Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Functional Succession of Growing Soil Microorganisms and Virus-Driven Mortality Following Rewetting in a California Grassland Soil


Steven J. Blazewicz1* (, Alexa Nicolas2, Ella T. Sieradzki2, Peter Chuckran2, Katerina Estera-Molina1,2, Rohan Sachdeva2, Mary K. Firestone2, Jillian Banfield2,3, and Jennifer Pett-Ridge1,2


1Lawrence Livermore National Laboratory; 2University of California–Berkeley; and 3Lawrence Berkeley National Laboratory



Microorganisms play key roles in soil carbon turnover and stabilization of persistent organic matter via their metabolic activities, cellular biochemistry, and extracellular products. Microbial residues are the primary ingredients in soil organic matter (SOM), a pool critical to Earth’s soil health and climate. Researchers hypothesize that microbial cellular chemistry, functional potential, and ecophysiology fundamentally shape soil carbon persistence and are characterizing this via stable isotope probing (SIP) of genome-resolved metagenomes and viromes. The team focuses on soil moisture as a master controller of microbial activity and mortality since altered precipitation regimes are predicted across the temperate United States. This science focus area’s ultimate goal is to determine how microbial soil ecophysiology, population dynamics, and microbe-mineral-organic matter interactions regulate the persistence of microbial residues under changing moisture regimes.


Rewetting of soil stimulates a succession of microbial growth and mortality, a process that could potentially become more frequent as climate change in semi-arid zones is predicted to lead to fewer rain events, potentially allowing for soil dry-down between events. It has been hypothesized that certain microbial traits, such as degradation of carbohydrates and acquisition of nitrogen, underlie this succession and confer advantages for growth as both the soil microbial community and available resources change over time. Researchers presume that the initial burst of mortality following wet-up is driven by osmotic lysis due to the rapid change in osmotic pressure, while continued mortality after the first few hours is driven by viruses or other biological factors. Researchers also hypothesized that the summer dry down would drive phages to integrate into host chromosomes and that wet-up of dry soil might serve as an environmental inducer of temperate phages.

To determine the mechanisms driving microbial growth and mortality during wet-up, researchers performed a wet-up experiment using soils that had been previously 13CO2-labeled and maintained under one of two precipitation regimes: the historical average precipitation (100%) and a 50% water reduction. Following the annual summer dry period, soils were collected and incubated with multiple isotopic treatments. Heavy water (18O-H2O) additions were used to specifically target the growing portion of the microbiome and virome. Samples were harvested at six times following rewetting (0, 3, 24, 48, 72, and 168 hr) for DNA–quantitative stable isotope probing (qSIP), metagenomics, metatranscriptomics, viromics, and CO2 production.

While total soil respiration did not vary between soils exposed to 100% versus 50% precipitation, respiration of new (labeled) rhizodeposits was higher in the 100% soils, implying functional differences between precipitation groups. This result was supported by large differences in taxon-specific responses for bacterial growth and mortality and differential abundance of traits found in growing (18O-labeled) microorganisms for the two precipitation treatments. Differential abundance of traits also revealed a large difference in the functional potential of the microbiome at the end of the dry season. Surprisingly this legacy effect disappeared after one week, indicating functional capacity converged regardless of prior conditions. Temporal changes were observed in the abundance of genes coding for carbohydrate active enzymes in growing organisms implying that substrate availability varied with time. Genes coding for synthesis and export of EPS were more abundant in growing organisms as compared to the total community in alignment with the hypothesis that this function could provide a fitness advantage during both the dry-down and wet-up.

In comparison to temporal abundance patterns in microorganisms, viruses displayed higher spatial heterogeneity in addition to temporal community changes. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicated that dry soil held a diverse but low biomass reservoir of virions, of which only a subset thrived following wet-up. Viral richness decreased by 50% within 24 hours post wet-up, while viral biomass increased at least four-fold within one week. Counter to recent hypotheses suggesting temperate viruses predominate in soil, the team’s evidence indicates that wet-up is dominated by viruses in lytic cycles. Researchers estimate that viruses drive a measurable and continuous rate of cell lysis with up to 46% of microbial death driven by viral lysis one week following wet-up. Results show that viruses contribute to a significant portion of soil microbial biomass turnover and the widely reported CO2 efflux following wet-up of seasonally dry soils.

In summary, the team observed temporal changes in growing microbial and viral communities following wet-up that were underpinned by succession of organic carbon degradation capabilities as well as by lytic infection by viruses.

Funding Information

This research is based upon work of the LLNL Microbes Persist Soil Microbiome science focus area supported by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research Genomic Science program under Award Number SCW1632 to the Lawrence Livermore National Laboratory with a subcontract to the University of California, Berkeley. Work at Lawrence Livermore National Laboratory was performed under U.S. Department of Energy Contract DE-AC52-07NA27344.