ReviewFrontiers in microbiology2022
Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations.
Review in Frontiers in microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Reciprocal transport of carbon and nitrogen between plants and the hyphosphere microbiome in a temperate grassland.The New phytologist · 2026Article
- Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients.Environmental microbiology reports · 2026Article
- Article
- Rhizosphere Bacterial Communities of Two Coastal Halophytes Under Salinity-Flooding Stress.Plants (Basel, Switzerland) · 2026Article
- Soil properties, rather than urbanization time, drive shifts in soil bacterial communities in a subtropical city of China.Applied and environmental microbiology · 2026Article
- Effects of Nutrient Limitation on Antarctic Microbial Community Diversity, Composition, and Interactions: A Cryoconite Microcosm Study.Microorganisms · 2026Article
- Host Species Mediate Distinct Seed Microbiome Responses to Restoration.Microbial ecology · 2026Article
- Compartment-specific assembly and genotype-associated differentiation of root microbiomes in saline-alkali-sensitive and -tolerant maize inbred lines.BMC plant biology · 2026Article
- Changes in the Microbial Communities ofPlants (Basel, Switzerland) · 2026Article
- Unexpected enrichment of antibiotic resistance genes in recirculating aquaculture effluents of rainbow trout (Frontiers in microbiology · 2026Article
- Article
- Environmental DNA sampling workflow matters: testing different approaches on marine microbial assemblages in three coastal areas of Greece.Frontiers in microbiology · 2026Article
- Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries.Frontiers in microbiology · 2026Article
- Integrating Microbiomes for Regenerative Food Systems: Recent Insights, Implementations, and Emerging Trends.Food science & nutrition · 2025Review
- Banana genotype-associated microbiomes play an essential role in suppressing Fusarium wilt.BMC plant biology · 2025Article
- Sharp but consistent fungi species composition transition during a 40-yr urbanization in a subtropical city of China.Environmental microbiome · 2025Article
- Compartment-specific microbial communities highlight the ecological roles of fungi in a subtropical seagrass ecosystem.Applied and environmental microbiology · 2025Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Article
- Integrating network analysis with in vivo-in situ manipulation to elucidate microbiome dynamics in Aedes albopictus.FEMS microbiology letters · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network's representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.