Predictive genomic traits for bacterial growth in culture versus actual growth in soil

Junhui Li, Rebecca L. Mau, Paul Dijkstra, Benjamin J. Koch, Egbert Schwartz, Xiao Jun Allen Liu, Ember M. Morrissey, Steven J. Blazewicz, Jennifer Pett-Ridge, Bram W. Stone, Michaela Hayer, Bruce A Hungate

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.

Original languageEnglish (US)
JournalISME Journal
DOIs
StatePublished - Jan 1 2019

Fingerprint

microbial growth
genomics
Soil
Genome Size
genome
soil bacteria
Microbial Genes
gene
glucose
Growth
gene dosage
soil
bacterium
ecosystems
nutrient
ecosystem
nutrients
Ecosystem
growth response
stress tolerance

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Predictive genomic traits for bacterial growth in culture versus actual growth in soil. / Li, Junhui; Mau, Rebecca L.; Dijkstra, Paul; Koch, Benjamin J.; Schwartz, Egbert; Liu, Xiao Jun Allen; Morrissey, Ember M.; Blazewicz, Steven J.; Pett-Ridge, Jennifer; Stone, Bram W.; Hayer, Michaela; Hungate, Bruce A.

In: ISME Journal, 01.01.2019.

Research output: Contribution to journalArticle

Li, Junhui ; Mau, Rebecca L. ; Dijkstra, Paul ; Koch, Benjamin J. ; Schwartz, Egbert ; Liu, Xiao Jun Allen ; Morrissey, Ember M. ; Blazewicz, Steven J. ; Pett-Ridge, Jennifer ; Stone, Bram W. ; Hayer, Michaela ; Hungate, Bruce A. / Predictive genomic traits for bacterial growth in culture versus actual growth in soil. In: ISME Journal. 2019.
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