Alliance of Hyphae Bacteria, AM Fungi, and Plants Could Be the Key to Enriching Soil with Nutrients

May 5, 2021. By Kolemann Lutz

Enabling the formation, colonisation, of soil fungus and hyphae bacteria subsurface microbiomes could be key to priming the hyphosphere and soil fertility, supporting enzyme and nutrient exchange, enabling plants with stress resistance and tolerance, and sustaining photosynthesis in Martian and Lunar soil.

Arbuscular mycorrhizal fungi (AMF or AM) evolved a symbiotic relationship with plants over 400 to 480 million years ago and are found in the Hyphosphere with around 72% of all land plants and with most crop plants on Earth. A soil borne fungi, AM fungi penetrate the cortical cells of the plant roots to enhance photosynthesis and significantly improve plant nutrient uptake, stress resistance and tolerance, soil structure and fertility.

AMF helps absorb nitrogen and phosphate from organic matter in soil to transfer the N and P to the plants. AM Fungi lack enzymes to free nitrogen and phosphorus from complex organic molecules as well as enzyme genes to encode phytases and phosphatases, lignin, and complex carbohydrates.

Therefore, AMF can proliferate hyphae, which are branching filaments that make up the ends of the mycelium as part of the fungi and bacteria. By accessing carbon from the plant root, hyphae bacteria (linear feeding lanes) are typically extended deeper into the soil from fungal root tips.

Researchers from Cornell University conducted an experiment, funded by a grant from the US Department of Energy, to determine the bacterial community closely associated with the extraradical mycelium (ERM) or hyphae (ERH) of the fungal network and whether these bacterial communities differed among artificial soils systems.

In three mesocosm experiments, we detail the bacterial community closely associated with AMF extraradical hyphae bacteria and ask whether this community varies across soils, changes with time, or is influenced by either fungal species or nutrient status of the soil.

Results indicate that soil sample type accounted for roughly 40% of the ERH hyphae variation among samples from three soils. Hyphae bacteria were dominated by proteobacteria with 50% relative abundance. Hyphal samples showed repeated enrichment and increase in relative abundance of betaproteobacteriales, myxococcales, fibrobacterales, and cytophagales. Betaproteobacteriales, are mostly heterotrophic bacteria and are a frequent and significant components of plant microbiomes.

There was a striking observation: the consistent enrichment of myxococcales, a bacterial soil species that feed on insoluble organic substances in the soil, which are known for their predatory and social behavior. It is believed a strong increase in bacterial predators could indicate changing trophic structure in the hyphosphere and contribute to mineralization of nutrients from microbial biomass. Although these organisms can be antagonistic to fungi as several myxococcales prey on fungi or inhibit fungal activity, there is no evidence for myxococcales grazing on AMF.

Reproducibility of the hyphal community was high with only 5% of the variation accounted for by interaction of soil and sample. There were increased rates of decomposition and nitrogen mineralization from soil and organic residue in the hyphosphere, the zone of soil influenced by hyphae bacteria.

The study demonstrates the existence of a core microbiome associated with the extraradical hyphae (ERH) of AMF fungi with variation among soils. Unique microbiome composition likely arises in response to site-specific constraints or microbe-microbe interactions, similar to the plant root and rhizosphere microbiomes. Findings and observations show bacteria’s ability to attach and colonize to the ERH in vitro, depending on matter and quality of fungal species, which influences soil composition and bacteria metabolism.

Many of the bacteria predators are well equipped with hydrolytic enzymes(cellulase, cellobiase, xylanase and amylase) for breaking down complex carbohydrates into sugars. These enzymes are also biochemical catalysts that use water to break the chemical bond and help regulate plant pathogens.

In a recent metagenome resolved transcriptomic 2020 study, both Burkholderiaceae and fibrobacteria upregulated transcription of carbohydrate active enzymes 3x greater in combined rhizosphere and detritosphere habitats. These bacterial groups are candidates for their contribution to hyphosphere priming of carbon and nitrogen mineralization.

“If AMF species vary in hyphal exudates, metabolites, or signaling that drives changes in composition and activity of hyphae bacterial communities, such variation could have important implications for nutrient cycling in soil”, mentioned by lead author, Dr. Bryan Emmett, a Research Microbiologist at US Department of Agriculture (USDA) Agricultural Research Service.

In a separate 2018 study, German researchers conducted a separate study

to cultivate petunias (flower similar to crops) and mycorrhizal fungi under low gravity conditions. A key challenge is that microgravity has been observed to affect the AMF microbiome and reduce protein intake for the plant. By introducing a chemical compound known as strigolactone, mycorrhiza formed and encouraged relationships between the plant and outside microbes, creating a beautiful blooming petunia flower.

Although planets like Mars and Moon don't yet have nutrients in the ground, arbuscular mycorrhizal fungi will play a critical role in plant nutrient acquisition and demand improved understanding of interactions with soil simulants and local soil biota.


Emmett, B.D., Lévesque-Tremblay, V. & Harrison, M.J. Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi. ISME J (2021).

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