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.
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.
“PROMISE” conceptual soil carbon model published in Global Change Ecology
Members of Microbes Persist participated in a unique collaboration to re-conceptualize how we think about, measure, and model soil carbon. Read more about this novel approach, which emphasizes the mechanistic controls on the flow of carbon between ecosystem pools, in LLNL’s news release, “A PROMISE to trace the path of individual carbon atoms.”
[B.G. Waring, B.N. Sulman, S. Reed, A.P. Smith, C. Averill, C.A. Creamer, D.F. Cusack, S.J. Hall, J.D. Jastrow, A. Jilling, K.M. Kemner, M. Kleber, X.‐J.A. Liu, J. Pett‐Ridge, and M. Schulz, From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world, Global Change Biology 26, 6631 (2020), doi: 10.1111/gcb.15365.]
Data resource: “Metagenomes and Metatranscriptomes of Glucose-Amended Agricultural Soil”
Northern Arizona University (NAU) postdoc Pete Chuckran, along with colleagues from NAU and the Joint Genome Institute, published a trove of metagenome and metatranscriptome data describing microbial ecophysiology in response to soil glucose additions.
[P.F. Chuckran, M. Huntemann, A. Clum, B. Foster, B. Foster, S. Roux, K. Palaniappan, N. Varghese, S. Mukherjee, T.B. Reddy, C. Daum, A. Copeland, N.N. Ivanova, N.C. Kyrpides, T. Glavina del Rio, E.A. Eloe-Fadrosh, E.M. Morrissey, E. Schwartz, V. Fofanov, B. Hungate, P. Dijkstra, Metagenomes and metatranscriptomes of a glucose-amended agricultural soil, Microbiology Resource Announcements 9, e00895-20 (2020), doi: 10.1128/MRA.00895-20.]
“Harvesting” soil at HREC
Digging a soil pit during a global pandemic, wildfire season, and 90°F heat is not everyone’s idea of fun, but LLNL postdoc Eric Slessarev, UC Berkeley student Christina Fossum, and Jennifer Pett-Ridge braved it all to collect soils from the “super-dry” season at the Hopland Research and Extension Center (HREC) in Hopland, California.
Welcome Kat Georgiou, Lawrence Fellow postdoc
Katerina Georgiou was recently awarded one of the prestigious LLNL Lawrence Fellowships to pursue her postdoctoral research. She will work in coordination with the Microbes Persist SFA on her project, “From Microbes to The Earth System—Upscaling Microbial Community Dynamics to Macro-Scale Soil Carbon Models.”
Insights into microbial population dynamics in response to rapid change in soil moisture
Steve Blazewicz (LLNL) and colleagues at the University of California, Berkeley and Northern Arizona University used quantitative stable isotope probing (qSIP) with heavy water (H218O) to quantify the growth and mortality rates of bacteria following early season wet-up of a Mediterranean grassland soil. Their article is published in the ISME Journal.
[S.J. Blazewicz, B.A. Hungate, B.J. Koch, E.E. Nuccio, E. Morrissey, E.L. Brodie, E. Schwartz, J. Pett-Ridge, and Firestone MK, Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil, The ISME Journal 14, 1520 (2020), doi: 10.1038/s41396-020-0617-3.]
LLNL bids farewell to Craig See
For the past six months, we have had the pleasure of hosting Craig See from Dr. Peter Kennedy’s laboratory at the University of Minnesota via a DOE Office of Science Graduate Student Research fellowship—and we are now sad to see him go. While at LLNL, Craig learned stable isotope probing, scanning electron microscope, and NanoSIMS, and he processed samples from a project focused on tracing carbon and nitrogen from decomposing fungal necromass in ecto-mycorrhizal versus arbuscular mycorrhizal hyphospheres.
ISRaD paper provides global dataset of soil 14C
With a large team of international colleagues, scientists Karis McFarlane (LLNL) and Christina Schädel (Northern Arizona University) released a new open-source soil data archive, the International Soil Radiocarbon Database (ISRaD) version 1.0. The database is a compilation of individual study datasets that include carbon and radiocarbon measurements for bulk soil depth profiles, soil fractions, soil gas, and interstitial water.
[C.R. Lawrence, J. Beem-Miller, A.M. Hoyt, G. Monroe, C.A. Sierra, S. Stoner, K. Heckman, J.C. Blankinship, S.E. Crow, G. McNicol, S. Trumbore, P.A. Levine, O. Vindušková, K. Todd-Brown, C. Rasmussen, C.E. Hicks Pries, C. Schädel, K. McFarlane, S. Doetterl, C. Hatté, Y. He, C. Treat, J.W. Harden, M.S. Torn, C. Estop-Aragonés, A.A. Berhe, M. Keiluweit, A.D.R. Kuhnen, E. Marin-Spiotta, A.F. Plante, A. Thompson, Z. Shi, J.P. Schimel, L.J.S. Vaughn, S.F. von Fromm, and R. Wagai, An open source database for the synthesis of soil radiocarbon data: ISRaD version 1.0, Earth System Science Data Discussions 12, 61 (2020), doi: 10.5194/essd-12-61-2020.]
Uncovering soil viral predators from rhizosphere metatranscriptomes
Very little is known about RNA viruses in the environment, and even less is known about their diversity and ecology in soil. Evan Starr, a UC Berkeley graduate student working with SFA principal investigators Mary Firestone and Jill Banfield has helped to show that RNA viruses are abundant and diverse in soil, where they prey upon organisms such as insects, nematodes, and fungi, and likely affect the carbon cycle. This cutting-edge study was featured in a recent article in the Economist.
[E.P. Starr, E.E. Nuccio, J. Pett-Ridge, J.F. Banfield, and M.K. Firestone, Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil, Proc. Natl. Acad. Sci. 116, 25900 (2019), doi: 10.1073/pnas.1908291116.]
“DRIP-SIP” (Detritusphere Rhizosphere Isotope Persistence-Stable Isotope Probing) study complete
LLNL postdoc Noah Sokol has been working long hours in the greenhouse with Megan Foley (Northern Arizona University) and Alex Greenlon (University of California, Berkeley) to complete a complex 13CO2-labeling study examining how drought affects the microbial ecophysiological traits that modulate soil carbon formation. The samples are all now safely in the -80°C freezer(s).
Sullivan Lab develops new viral sequence classifier
Classification of environmental viruses, specifically uncultivated viral genomes, is a key step to organizing the virosphere and isolating viral groups of potential interests. Our SFA partners in the Sullivan Lab at Ohio State University developed a genome-based, automatic phage and archaeal virus classifier, called vConTACT2, and described in Nature Biotechnology.
[H.B. Jang, B. Bolduc, O. Zablocki, J. Kuhn, S. Roux, E. Adriaenssens, J. Brister, A. Kropinski, M. Krupovic, R. Lavigne, D. Turner, and M. Sullivan, Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks, Nature Biotechnology 37, 632 (2019), doi: 10.1038/s41587-019-0100-8.]
A first-principles theory to predict moisture sensitivity of soil heterotrophic respiration
Jinyun Tang (Lawrence Berkeley National Laboratory), a Microbes Persist principal investigator, has co-developed a theory to predict microbial substrate affinity in variably saturated soils. The theory uses measured soil physical parameters and microbial parameters to explain the large variability in affinity parameters used in many existing land biogeochemistry models.
[J.-Y. Tang and W.J. Riley, A theory of effective microbial substrate affinity parameters in variably saturated soils and an example application to aerobic soil heterotrophic respiration, JGR Biogeosciences 124, 918 (2019), doi: 10.1029/2018JG004779.]
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 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
To meet this objective, we are applying SIP-metagenomics to measure how changing water regimes shape the activity of individual microbial populations and the expression of ecophysiological traits that affect the fate of microbial and plant carbon.
In Mediterranean-climate grasslands, indigenous microbes must survive extreme desiccation during long hot summers and mineralize carbon minutes after “wet-up,” when fall rains begin. The characteristics that allow these groups to survive under dry conditions and persist through rapid changes in water potential are likely important traits for soil carbon dynamics.
To determine how soil moisture shapes microbial ecophysiological traits, we study the three seasonal moisture periods characteristic of Mediterranean grasslands: the wet “spring” growing season, the “summer” drought, and “fall” wet-up. Our experiments show how soil moisture-driven changes in microbial ecophysiology control the persistence of soil carbon.
To meet this objective, we are identifying and measuring mechanisms of mortality in the soil microbiome—focusing on phage lysis and water stress—and their contribution to carbon turnover and the biochemistry of microbial residues.
Soils represent an enormous reservoir of viruses, yet we know remarkably little about their diversity and activity. Our tools and experience position us to substantially expand this nascent field. In our experiments, we track viromes, phage–host links, and viral population dynamics throughout growth, drought, and wet-up periods. With the discovery and ecological characterization of new virus-encoded auxiliary metabolic genes, we can better understand, and better model, how viruses modulate ecosystem biogeochemical processes.
To meet this objective, we are measuring how the soil microbiome and its products interact with contrasting mineral assemblages to control both short- and long-term soil carbon persistence.
Changes in soil moisture can dramatically impact how the soil microbiome and its biochemical residues interface with the soil matrix. To determine the mechanisms that regulate how microbial carbon persists on soil minerals, we conduct sorption experiments using pure minerals incubated with microbes under a range of conditions. In these microcosm and field studies, we use spectroscopy and mass spectroscopy imaging to better understand the nature of mineral associations with biochemical residues produced by classes of microbial isolates. These experiments are intended to characterize features of SOM and cell surface moieties that may affect persistent SOM–mineral associations.
To meet this objective, we are synthesizing genome-scale ecophysiological trait data, SOM chemistry, and population-specific growth and mortality to build models of microbial functional guilds and SOM turnover. Our long-range goal is to predict the long-aspired connection between soil microbiomes and the fate of soil carbon.
We predict that in grassland ecosystems, shifts in microbiome structure and ecophysiological traits due to moisture regime are critical predictors of soil C turnover and composition. Over time, microbial recycling and reuse of SOM imposes a strong filter and narrows the diversity of molecular classes sorbed to minerals. This microbial filter results in the differential persistence of microbial-derived and plant-derived residues.
To test these hypotheses, synthesize our data, and inform predictive models of ecosystem function, we are using:
- Statistical analyses of microbial ecophysiological traits and carbon composition and turnover
- Mechanistic simulations of the sensitivity of carbon composition and turnover to variations in these ecophysiological traits
- Meta-analysis and modeling of carbon turnover constrained by extensive 14C data
In collaboration with DOE’s Systems Knowledgebase (KBase), we are developing a suite of new tools for automated curation of metagenomes and integrating this capability, along with our existing virus genome tools, into KBase. Our curation tool will massively increase the rate at which genome closure can be achieved—automating steps that are currently used to “hand finish” genomes, extending assembled scaffolds into larger assemblies, and correcting misassembled scaffold regions. Our goal is to develop an automated assembly curation procedure to reconstruct long, accurate sequences that can be binned more confidently than fragmented data.
We are also working to port the “iVirus” suite of applications and data resources and the LLNL-developed PhATE phage functional annotation pipeline into KBase. Together, these tools aim to identify, characterize, and ecologically contextualize viruses in large-scale sequence datasets.
These new open source tools will broadly benefit KBase users and will specifically benefit our SFA by creating a faster workflow for metagenome–genome curation and an integrated suite of KBase-hosted viral sequence analysis tools.
A. Aigle, C. Gubry-Rangin, C, Thion, K. Estera, H. Richmond, J. Pett-Ridge, M. Firestone, G. Nicol, and J. Prosser
B.G. Waring, B.N. Sulman, S. Reed, A.P. Smith, C. Averill, C.A. Creamer, D.F. Cusack, S.J. Hall, J.D. Jastrow, A. Jilling, K.M. Kemner, M. Kleber, X.‐J.A. Liu, J. Pett‐Ridge, and M. Schulz
E.T. Sieradzki, B.J. Koch, A. Greenlon, R. Sachdeva, R.R. Malmstrom, R.L. Mau, S.J. Blazewicz, M.K. Firestone, K. Hofmockel, E. Schwartz, B.A. Hungate, and J. Pett-Ridge
Metagenomes and metatranscriptomes of a glucose-amended agricultural soil | Microbiology Resource Announcements
P.F. Chuckran, M. Huntemann, A. Clum, B. Foster, B. Foster, S. Roux, K. Palaniappan, N. Varghese, S. Mukherjee, T.B. Reddy, C. Daum, A. Copeland, N.N. Ivanova, N.C. Kyrpides, T. Glavina del Rio, E.A. Eloe-Fadrosh, E.M. Morrissey, E. Schwartz, V. Fofanov, B. Hungate, and P. Dijkstra
Quantifying the effects of switchgrass (Panicum virgatum) on deep organic C stocks using natural abundance 14C in three marginal soils | Global Change Biology Bioenergy
E.W. Slessarev, E.E. Nuccio, K.J. McFarlane, C. Ramon, M. Saha, M.K. Firestone, and J. Pett-Ridge
Rewetting of soil: Revisiting the origin of soil CO2 emissions | Soil Biology and Biochemistry
R.L. Barnard, S.J. Blazewicz, and M.K. Firestone
S.J. Blazewicz, B.A. Hungate, B.J. Koch, E.E. Nuccio, E. Morrissey, E.L. Brodie, E. Schwartz, J. Pett-Ridge, and Firestone MK
J.-Y. Tang and W.J. Riley
An open source database for the synthesis of soil radiocarbon data: ISRaD version 1.0 | Earth System Science Data Discussions
C.R. Lawrence, J. Beem-Miller, A.M. Hoyt, G. Monroe, C.A. Sierra, S. Stoner, K. Heckman, J.C. Blankinship, S.E. Crow, G. McNicol, S. Trumbore, P.A. Levine, O. Vindušková, K. Todd-Brown, C. Rasmussen, C.E. Hicks Pries, C. Schädel, K. McFarlane, S. Doetterl, C. Hatté, Y. He, C. Treat, J.W. Harden, M.S. Torn, C. Estop-Aragonés, A.A. Berhe, M. Keiluweit, A.D.R. Kuhnen, E. Marin-Spiotta, A.F. Plante, A. Thompson, Z. Shi, J.P. Schimel, L.J.S. Vaughn, S.F. von Fromm, and R. Wagai
E.P. Starr, E.E. Nuccio, J. Pett-Ridge, J.F. Banfield, and M.K. Firestone
Microbial taxon-specific isotope incorporation with DNA quantitative stable isotope probing | Stable-Isotope Probing
B.K. Finley, B.J. Koch, M. Hayer, R.L. Mau, and B.A. Hungate
Quantitative Stable Isotope Probing with H218O to Measure Taxon-Specific Microbial Growth | Methods of Soil Analysis
A.M. Purcell, P. Dijkstra, B. Finley, M. Hayer, B.J. Koch, R.L. Mau, E. Morrissey, K. Papp, E. Schwartz, B.W. Stone, and B.A. Hungate
H.B. Jang, B. Bolduc, O. Zablocki, J. Kuhn, S. Roux, E. Adriaenssens, J. Brister, A. Kropinski, M. Krupovic, R. Lavigne, D. Turner, and M. Sullivan
Performance metric reports
LLNL Soil Microbiome Performance Metric Q1 2021 Report, January 2021
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.