Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

• 成果类型: Article
• 署名作者: Chuckran, Peter F.; Estera-Molina, Katerina; Nicolas, Alexa M.; Sieradzki, Ella T.; Dijkstra, Paul; Firestone, Mary K.; Pett-Ridge, Jennifer; Blazewicz, Steven J.
• 署名单位: University of California System; University of California Berkeley; United States Department of Energy (DOE); Lawrence Livermore National Laboratory; University of California System; University of California Berkeley; Columbia University; Universite Claude Bernard Lyon 1; Institut National des Sciences Appliquees de Lyon - INSA Lyon; Ecole Centrale de Lyon; Northern Arizona University; University of California System; University of California Merced; University of California System; University of California Berkeley
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-12971
• DOI: 10.1073/pnas.2413032122
• 发表日期: 2025-01-15
• 关键词: carbon-dioxide pulses; gene-expression; ribosomal-rna; usage; strategies; CONSEQUENCES; respiration; determinant; exploration; EFFICIENCY

摘要

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with O-18-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.