Spaceflight Metatranscriptomics Arabidopsis thaliana NASA GeneLab Plant AWG BLSS Biosecurity

Mining the Extraterrestrial Seedling Microbiome

Uncovering endophytic and commensal microbial communities hidden within archival plant RNA-seq data from the International Space Station. Meta-analysis of NASA OSDR accessions spanning BRIC-19, BRIC-20, APEX-03-2, and BRIC-PDF.

6
OSDR Studies Mined
35+
Microbial Species Profiled
4
Arabidopsis Ecotypes
100%
Ralstonia Dominance in Cvi-0

Target Spaceflight Accessions

Curated spaceflight missions analyzed for seedling-associated non-host microbial transcripts.

OSD-37 (GLDS-37) BRIC-19
ISS Petri Dish • 8-day Seedlings

Multi-ecotype comparison (Col-0, Cvi-0, Ler-0, WS-2) dark-germinated in BRIC hardware. Exhibited overwhelming dominance of Ralstonia pickettii across all genotypes.

4 Ecotypes RNAlater Fixation Whole Seedling
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OSD-38 (GLDS-38) BRIC-20
ISS Petri Dish • 3–4-day Seedlings

Early developmental kinetics in Col-0 seedlings. Identified novel presence of Weizmannia ginsengihumi, a potent antioxidant-producing plant growth promoter.

Col-0 WT Liquid N2 Control Time Course
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OSD-120 (GLDS-120) APEX-03-2
ISS Petri Plates • Micro-dissected Roots

Targeted root tip apical meristem sequencing in Col-0, WS, and phyD mutants. Demonstrated near-zero microbial taxa detection, proving root apical zones maintain endophyte exclusion.

Root Tips Light & Dark 11–13 days
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OSD-217 (GLDS-217) BRIC-PDF
ISS Light-grown • Dissected Organs

Organ-resolved metatranscriptomics in WS ecotype. Distinctly separated leaf mesophyll endophytes (Delftia, Bradyrhizobium) from root vascular communities.

Leaves vs Roots Light Regimes WS Ecotype
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OSD-321 (GLDS-321) BRIC-22 Canister
BRIC-22 / SpaceX CRS-12 (Dark Confinement vs Ground Control)

Unfolded Protein Response (UPR) and ER stress adaptation in sealed BRIC-PDFU canisters. Profiles microbial persistence and community shifts during dark canister orbital confinement across Col-0 and UPR mutants.

BRIC-PDFU Col-0 & UPR Mutants SpaceX CRS-12
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OSD-522 (GLDS-522) Spaceflight Light
ISS Spaceflight • Whole Seedling

Light-grown Col-0 spaceflight seedlings. Validates detection of Cutibacterium acnes, Rhodococcus fascians, and Herbaspirillum huttiense.

Flight vs Ground Light-Grown Col-0
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Microbial Taxa Directory & Provenance

Comprehensive catalog of detected microorganisms classified by putative origin (seed-borne endophytes vs human/hardware commensals) and physiological characteristics.

Organism Phylum / Class Putative Origin Morphology Functional Attributes Biofilm Plant Pathogen

Analytical Visualizations

Intersectional set distributions, pairwise community correlations, and study selection parameters.

Interactive Krona Taxonomic Viewer

Explore the hierarchical taxonomic breakdown (Domain → Phylum → Class → Order → Family → Genus → Species) generated from the spaceflight seedling unmapped read assemblies.

📊 Krona Metagenomic Sunburst Chart Open in Full Window ↗

Metatranscriptomic Mining Pipeline

Systematic extraction of microbial dark matter from eukaryotic host RNA sequencing data.

STEP 01
OSDR FASTQ Ingestion
Automated retrieval of raw paired/single-end FASTQ files from NASA OSDR using Python REST API scripts.
STEP 02
QC & Adapter Trimming
Quality verification with FastQC and low-quality/adapter removal via Trim Galore! (Q ≥ 25, len ≥ 35 bp).
STEP 03
Host Subtraction
Splice-aware alignment against A. thaliana TAIR10 genome (STAR & Bowtie2). Unmapped reads extracted with SAMtools.
STEP 04
Taxonomic Profiling
Profiling unmapped reads against 5.1M clade-specific marker genes using MetaPhlAn4 and Bowtie2 mapping matrices.
STEP 05
Ecological Synthesis
Functional trait lookup via The Microbe Directory & BacDive, UpSet intersection, and HAllA association testing.

Full Manuscript & LaTeX Source Suite

Complete research article titled "Mining the Extraterrestrial Seedling Microbiome: Meta-transcriptomic Discovery of Endophytic and Commensal Communities in Spaceflight Arabidopsis thaliana", compiled with bibliography, publication-ready tables, and vector figures.