Edaphic controls on genome size and GC content of bacteria in soil microbial communities

Journal Article · Tue Dec 27 00:00:00 EST 2022 · Soil Biology and Biochemistry

DOI:https://doi.org/10.1016/j.soilbio.2022.108935· OSTI ID:2204106

Chuckran, Peter F. ^[1]; Flagg, Cody ^[2]; Propster, Jeffrey ^[3]; Rutherford, William A. ^[4]; Sieradzki, Ella T. ^[5]; Blazewicz, Steven J. ^[6]; Hungate, Bruce ^[3]; Pett-Ridge, Jennifer ^[7]; Schwartz, Egbert ^[3]; Dijkstra, Paul ^[3]

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1. Northern Arizona Univ., Flagstaff, AZ (United States); Univ. of California, Berkeley, CA (United States)
2. National Ecological Observation Network (NEON), Boulder, CO (United States)
3. Northern Arizona Univ., Flagstaff, AZ (United States)
4. Univ. of Arizona, Tucson, AZ (United States)
5. Univ. of California, Berkeley, CA (United States)
6. Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
7. Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Univ. of California, Merced, CA (United States)

Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition; however, much of this work has been conducted in marine systems and the factors which shape soil bacterial genomic traits remain largely unknown. Here, for this work, we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across a broad geographic range and used machine-learning to determine the environmental parameters that most strongly explain the distribution of these traits. We found that genomic trait averages were most related to pH, which we suggest is primarily due to the correlation of pH with several environmental parameters, particularly soil carbon content. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with lower GC content and larger genomes, potentially a response to increased physiological stress and a requirement for metabolic diversity. Conversely, communities in high pH and low soil C:N had smaller genomes and higher GC content—indicating potential resource driven selection against AT base pairs, which have a higher C:N than GC base pairs. Similarly, we found that nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with low C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms that underpin genome size, and nucleotide and amino acid selection in soil bacteria.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDA; USDOE; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC52-07NA27344
• OSTI ID: 2204106
• Alternate ID(s): OSTI ID: 1908033
• Report Number(s): LLNL--JRNL-826457; 1041096
• Journal Information: Soil Biology and Biochemistry, Journal Name: Soil Biology and Biochemistry Vol. 178; ISSN 0038-0717
• Publisher: Elsevier
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
Amino acid stoichiometry
C:N ratios
Genomic traits
Metagenomics
pH