ArticleMicrobiome2022
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
- Metagenomic Insights into Microbial Functional Potential Associated with Soil Carbon, Nitrogen, and Phosphorus Cycling Along an Elevational Gradient in a Warm-Temperate Forest.Microorganisms · 2026Article
- Decadal Resampling Reveals Widespread Increases in Soil Microbial Diversity Associated With Nitrogen Deposition.Global change biology · 2026Article
- Unraveling the coastal marine plastisphere archaeome.Nature communications · 2026Article
- Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.Nature communications · 2026Article
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- Soil to Cytoplasm: The Mycorrhizal Phosphorus Express and Its Regulatory Steps.Journal of fungi (Basel, Switzerland) · 2026Review
- Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.Applied and environmental microbiology · 2026Article
- A 'Genome-First' Framework for Next-Generation Bioinputs: From Functional Mining to Rational Synthetic Microbial Communities.Environmental microbiology · 2026Review
- Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.Environmental microbiome · 2026Article
- Phenotypic, Pot-Experimental, and Genomic Characterization ofMicroorganisms · 2026Article
- Unveiling the hidden viral biodiversity and potential ecological functions with global coral holobiont virome database.NPJ biofilms and microbiomes · 2026Article
- Reactive oxygen species in the rhizosphere orchestrate the recruitment of beneficial bacteria.The EMBO journal · 2026Article
- Rhizosphere microbial functions drive ecological stoichiometry in soils across an elevational gradient of a temperate mountain ecosystem.Communications biology · 2026Article
- Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient.mSystems · 2026Article
- Divergent Successional Patterns ofMicroorganisms · 2026Article
- Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries.Frontiers in microbiology · 2026Article
- Annotation of glycoside hydrolases in unassembled metagenomes using CAZyOBioinformatics advances · 2026Article
- Coordinated plant and microbial transcriptional responses to oil-sands process-affected water.ISME communications · 2026Article
- Organic amendments boost maize yield (Frontiers in plant science · 2026Article
5 more citing papers are in PubMed but not listed here.
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12 authors.
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Abstract
backgroundPhosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.
resultsIn this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.
conclusionsWe demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.
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