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

Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon Cycling


Vanessa Brisson1* (, Jeff Kimbrel1, Megan Kan1, Joshua White1, Edith Lai1, Eric Slessarev1, K. J. Min2, Jessica Wollard1, Peter Kim3, Trent Northen3, Karis McFarlane1, Mary Firestone3,4, Vanessa Brisson1, Jennifer Pett-Ridge1,5, Erin Nuccio1


1Lawrence Livermore National Laboratory; 2Seoul National University; 3Lawrence Berkeley National Laboratory; 4University of California–Berkeley; 5University of California–Merced


Arbuscular mycorrhizal fungi (AMF) are ancient symbionts that form root associations with most plants. AMF play an important role in global nutrient and carbon (C) cycles, and understanding their biology is crucial to predict how C is stored and released from soil. This Early Career research investigates the mechanisms that underpin synergistic interactions between AMF and microbes that drive nitrogen (N) and C cycling, addressing DOE’s mission to understand and predict the roles of microbes in Earth’s nutrient cycles. By coupling isotope-enabled technologies with next-generation DNA sequencing techniques, the project investigates soil microbial interactions in situ using natural levels of soil complexity. This work will provide a greater mechanistic understanding needed to determine how mycorrhizal fungi influence organic matter decomposition and will shed light on nutrient cycling processes in terrestrial ecosystems.


The arbuscular mycorrhizal association between Glomeromycota fungi and land plants is ancient and widespread; 72% of all land plants form symbiotic associations with AMF. While AMF are obligate symbionts that depend on host plants for C and cannot decompose soil organic matter (SOM), AMF can stimulate the decomposition of SOM and dead plant tissue. Prior Early Career Program research strongly suggests that AMF partner with their microbiome in the zone surrounding hyphae (or “hyphosphere”) to encourage decomposition (Nuccio et al. 2022). The team examined AMF-microbial interactions in reduced-complexity microcosms and the field to assess the impact of AMF on terrestrial C and N cycling processes. In the laboratory, researchers are assessing how AMF and their microbiome impact litter decomposition, while in the field researchers assess how a deeply rooted perennial grass alters the “zone of influence” of AMF in soil depth profiles.

The molecular mechanisms that underpin interactions between AMF and the microbial community during SOM decomposition is a key knowledge gap. To facilitate metabolomics and mechanistic studies of the hyphosphere, the team has developed the MycoChip, a sterile plant-mycorrhizal microcosm for interrogating hyphal-microbial interactions in situ. The MycoChip allows both destructive and nondestructive resampling of hyphosphere communities over time and is optically clear to permit microscopy. This system has two chambers separated by a “raised airgap” containing a dam to prevent solute exchange between chambers and flanked by mesh barriers to block root entry and create a hyphosphere chamber isolated from the rhizosphere. Researchers used the MycoChip to examine how a living microbiome alters AMF exudation and the exometabolome during SOM decomposition. AMF were either allowed or denied access to nutrients (plant litter and bone meal) in the hyphal chamber by using different mesh sizes (31 micrometers and 0.45 µm respectively). To investigate how fungal-microbial interactions impact decomposition, AMF were exposed to “live” vs. “dead” soil in the hyphal chamber. Data analysis is ongoing to investigate how AMF impacts the detritusphere metabolome, microbiome, and plant photosynthesis and growth.

Most knowledge about physiology and ecology of AMF (and most soil organisms) has been learned from surface soils that are less than 20 cm deep. In a national field study, researchers assessed how the rhizosphere of a deep-rooted perennial bioenergy grass—switchgrass (Panicum virgatum)—alters the “zone of influence” of AMF in depth profiles and impacts soil C stocks. Rhizosphere and bulk samples from paired switchgrass and shallow-rooted fields were collected from 2.5 m deep soil cores across nine field sites in the eastern United States. The team characterized the impact of switchgrass on AMF communities, soil organic C, radiocarbon (14C), root abundance, and a range of soil physical and chemical properties. AMF diversity decreases linearly below 40 cm depth. At most sites, deeply rooted switchgrass extended the habitat of AMF down the soil profile compared to the shallow-rooted controls (maximum AMF depths under switchgrass ranged from ~25 cm to 175 cm). By moving AMF down the soil profile, deep root systems can potentially extend the influence of AMF to impact subsoil C cycling and weathering processes.


Nuccio, E. E., et al. 2022. “HT-SIP: A Semi-Automated Stable Isotope Probing Pipeline Identifies Cross-Kingdom Interactions in the Hyphosphere of Arbuscular Mycorrhizal Fungi,” Microbiome 10, 199.

Funding Information

This research is supported by the U.S. DOE Office of Science, BER program’s GSP under Early Career award SCW1711 and Lawrence Livermore National Laboratory (LLNL) Laboratory Directed Research and Development grant 19-ERD-010. Work conducted at LLNL was supported under the auspices of the U.S. DOE under Contract DE-AC52-07NA27344. Work at Lawrence Berkeley National Laboratory is supported by the m-CAFEs (Microbial Community Analysis and Functional Evaluation in Soils; Science Focus Area and was performed under the auspices of the U.S. DOE Contract No. DE-AC02-05CH11231.