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

Unraveling Microbial and Viral Responses to Wetting Using Multiomics

Authors:

Steven J. Blazewicz1* (blazewicz1@llnl.gov), Peter Chuckran2* (pete.chuckran@berkeley.edu), Linnea K. Honeker1, Gareth Trubl1, Rebecca Mau3, Nicole DiDonato4, Jeff Kimbrel1, Alexa Nicolas2, Ella T. Sieradzki2, Katerina Estera-Molina1,2, Rohan Sachdeva2, G. Michael Allen1, Egbert Schwartz3, Mary K. Firestone2, Jillian Banfield2,5, Jennifer Pett-Ridge1,6

Institutions:

1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory; 2University of California–Berkeley; 3Northern Arizona University; 4Pacific Northwest National Laboratory; 5Lawerence Berkeley National Laboratory; 6Life and Environmental Sciences Department, University of California–Merced

URLs:

Goals

Microorganisms play key roles in soil carbon (C) 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, a pool critical to Earth’s soil health and climate. The team hypothesizes that microbial cellular chemistry, functional potential, and ecophysiology fundamentally shape soil C persistence, and researchers are characterizing this via stable isotope probing (SIP) of genome-resolved metagenomes and viromes. The project focuses on soil moisture as a “master controller” of microbial activity and mortality, since altered precipitation regimes are predicted across the temperate United States. The Science Focus Area’s (SFA) 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.

Abstract

The intensity and timing of precipitation not only affects soil microbial community composition and microbial ecological strategies, but also microbial-controlled decomposition and soil carbon dioxide efflux. However, scientists do not have a mechanistic understanding of how altered soil moisture regimes will affect soil C persistence or microbial population dynamics. Conducting a wet-up experiment on soils previously subjected to either historical average precipitation (100%) or a 50% water reduction, researchers employed a multiomics approach (16S-quantitative stable-isotope probing, metagenomics, viromics, metatranscriptomics, metabolomics, and lipidomics) to elucidate the mechanisms governing microbial response following wet-up.

Determining the relationship between bacterial traits and life strategies is a crucial step in linking soil microbial communities to ecosystem function. Genomic traits, such as genome size, codon usage, and nucleotide selection, may be particularly useful trait dimensions as they are relatively easy to measure and provide insight into the evolutionary forces which shape bacteria. In response to rewetting, researchers found that metagenome assembled genomes (MAGs) with high levels of codon bias and cheaper nucleotides in their ribosomal protein genes had high growth rates shortly after rewetting. The team also found that MAGs with smaller genomes had higher growth rates than larger genomes one week post rewetting. Together, these results point towards a set of genomic characteristics that are potentially important for bacteria in highly dynamic soil environments.

The project found that legacy precipitation (50 vs. 100% mean annual precipitation; MAP) had the largest impact on microbial population dynamics, where 100% MAP was associated with higher overall growth and mortality rates and greater changes in gene expression across multiple metabolic pathways. Similarly, metabolomics data showed a greater magnitude of changes in metabolite composition after rewetting at 100% MAP. Results suggest that decreased legacy moisture leads to decreased metabolic and growth potential for microbes following dry down, impacting which taxa are able to rapidly respond to rewetting.

The team posits that interactions between the soil water cycle, nutrient availability, and microbial predators (bacterivores, viruses) may also control a significant proportion of soil C flux, but this nascent research area is another major knowledge gap. Researchers detected 172 protist taxa and found that average population growth at 80% field capacity was 4.4 times greater than at 20% field capacity (3.2% vs. 0.15% per day, respectively), suggesting that protists’ growth activity is highly sensitive to soil moisture. Further, researchers found soil viruses exhibited sensitivity to nutrient availability upon rewetting. The introduction of phosphorus diminished the overall richness of RNA viruses, yet it concurrently triggered an upsurge in specific bacterial viruses. The increase of bacterial viruses may be attributed to the alleviation of stress experienced by bacterial hosts due to phosphorus limitation. Conversely, fungal viruses exhibited no significant change, potentially indicating the resilience of fungal mycelial networks in nutrient movement.

In summary, the project identified important genome-level traits predictive of microbial growth response to rewetting. The team also found that differences in legacy precipitation can influence microbial activities long after changes in soil moisture are no longer detectable, and microbial predators are sensitive to changes in soil moisture and nutrient changes.

Funding Information

This research is based upon work of the Lawrence Livermore National Laboratory (LLNL) “Microbes Persist” Soil Microbiome SFA, supported by the U.S. DOE Office of Science, BER program’s GSP under Award Number SCW1632 to the LLNL and subcontracts to Northern Arizona University, University of California–Berkeley, and the Pacific Northwest National Laboratory. Work at LLNL was performed under U.S. DOE Contract DE-AC52-07NA27344.