Student Digest

A novel hypothesis to explain why some legume lineages retained the ability to fix nitrogen, while others did not.

Rachel Souza Ferreira, PhD student
German Centre for Integrative Biodiversity Research, iDiv,
& Leipzig University, Germany

All organismic groups across the Tree of Life – plants, animals, protists and fungi – depend on nitrogen to grow and build proteins. Although Earth’s atmosphere is rich in nitrogen (N2), many soils are relatively nitrogen-poor. A small subset of plants, restricted to the N2-fixing clade of angiosperms evolved specialized organs known as nodules, within which they house intracellular diazotrophic bacteria, collectively known as Rhizobia, which allows them to fix and capture atmospheric nitrogen directly (Wagner, 2011). Given the massive economic and ecological importance of N2-fixing root nodule symbiosis, it is surprising that the evolution of nodulation remains poorly understood. Indeed, there is continued debate surrounding two contrasting evolutionary hypotheses: (i) a scenario of multiple independent parallel evolutionary origins of nodulation with few losses, vs (ii) a single gain followed by multiple independent secondary losses of nodulation potentially triggered by global scale geological and environmental change (e.g., van Velzen et al., 2019). One might expect that a functional trait that potentially confers such obvious advantages would be widespread and universally successful, but only a small subset of species in the N2-fixing clade are able to nodulate (Werner et al., 2014). Within legumes the majority, but not all genera in subfamilies Papilionoideae and Caesalpinioideae (sensu LPWG, 2017) are generally nodulated, but nodulation is unknown in the other four legume subfamilies. The reasons for this very uneven phylogenetic distribution of nodulation remain poorly understood. Furthermore, the high diversity of nodule anatomies, morphologies and development across nodulating lagumes means that it is extremely difficult to determinate whether nodules in legumes are strictly homologous or not (Doyle, 2016), adding a further layer of debate about the evolutionary origins of nodulation.

In a recently published paper in the New Phytologist focusing on the legume subfamily Caesalpinioideae, Faria et al. (2022) explore these questions and suggest a novel hypothesis to explain this very uneven phylogenetic distribution of nodulation. Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, Faria et al. (2022) reconstructed the evolution of two distinct nodule anatomy types: (i) fixation thread-type nodules (FT), where the bacteria are retained within the cell wall and the plasmalemma, and (ii) symbiosome-type nodules (SYM) where the bacteroids are surrounded by symbiosomes. Faria et al. showed that all confirmed nodulating genera in the mimosoid clade have SYM-type nodules, while almost all nodulating species from the non-mimosoid grade subtending the mimosoid clade have FT-type nodules (except a subset of species of the genus Chamaecrista). This striking distribution of nodule anatomy across Caesalpinioideae provides a possible explanation for the pattern suggested by Werner et al. (2014) that the mimosoid clade have a ‘moderate stable fixing state’ compared to the non-mimosoid grade where nodulation is more sporadically distributed across lineages. Faria et al. (2022) documented a six-fold greater rate of evolutionary loss of nodulation through time associated with FT-type lineages than SYM-type lineages, suggesting that the evolution of SYM-type nodules resulted in a significantly more stable occurrence of nodulation compared to lineages with FT-type nodules which appear to be much more susceptible to evolutionary loss of nodulation across Caesalpinioideae.

Left to right: Nodules of the genera Dimorphandra, Erythrophleum, Chidlowia and Indopiptadenia. Faria et al. (2022) showed that the first two genera have fixation-thread-type nodules and are placed in the non-mimosoid grade of the legume subfamily Caesalpinioideae, while the latter two have symbiosome-type nodules and are placed in the mimosoid clade. Photos, Dimorphandra and Erythrophleum: Euan James, James Hutton Institute, Dundee, U.K.; Chidlowia: George Ametsitsi, FORIG, Kumasi, Ghana; Indopiptadenia: HS Gehlot, JNVU, Jodhpur, India.

Few studies of plant functional trait evolution have hypothesized the sort of massive evolutionary losses that have been suggested for nodulation, nor demonstrated that trait innovation can mitigate against evolutionary loss as elegantly as Faria et al. They attributed this greater evolutionary stability to the greater control conferred by tighter compartmentalisation of the symbiont in SYM-type nodules. It is well established that N2 fixation is highly energy demanding and only beneficial under certain environmental conditions in which nitrogen limits growth (McKey, 1994; Hoffman et al., 2014; van Velzen et al., 2019), and this is manifest in phenotypic plasticity of nodulation (Goh et al., 2013). This suggests that any innovation which promotes a closer relationship between the host and the symbiont is likely to be critical in maintaining the evolutionary advantages of nodulation.

Faria et al. (2022) highlight the non-mimosoid grade of subfamily Caesalpinioideae as a hotspot of evolutionary transitions including two shifts from FT- to SMY-type nodules and numerous evolutionary losses of nodulation, opening the way for wider genomic studies. Faria et al.’s study also paves the way for wider exploration of nodule anatomy across legumes to see whether similar patterns of evolutionary loss of nodulation in subfamily Papilionoideae are also associated with FT-type nodules, which are also known to occur in a subset of lineages within that subfamily. It appears that there is still much to be done to fully understand the evolution of the prominent functional trait of nodulation.


Doyle, J. J. (2016) Chasing unicorns: Nodulation origins and the paradox of novelty. American Journal of Botany 103: 1865–1868.

Faria, S. M., Ringelberg, J. J., Gross, E., Koenen, E. J., Cardoso, D., Ametsitsi, G. K., Akomatey, J., Maluk, M., Tak, N., Gehlot, H.S. and Wright, K.M., Teaumroong, N., Songwattana, P., de Lima, H.C., Prin, Y., Zartman, C.E., Sprent, J.I., Ardley, J., Hughes, C.E. & James, E.K. (2022) The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes. New Phytologist 235: 2365–2377.

Goh, C. H., Veliz Vallejos, D. F., Nicotra, A. B., & Mathesius, U. (2013) The impact of beneficial plant-associated microbes on plant phenotypic plasticity. Journal of Chemical Ecology 39: 826–839.

Hoffman, B. M., Lukoyanov, D., Yang, Z. Y., Dean, D. R., & Seefeldt, L. C. (2014) Mechanism of nitrogen fixation by nitrogenase: the next stage. Chemical Reviews 114: 4041–4062.

LPWG. (2017) A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG). TAXON 66: 44–77.

McKey, D. (1994) Legumes and nitrogen: the evolutionary ecology of a nitrogen-demanding lifestyle. In: Sprent JI, McKey D, Eds. Advances in Legume Systematics 5: The Nitrogen Factor. Kew, UK: Royal Botanic Gardens, 221–228.

van Velzen, R., Doyle, J. J., & Geurts, R. (2019) A resurrected scenario: single gain and massive loss of nitrogen-fixing nodulation. Trends in Plant Science 24: 49–57.

Wagner, S. C. (2011) Biological Nitrogen Fixation. Nature Education Knowledge 3: 15.

Werner, G. D., Cornwell, W. K., Sprent, J. I., Kattge, J., & Kiers, E. T. (2014). A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nature Communications 5: 1–9.