We first conducted an experiment testing the effect of Si on heat, cold and freeze-thaw cycling stress in an emblematic Si-accumulating species, namely rice (see Materials and Methods for details). After planting rice in a nutrient solution containing 1mM silicic acid for 15 days, no differences in shoot length, root length, and chlorophyll concentrations between the -Si and + Si groups were observed (Table S1). However, when rice plants were placed under three types of stress (heat, cold, and freeze thawing) for three days, a pronounced effect of Si fertilization was observed (Fig. 1a). Under heat stress, Si-fertilized rice had significantly higher shoot length, root length, and fresh weight than the -Si group (Fig. 1b-d). In contrast, root length and shoot fresh weight of the + Si group were lower than those of the -Si group under cold stress (Fig. 1). Under freeze thawing, the + Si group even showed significant wilting (Fig. 1).
Following this experiment, we used a recently published database with leaf Si concentrations in about 1800 species12 that we combined with information on species distribution obtained from the GBIF (Global Biodiversity Information Facility) to check whether high-Si and low-Si plant orders were associated with locations with different climatic conditions (see Fig. S2 and Table S2 for details). Specifically, we selected 10 orders with high-Si concentrations (mean more than 2 mg g− 1) and 10 orders with low-Si concentrations (mean less than 1 mg g− 1). The high-Si orders were Poales, Saxifragales, Schisandraceae, Arecales, Boraginaceae, Fagales, Rosales, Nymphaeaceae, Asterales, Alismatales. The low-Si orders were Acorales, Brassicales, Liliales, Asparagales, Aquifoliales, Santalales, Pandanales, Celastraceae, Cornales, Bromeliaceae. We randomly selected the distribution information of 1000 occurences from each order (using rgbif package in R, see Table S2 for species information), and drew distribution maps of high-Si and low-Si plants. The data in Fig. 2a suggest that high-Si plants occur to a greater extent in areas of lower latitude while low-Si plants are more noticeably present in higher latitude regions. This is confirmed by the analysis in Fig. 2b: the average temperature of the distribution of high-Si plants was 1.2°C higher than that of low-Si plants. In addition, the distribution of the data indicated that high-Si plants were mainly concentrated in environments with a mean annual temperature near 17°C, while low-Si plants were predominantly concentrated in environments with a mean annual temperature near 11°C (Fig. 2b).
In addition to this global analysis, we conducted field sampling of two typical high-Si species, wheat and rice, in the main grain producing areas of China (Fig. 3). We found a significant positive correlation between both wheat and rice phytolith concentrations and air temperature, especially for wheat (Fig. 3). Samples from two regions were analyzed separately because of important differences in climate and soil types, but the results still showed that the phytolith concentrations were positively correlated with temperature (Fig. S3). Overall, this evidence suggests that present-day temperature influences both the distribution of high- and low-Si species worldwide, and also affects intraspecific variation in leaf Si concentrations.
We then constructed evolutionary trees of Si transporter proteins (encoded by the genes Lsi1, Lsi2, Lsi3, Lsi6)16. We searched for the homologous sequences of these proteins using NCBI BLASTp (Basic Local Alignment Search Tools for proteins)26, and then downloaded the protein sequences of the top 15–20 species with the highest homology for evolutionary tree construction. Results showed that the Si transporter proteins of high-Si species evolved mainly during warm periods (Fig. 4a). However, the evolutionary trees include only a few species, and we still need evidence from more taxa.
Using data from Angiosperm Phylogeny Website, we investigated the occurrence of plant families with contrasted Si concentrations during warm and cold periods. We found that 77% of high-Si families (> 10 mg g− 1) emerged during warm periods, while 75% of low-Si families (< 1 mg g− 1) emerged during cold periods (Fig. 4b). The historical temperature of the Earth during the emergence of high-Si families was 3°C higher than that of low-Si families (p < 0.001) (Fig. 4c, see Table S3 for specific information on the plant families). In order to correct for species differentiation time, we selected another set of data from Li et al. (2019) for analysis. Unlike the evolutionary information collected from different literature sources on Angiosperm Phylogeny Website, Li et al. (2019) data was from their plastid phylogenomic tree based on 80 genes from 2881 plastid genomes and 62 fossil calibrations. A similar result was obtained, where high-Si families were more likely to appear during high temperature periods (65%), while low-Si families mainly appeared during cold periods (57%) (Fig. S4 and S5).
In addition, we analyzed the divergence times of different subfamilies in the five major families of angiosperms (Asteraceae, Orchidaceae, Fabaceae, Rubiaceae, and Poaceae). In Asteraceae, species with high Si concentrations (> 10 mg g− 1) are found in the Asteroideae subfamily, which emerged during the Middle Eocene Thermal Maximum28,29, while low Si concentrations (< 2 mg g− 1) are typical of the Carduoideae and Cichorioideae subfamilies, which emerged in cooler periods30,31. In Orchidaceae, Si-rich species are found in the Apostasioideae and Cypripedoidoidae subfamilies, which thrived during a warm climate, whereas Si is notably absent in the Vanilloideae, Orchidoideae, and Epidendrioideae subfamilies that emerged during a cooler phase32,33. Fabaceae exhibits low Si concentrations (< 1 mg g− 1) in subfamilies like Caesalpinioideae and Cercidoideae that appeared during cold periods, while high-Si species are mainly in the Papilionoideae, particularly the Phaseoleae subclade that emerged during a warm period34,35. In Rubiaceae, high-Si species are found in the Rubioideae, which emerged in a warm era, while low-Si species appear in the Ixoroideae and Cinchonoideae, which emerged during a colder period36. Among Poaceae, low-Si species distributed among five subfamilies (Poodinae, Panicoideae, Poeae, Chloridoideae, and Paspaleae) all emerged during cold periods, except Chloridoideae. By contrast, high-Si species mainly belong to the Arundinarieae, Panicoideae, Cynodonteae, Andropogoneae, and Molinieae, of which all but the Cynodonteae emerged during warm periods. Detailed information on the emergence and mean leaf Si concentrations of these subfamilies is provided in Table S4. Overall, our analysis of the subfamilies from five different major families of angiosperms showed that the leaf Si concentrations in subfamilies seemed to closely relate to the Earth’s temperature during their appearance period. This suggests that silicification might have been favored during warm and interglacial periods and/or avoided during glacial periods.