Plants & Nitrogen

If you’ve ever sifted through fertilizers at a garden store, you’re likely familiar with NPK ratios. These elements – nitrogen (N), phosphorus (P), and potassium (K) – are the three biggies, the primary elements that all plants need. The first of these, nitrogen, is a key element in amino acids (the building blocks of proteins, enzymes, and DNA) and central to the photosynthetic macromolecule chlorophyll. When nitrogen levels in the soil are low, chlorophyll production is stunted and plant leaves pale to a sickly yellow. To compensate for low nitrogen levels, a plant will slow stem growth and put more resources into root development, allowing the roots to forage in the soil for limiting nutrients.

The vast majority of nitrogen in the biosphere is in the form of gaseous N2 (dinitrogen). When you take a big deep breath of air, most of what you’re inhaling is this form of nitrogen (about 78% of the atmosphere is dinitrogen). And when you exhale, out comes the nitrogen, unchanged, unused, as unfortunately for most organisms, a triple bond binds the two nitrogen molecules together and is just about impossible to break.

Rhizobia root nodes on red clover
Nitrogen fixation

This unusable nitrogen needs to be “fixed” into a biologically useful form like nitrate (NO3) or ammonia (NH4) before organisms can use it to build proteins and other important macromolecules. A small amount of soil nitrogen (<10%) is fixed by lightning. The rest is fixed biologically (called diazotrophy) by a variety of different species of bacteria. While most of these bacteria are free-living (like cyanobacteria, including the blue green algae responsible for that pea soup-like slurry that appears in the summer), some plants have very casual associations with these bacteria, and they’re often found in closer proximity. In these associative nitrogen fixation relationships, small clusters of bacteria live in the soil immediately around the roots of plants. Excess nitrogen products are absorbed by the plant’s roots, while excess photosynthates (carbohydrates) are exuded into the root zone

Frankia spp.

Another genus of bacteria, Frankia, have symbioses with over 200 species of plants in various families. And as with associative nitrogen fixation, the same exchange of ammonia for photosynthates drives the relationship. But here the bacteria live in nodules that form on the roots of the host plant. This symbiosis allows the host plants to compete on nutrient-poor soils. To initiate the symbiosis, both the bacteria and host plant release chemical signals into the soil (source). If the signal is accepted, a cluster of Frankia extend their hyphae through the cell wall of root hairs along the epidermal layer of the roots. The bacterial hyphae then branch into these cells, ultimately causing the root hairs to deform. Within about 10-14 days the deformed root hairs develop into a nodule that fully encapsulates the cluster of bacteria. The largest cluster of these nodules that I dug up was about the size of a golf ball (see below), but apparently the clusters on some species can be as large as a soccer ball. Here in Vermont, these root nodules form in few species – e.g. Alnus incana (speckled alder), Comptonia peregrina (sweet fern), Myrica gale (Bog myrtle), and Elaeagnus umbellata (autumn olive) – all of which tend to grow in sandy soils in or adjacent to water. It’s possible that flooding in these habitats may be the dispersal agent for Frankia, allowing the bacteria to invade new areas (source).

Cluster of Frankia root nodules on speckled alder roots, exposed at the surface (Centennial Woods, Burlington)


Also of note is Rhizobia, a diverse group of bacteria that exclusively invade legumes (Fabaceae). Here in Vermont, this is represented in a range of herbaceous plants (like the clovers) and trees (both black locust and honey locust form root nodules). The nodules are small (about the size of a grain of rice) and scattered across the outer section of roots. Black locust is extremely shade-intolerant, and its growth is limited not by photosynthesis, but by soil nutrients and water. It tends to colonize sandy, nutrient-poor and drought-prone soils (drought also slows the uptake of nutrients, so having a built-in fertilizer can help the plant cope with low water levels). Again, the symbiosis with rhizobia allows locusts to outcompete other early succession trees by trading photosynthates for ammonia or amino acids. But pea family plants aren’t wasteful, and in soils high in nitrogen they will resist invasion by rhizobia.

Root nodules from Rhizobia on black locust roots (Centennial Woods, Burlington)

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