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

How Microbes and Minerals Make Necromass that Persists

Authors:

Cam G. Anderson1* (cganderson@umass.edu), Li Han Chan1, Maria Montero Sanchez1, Hannah Vanderscheuren2, Rachel Moser3, Emil Ruff2, Manuel Kleiner3, Melanie Mayes4, Kristen M. DeAngelis1

Institutions:

1University of Massachusetts–Amherst; 2Marine Biological Laboratory; 3North Carolina State University; 4Oak Ridge National Laboratory

Goals

Most of the Earth’s terrestrial carbon is stored in soil organic matter (SOM), and new SOM is derived largely from microbial necromass (Liang and Balser 2011). Necromass forms when microbes produce extracellular compounds, like extracellular polysaccharides and enzymes, or succumb to environmental stress and lyse. Because most soil microbes live attached to surfaces, necromass tends to remain associated with minerals, eventually persisting as SOM (Creamer et al. 2019). New necromass is the most sensitive to decomposition (Dong et al. 2021), so understanding new necromass decomposition directly informs long-term SOM stability and persistence.

Including microbial parameters in ecosystem models improves projections of soil carbon (C) stocks (Wieder et al. 2015). Soils with large C stores generally have large and active microbiomes (Liang et al. 2019), suggesting that yield or turnover drives necromass formation and persistence. However, growth is constrained by the acquisition of limiting resources. Soil microbes are primarily C limited, but soil minerals affect nutrient limitation, in turn affecting the ability to make new extracellular enzymes or dictating the size of cells and even genomes (Sorensen et al. 2019). Stress can also divert resources away from growth and nutrient acquisition, altering necromass deposition and microbial biomass composition (Fernandez and Kennedy 2018).

Mineral-organic associations are the most quantitatively important C storage mechanism in soils (Oldfield et al. 2018). Soil minerals modulate availability of energy and nutrients to microbes by restricting water and oxygen flow (Keiluweit et al. 2017). Clay minerals also slow microbial growth by sorbing added exogenous substrates (Finley et al. 2021). Both soil pore size and clay composition are intertwined with microbial traits to regulate growth and nutrient acquisition. By exploring traits associated with growth and resource acquisition from necromass biomolecules in soils and soil communities, researchers can better predict necromass persistence.

The goal is to better define the interactive roles of soil mineralogy and microbiomes that contribute to the persistence of necromass as SOM. The project’s overarching hypothesis is that necromass biomolecules are sensitive to decomposition depending on microbiome traits, nutrient bioavailability, and soil types. This work has four specific objectives:

  • Define microbial populations capable of degrading necromass macromolecules.
  • Define the mineral characteristics and microbial traits that drive necromass decomposition.
  • Define the food webs and fates of necromass macromolecules in soils over time.
  • Model the microbial or metabolic traits that best predict necromass formation.

Three experiments explore how microbes and minerals make persistent necromass, followed by statistical and mechanistic modeling to define conditions conducive to persistent necromass.

Abstract

Some soil C persists, sometimes for a long time, but scientists don’t know enough about this process to predict the long-term storage of C. New organic matter enters soil through plant detritus, and similar amounts enter soil through the continuous recycling of nutrients by microbial turnover, which generates microbial necromass. This microbial necromass represents a steady stream of new organic matter to soil, but new necromass is very sensitive to decomposition and loss as carbon dioxide (CO2). Surface attachment to minerals and other organic matter is the prevailing theory on the mechanism of soil C stabilization. However, reactive surfaces and soil pores reduce the bioavailability of nutrients that drive microbial turnover. How do microbes and minerals make necromass that persists?

Here, the project shows preliminary results from an ongoing experiment that assesses the impact of soil pore size and clay activity on the formation and cycling of necromass. The team has established nine artificial soils that consist of 90% acid-washed sand and 10% clay, which vary in both pore size (25 to 45, 75 to 105, and 150 to 250 micrometer particle sizes, using silica quartz sand) and clay activity (kaolinite and montmorillonite in 1:1, 1:9, and 9:1 mass ratios). These model soils were inoculated with soil microbes extracted from a temperate deciduous forest soil (Harvard Forest, Petersham, MA) and have been fed weekly since February 2023 with 0.5 milligram C g soil-1 cellobiose and 0.05 mg nitrogen g soil-1 ammonium nitrate and maintained at 45% soil moisture.

Preliminary results show that soils with smaller particle sizes and more active clays differ in microbial biomass (DNA yields), community composition (amplicon sequencing), and activity (CO2 production) compared to coarser textured soils with less active clays. The team additionally presents an upcoming experiment that incubates the mature model soils with representative necromass biomolecules (carbohydrates, protein, nucleic acid, and lipids). Researchers will use oxygen-18 (18O) water to follow 18O incorporation into proteins in response to each necromass biomolecule. A novel combination of stable isotope probing–metaproteomics and metagenomics can be used to define the metabolic pathways and microbial populations active across soil and macromolecule types, as well as substrate-specific C use efficiency. Additionally, the team will track the fate of necromass C through continuous monitoring of CO2 production and assessment necromass C stocks in microbial biomass (via chloroform fumigation) and particulate vs. mineral-associated pools (via density fractionation).

References

Creamer, C. A., et al. 2019. “Mineralogy Dictates the Initial Mechanism of Microbial Necromass Association,” Geochimica et Cosmochimica Acta 260, 161–76. DOI:10.1016/j.gca.2019.06.028.

Dong, W., et al. 2021. “Decomposition of Microbial Necromass Is Divergent at the Individual Taxonomic Level in Soil,” Frontiers in Microbiology.12, 679793. DOI:10.3389/fmicb.2021.679793.

Fernandez, C. W., and P.G. Kennedy. 2018. “Melanization of Mycorrhizal Fungal Necromass Structures Microbial Decomposer Communities,” Journal of Ecology 106(2), 468–79. DOI:10.1111/1365-2745.12920.

Finley, B. K., et al. 2021. “Soil Minerals Affect Taxon-Specific Bacterial Growth,” The ISME Journal 16, 1318–26. DOI:10.1038/s41396-021-01162-y.

Keiluweit, M., et al. 2017. “Anaerobic Microsites Have an Unaccounted Role in Soil Carbon Stabilization,” Nature Communications 8, 1771. DOI:10.1038/s41467-017-01406-6.

Liang, C., and T. C. Balser. 2011. “Microbial Production of Recalcitrant Organic Matter in Global Soils: Implications for Productivity and Climate Policy,” Nature Reviews Microbiology 9, 75. DOI:10.1038/nrmicro2386-c1.

Liang, C., et al. 2019. “Quantitative Assessment of Microbial Necromass Contribution to Soil Organic Matter,” Global Change Biology 25(11), 3578–90. DOI:10.1111/gcb.14781.

Oldfield, E. E., et al. 2018. “Substrate Identity and Amount Overwhelm Temperature Effects on Soil Carbon Formation,” Soil Biology and Biochemistry 124, 218–26.

Sorensen, J. W., et al. 2019. “Ecological Selection for Small Microbial Genomes Along a Temperate-to-Thermal Soil Gradient,” Nature Microbiology 4, 55–61. DOI:10.1038/s41564-018-0276-6.

Wieder, W. R., et al. 2015. “Explicitly Representing Soil Microbial Processes in Earth System Models,” Global Biogeochemical Cycles 29(10), 1782–800. DOI:10.1002/2015GB005188.

Funding Information

This research was supported by the DOE Office of Science, BER program, grant no. DE‐SC0022996. The soil warming experiments at Harvard Forest are supported by the National Science Foundation (DEB-1832110, DEB-1456610). The team is grateful to Drs. Serita Frey and Mel Knorr for maintaining this infrastructure for the community.