“Microbes Persist” Soil Microbiome Scientific Focus Area

Exploring the role microbes play in the stabilization and persistence of soil carbon.

The LLNL Soil Microbiome Scientific Focus Area (SFA)—Microbes Persist: Systems Biology of the Soil Microbiome—seeks to understand how microbial ecophysiology, population dynamics, and microbe–mineral–organic matter interactions regulate the persistence of microbial residues in soil under changing moisture regimes. Members of the soil microbiome (bacteria, archaea, fungi, microfauna, and viruses) play key roles in soil carbon turnover and the stabilization of persistent organic matter via their metabolic activities, cellular biochemistry, and extracellular products. Soils store more carbon than the atmosphere and biosphere combined, yet the mechanisms that regulate soil carbon remain elusive. Microbial residues are a primary ingredient in soil organic matter (SOM), a pool that is critical to agriculture, healthy ecosystems, and Earth’s climate.

We hypothesize that microbial cellular chemistry, functional potential, and ecophysiology fundamentally shape soil carbon persistence and are characterizing these phenomena via stable isotope probing (SIP) of genome-resolved metagenomes and viromes. Our current projects focus on soil moisture as a “master controller” of microbial activity and mortality, since altered precipitation regimes are predicted across the temperate United States. Learn more about our primary objectives in the Research section.

News highlights

November 2020

Ben Bolduc gives KBase webinar about viral KBase apps

Dr. Ben Bolduc of the Sullivan Lab at Ohio State University gave a webinar for DOE’s Systems Biology Knowledgebase (KBase) describing apps for viral analysis that he developed as part of our Microbes Persist–KBase partnership. Watch the KBase webinar recording.

Read more about our viral informatics collaboration on the KBase Soil Microbiome SFA website.

KBase website home page

More news


Overview of the Microbes Persist SFA, illustrating our four primary objectives, which explore how microbial ecophysiology, population dynamics, and mineral-microbe interactions regulate cellular carbon persistence under changing moisture regimes.

Although soils store more carbon than the atmosphere and biosphere combined, little is known about the mechanisms that regulate soil carbon. Plant roots are the initial source of carbon in soil, allocating carbon captured from the atmosphere to the soil system. Our project’s premise is that microbial transformations of this carbon determine whether it is returned back to the atmosphere or stored as SOM. Since soil carbon and associated organic molecules are critical to agriculture, healthy ecosystems, and Earth’s climate, a predictive understanding of soil carbon’s residence time and turnover (i.e. “persistence”) in the soil is essential, especially as climate conditions change.

Our projects focus on soil moisture as a master controller of organic matter stabilization processes and soil microbial growth and death in soil. The current paradigm in soil organic matter is that microbial cell materials (necromass) are a primary starting material in the process of carbon stabilization. We presume that microbial ecophysiology is a key factor in controlling soil carbon dynamics as water availability changes because the intensity and timing of precipitation not only significantly affects soil microbial community composition and microbial ecological strategies, but also microbial-controlled decomposition, carbon use efficiency, and soil carbon dioxide efflux.

Through our research, we address three critical needs:

  • Learn more about how microorganisms grow and die in soil and how those factors mediate SOM formation
  • Predict more accurately the impacts of shifting climate conditions on carbon cycling and biosequestration in ecosystems
  • Examine potential means of biological sequestration of carbon

Our approaches

Our SFA’s key strength is an interdisciplinary and multi-scale approach. In both our complex “wild” soil studies and our pure culture experiments, we rely on isotope tracing and informatics tools that are unique to our team, allowing us to study individual genomes, their expression, and metabolic products within the soil habitat. These methods include:

  • High-throughput stable isotope probing (SIP) metagenomics (HT-SIP), ChipSIP, and qSIP to quantitatively resolve strain-level assimilation of specific biomolecules
  • 18O-SIP for taxon-specific growth and death rates
  • SIP-viromics and in-house informatics tools for genomic tracking of phage–host linkages
  • NanoSIMS-STXM (combined high-resolution secondary ion mass spectrometry and scanning transmission electron microscopy) to trace the molecular fate of specific cell-derived molecules
  • FTICR-MS (Fourier-transform ion cyclotron resonance mass spectrometry) for high resolution characterization of soil solution molecular components
  • 13C-NMR (nuclear magnetic resonance) to characterize solid and liquid phases of soil organic matter
  • Compound specific 14C AMS (accelerator mass spectrometry) to measure the residence time of specific molecular classes of organic matter
  • Field 14C measurements used for modelling of mineral-associated SOM stability under varying edaphic conditions
  • Trait-based and DEB (dynamic energy budget) models to test the predictive power of microbial ecophysiological traits

Our objectives



Jennifer Pett-Ridge

Jennifer Pett-Ridge

Lead Scientist

Microbes persist team

Our multi-institutional team includes experts in soil microbiology, ecophysiology and biogeochemistry, metagenomics and viral ecology, organic matter–mineral chemistry, isotope and compound-specific mass spectrometry, and multiscale modeling.

Expand the sections below to meet more team members.