Year: 2026
Type: preprint
Abstract: Plant microbiome engineering remains a significant challenge due to challenges associated with accurately predicting microbiome assembly and function in complex, heterogeneous soil environments. However, host-mediated selection can simplify the process by using plant host phenotype as a reporter of microbiome function; by iteratively selecting microbiomes from hosts with desired phenotypes and using them to inoculate subsequent cohorts of hosts, artificial selection can steer the microbiome towards a composition producing optimized plant phenotypes. In this study, we inoculated rice with wild microbial communities from fallow rice field, desert, and serpentine seep field soils. By challenging these plants with drought and iteratively selecting microbiomes from the least drought stressed plants across multiple generations, we derived simplified microbiomes that enhanced both the growth and drought tolerance of rice. Across selection cycles, microbiomes within and between soil treatments became increasingly similar, implicating both dispersal and selection as drivers of community composition. With amplicon sequencing data we identified specific bacterial taxa associated with improved rice drought phenotypes; while many of these taxa have been previously described as plant growth promoters, we also identified novel taxa exhibiting strong positive correlation with improved drought performance. Lastly, we resolved 272 metagenome-assembled genomes (MAGs) and used these MAGs to identify functions enriched in bacteria driving enhanced drought tolerance. The most significantly enriched functions—particularly glycerol-3-phosphate and iron transport—have been previously implicated as potential mediators of plant-microbe interactions during drought. Altogether, these data demonstrate that host-mediated selection provides an efficient framework for microbiome engineering through the identification of both individual taxa and simplified communities associated with enhanced plant phenotypes.
Source: eLife
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $2,500
Awards: WE PROPOSE THE CENTER FOR THE UTILIZATION OF BIOLOGICAL ENGINEERING IN SPACE (CUBES) TO SUPPORT BIOMANUFACTURING FOR DEEP SPACE EXPLORATION THAT REALIZES THE INHERENT MASS POWER AND VOLUME ADVANTAGES OF SPACE BIOTECHNOLOGY OVER TRADITIONAL ABIOTIC APPROACHES. CUBES WILL ADVANCE THE PRACTICALITY OF AN INTEGRATED MULTI-FUNCTION MULTI-ORGANISM BIOMANUFACTURING SYSTEM ON A MARS MISSION. HIGHLY MULTIDISCIPLINARY RESEARCH WILL CULMINATE IN A CONTINUOUS BIOMANUFACTURING DEMONSTRATION OF FUEL MATERIALS PHARMACEUTICALS AND FOOD. OUR TEAM CAN EXECUTE THIS VISION BECAUSE OF OUR DEEP EXPERIENCE IN HYBRID BIOINORGANICS FOR LIGHT-DRIVEN CARBON AND NITROGEN FIXATION ENZYMOLOGY POLYMER CHEMISTRY SYNTHETIC BIOLOGY EXTREMOPHILE ENGINEERING ADDITIVE MANUFACTURING AEROSPACE ENGINEERING PLANT/MICROBIOME FOOD AND CHEMICAL MANUFACTURE AND SPACE CROP PHYSIOLOGY. CUBES ENDEAVORS WILL INCLUDE (1) MEDIA GENERATION: ARTIFICIAL PHOTOSYNTHESIS THAT TURNS CARBON DIOXIDE INTO METHANE AND ACETATE; NITROGENASE-CATALYZED CONVERSION OF NITROGEN INTO AMMONIA AND CARBON DIOXIDE TO OTHER C1 COMPOUNDS; AMMONIA NITRIFICATION; REGOLITH DETOXIFICATION AND ENRICHMENT; RECYCLING MISSION MATERIALS; (2) FUEL PRODUCTION: THE AFOREMENTIONED METHANE; C2/C3 ALKANES; NITROUS OXIDE FROM NITRITE AND ACETATE; DIESELLIKE FUELS FROM RECYCLED INEDIBLE PLANT MASS; HYDRAZINE VIA ANAMMOX BACTERIA FROM AMMONIA; (3) BIOPOLYMER PRODUCTION USE AND RECYCLING: GENERATION FROM METHANE AND C1 SUBSTRATES; ADDITIVES PRODUCTION; TESTING IN ADDITIVE MANUFACTURING DEVICES; CHEMICAL/ BIOLOGICAL RECYCLING; (4) PROCESS ENGINEERING: OPTIMIZATION OF PLATFORM ORGANISMS FOR MAXIMAL YIELD AND TOLERANCE INCLUDING MESOPHILIC AND EXTREMOPHILE BIOPROCESSING IN NOVEL BIOREACTORS; PLATFORM CHEMICALS FOR DOWNSTREAM BIOLOGICAL PROCESSES; (5) PHARMACEUTICAL SYNTHESIS BY MICROBES AND PLANTS FOR ANALGESICS BONE REGENERATION AND ANTICANCER; (6) INCREASED FOOD PRODUCTION BY MICROBES AND PLANTS THROUGH SELECTION PLANT/MICROBE SYNERGIES IN RESTRICTED ROOT-ZONE VOLUMES GENETIC ENGINEERING PLANT-MICROBIOME ENHANCEMENT AND INNOVATIVE LIGHT DELIVERY SYSTEMS FOR PHOTOSYNTHESIS IN EFFICIENT SPACE-READY PLANT GROWTH CHAMBERS; (7) PLANT SYSTEM WASTE RECYCLING AND PLANT CELL WALL DECONSTRUCTION; AND (8) DEMONSTRATION SYSTEM INTEGRATION TESTING SEEDING AND INCORPORATION OF AUTONOMY. OUR INNOVATIONS INCLUDE: NOVEL ARTIFICIAL PHOTOSYNTHETIC SUBSTRATES COUPLED TO MICROBES AND ENZYMES TO EFFECTIVELY HARVEST LIGHT AND SPLIT WATER TO FIX BOTH CARBON DIOXIDE AND NITROGEN INTO CRITICAL FEEDSTOCKS FOR MICROBIAL AND PLANT BIOMANUFACTURING; THE DESIGN OF EFFECTIVE MICROBIAL COMMUNITIES AND BIOPROCESSING TECHNIQUES FOR A RANGE OF MICROBIALLY-PRODUCED PLASTICS WITH TUNABLE PROCESSING AND MECHANICAL PROPERTIES DERIVABLE FROM AVAILABLE FEEDSTOCKS AND RECYCLING MATERIALS; THE LEVERAGING OF A UNIQUE REPRODUCIBLE MARS ENVIRONMENT-SIMULATION CHAMBER TO EXPLORE THE BOUNDS OF OPERATION OF MESOPHILIC AND EXTREMOPHILIC MICROBES TO REDUCE COST FOR CONDITIONING IN MARS ENVIRONMENTS; CHARACTERIZING ENGINEERING AND OPTIMIZING DIVERSE NON-MODEL MICROBES THAT WILL SUPPORT BENEFICIAL PLANT PHENOTYPES; CUTTING-EDGE TECHNIQUES IN USING PLANTS AND INEDIBLE PLANT BIOMASS TO QUICKLY AND EFFICIENTLY PRODUCE IMPORTANT CLASSES OF HUMAN DRUGS THAT REQUIRE CHEMISTRIES UNAVAILABLE IN MICROBIAL CELLS; OPTIMIZED PLANTS AND PLANT GROWTH CHAMBERS THAT ADDRESS THE AVAILABILITY OF LIGHT STRESSORS AND ENERGY LIKELY TO BE ENCOUNTERED IN A DEEP SPACE CULTIVATION ENVIRONMENT; AND NOVEL COMPUTATION SYSTEMS TO CAPTURE MODEL ANALYZE TEST AND DISSEMINATE BIOLOGICAL DATA ACROSS CUBES INTEGRATED PROCESSES AND SUBSYSTEM MODULES. CUBES' INDIVIDUAL APPROACHES TO MEDIA PRODUCTION MISSION PRODUCT MANUFACTURE AND FOOD AND PHARMACEUTICAL SYNTHESIS AMPLIFIED BY A FOCUS ON INTEGRATION AND OPTIMIZATION WILL LEAD TO A STRONG DATA-DRIVEN TECHNOLOGICALLY-BACKED PLATFORM FOR SPACE BIOMANUFACTURING., G4560531565
OpenAlex ID: W7213458191