will not be able to compensate for the reduced weightlessness such as the one encountered on the Moon. Unfortunately, growth in altered gravity has a detrimental effect on plants' growth and yield. In addition, most crops of human interest require fertilizer supplementation to ensure a profitable yield. Indeed, although nitrogen is very abundant in the atmosphere (78% of the air is N2), plants cannot metabolize it. This causes another issue, as importing N-fertilizers regularly will not be compatible with extraterrestrial settlements being as self-sufficient as possible.

An alternative solution for providing crops with essential nutrients is to use the mutualistic relationship between nitrogen-fixing bacteria called rhizobia and legumes. Indeed, rhizobia can form a symbiosis with legumes and provide plants with reduced nitrogen in a process called nitrogen fixation. In addition, some rhizobia have additional plant-beneficial properties like protection against pests or abiotic stresses and growth stimulation. Paraburkholderia phymatum STM815T, the rhizobium used in our study, stands out for its ability to nodulate more than 50 legumes and being highly competitive against other soil bacteria for root infection. Moreover, P. phymatum produces auxin and endure harsh soil conditions such as stress and salt stress.

 Representation of the interaction between legumes and rhizobia in prospective extraterrestrial settlements

Rhizobia secrete nodulation factors (orange diamond) that induce the formation of nodules in legumes. The bacteria can then establish endosymbiosis with the plant, where they fix atmospheric dinitrogen and trade it to the plant in exchange for carbon sources. Rhizobia can also produce phytohormones (green diamonds), antibiotics (purple diamonds), and siderophores (blue diamonds) that can stimulate plant growth and protect them against pathogens.
Rhizobia secrete nodulation factors (orange diamond) that induce the formation of nodules in legumes. The bacteria can then establish endosymbiosis with the plant, where they fix atmospheric dinitrogen and trade it to the plant in exchange for carbon sources. Rhizobia can also produce phytohormones (green diamonds), antibiotics (purple diamonds), and siderophores (blue diamonds) that can stimulate plant growth and protect them against pathogens. 

In this study, we investigated the impact of artificial microgravity (s0-g) on P. phymatum growth and gene expression. We first used RNA-Sequencing to look at global transcript changes occurring in P. phymatum cells grown in simulated microgravity compared to terrestrial gravity (1g). Interestingly, the global transcript profile displays drastic changes, with around 23% of genes being differentially expressed.  Among the genes mostly downregulated in simulated microgravity we found a gene cluster coding for a putative iron chelator (siderophore) named phymabactin. Indeed when P. phymatum cells were incubated in simulated microgravity, a decreased amount of siderophores was produced. The fact that a phymabactin mutant strain did not produce any siderophore suggests that phymabactin is the only siderophore produced by P. phymatum.

Importantly, the fact that this promiscuous and stress-resistant beta-rhizobial strain P. phymatum grew in simulated microgravity as well as in normal gravity suggests that it also adapts very well to space-like conditions, makes it an excellent candidate for an inoculant for crops grown in future lunar or Martian colonies.

To learn more about our project, please refer to our article here: https://www.nature.com/articles/s41526-024-00391-7

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