ArticleNPJ biofilms and microbiomes2023
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis.
Article in NPJ biofilms and microbiomes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Harnessing synthetic microbial communities for desert vegetation restoration.Synthetic and systems biotechnology · 2027Review
- Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients.Applied and environmental microbiology · 2026Article
- Uncovering the Community Structure and Adaptive Characteristics of Soil Protists Across Natural, Semi-Natural and Highly Degraded Habitats.Environmental microbiology · 2026Article
- Nature Already Did the Screening: Drought-Driven Rhizosphere Recruitment Enables Inoculant Discovery in Tomato and Reveals a Candidate NovelMicroorganisms · 2026Article
- Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.Microbiome · 2026Article
- Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems.Applied and environmental microbiology · 2026Article
- High-throughput single-cell isolation ofMicrobiology spectrum · 2026Article
- Genome-based reassessment ofCurrent research in microbial sciences · 2026Article
- Metabarcoding insights into the fungal diversity and biotechnological potential of mangrove sediments in Ecuador's Reserva Ecológica Manglares Churute.Frontiers in fungal biology · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.ISME communications · 2026Article
- Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.Frontiers in plant science · 2026Review
- Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.Environmental microbiome · 2025Article
- Rare and abundant taxa in Artemisia desertorum rhizosphere soils demonstrate disparate responses to drought stress.Advanced biotechnology · 2025Article
- Fungi and Myxomycetes of the Tehuacán-Cuicatlán Biosphere Reserve, Mexico: A Comprehensive Review and Future Perspectives.IUBMB life · 2025Review
- Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.BMC microbiology · 2025Article
- Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.Journal of microbiology and biotechnology · 2025Review
- Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.Microorganisms · 2025Article
- Spatiotemporal Dynamics of Bacterial Community Assembly and Co-Occurrence Patterns in Biological Soil Crusts of Desert Ecosystems.Microorganisms · 2025Article
- Culture-dependent and -independent analyses reveal unique community structure and function in the external mycelial cortices of Ophiocordyceps sinensis.BMC microbiology · 2025Article
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Authors and funding
11 authors.
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Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
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