The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone

Abstract

For decades, rhizobia were thought to be the only nitrogen-fixing inhabitants of legume nodules, and biases in culture techniques prolonged this belief. However, other bacteria, which are not typical rhizobia, are often detected within nodules obtained from soil, thus revealing the existence of a phytomicrobiome where the interaction among the individuals is not only complex, but also likely to affect the behavior and fitness of the host plant. Many of these nonrhizobial bacteria are nitrogen fixers, and some also induce nitrogen-fixing nodules on legume roots. Even more striking is the incredibly diverse population of bacteria residing within nodules that elicit neither nodulation nor nitrogen fixation. Yet, this community exists within the nodule, albeit clearly out-numbered by nitrogen-fixing rhizobia. Few studies of the function of these nodule-associated bacteria in nodules have been performed, and to date, it is not known whether their presence in nodules is biologically important or not. Do they confer any benefits to the Rhizobium-legume nitrogen-fixing symbiosis, or are they parasites/saprophytes, contaminants, or commensals? In this review, we highlight the lesser-known bacteria that dwell within nitrogen-fixing nodules and discuss their possible role in this enclosed community as well as any likely benefits to the host plant or to the rhizobial inhabitants of the nodule. Although many of these nodule inhabitants are not capable of nitrogen fixation, they have the potential to enhance legume survival especially under conditions of environmental stress. This knowledge will be useful in defining strategies to employ these bacteria as bioinoculants by themselves or combined with rhizobia. Such an approach will enhance rhizobial performance or persistence as well as decrease the usage of chemical fertilizers and pesticides.

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth‐promoting bacteria and promote restoration of eroded desert soil

“…This was revealed by the abundance of Rhizobium in the rhizosphere of soil of inoculated seedlings. This finding supports the well‐known role of rhizobia on the growth of native legumes of arid lands (Jorquera et al, ) and the documented interactions of rhizobia with many species of PGPB in agriculture (Martínez‐Hidalgo & Hirsch, ). Inoculation with B. pumilus ES4 also seems to have slightly reduced the abundance of several members of its own phylum (Firmicutes).…”

Conjugative transfer betweenRhizobium etliendosymbionts inside the root nodule

“…Nodulation is usually a specific process, where certain bacteria interact with certain legumes (Gage, 2004;Popp and Ott, 2011;Westhoek et al, 2017) however, nodules have been shown to contain other endogenous bacteria, including diverse rhizobial and non-rhizobial genera, such as Agrobacterium, Enterobacter, Chryseobacterium, Sphingobacterium, Actinobacteria and unclassified Enterobacteriaceae (Dudeja et al, 2012;Mora et al, 2014;De Meyer et al, 2015;Leite et al, 2016;Lu et al, 2017). Nodules contain a high number of bacteria, about 10 9 (Downie, 2014); even if the most abundant are rhizobia, 10 5 -10 8 may belong to other genera (Sturz et al, 1997;Martínez-Hidalgo and Hirsch, 2017). These bacteria may be natural recipients, or donors, in conjugative transfer events, contributing to evolution and diversification of bacteria, not restricted to symbiotic information.…”

Microvirgasp. symbiovar mediterranense nodulatesLupinus cosentiniigrown wild in Morocco

“…The remaining nine isolates did not form nodules and were not used for further identification. The presence of non‐nodulating bacteria in the nodule interior is now well‐documented though their role is not yet understood (Martínez‐Hidalgo and Hirsch ; Velázquez et al . ).…”