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. 2020 Jun 3;15(6):e0234216. doi: 10.1371/journal.pone.0234216

Role of root exudates on assimilation of phosphorus in young and old Arabidopsis thaliana plants

Hugo A Pantigoso 1, Jun Yuan 2, Yanhui He 1,3, Qinggang Guo 1,4, Charlie Vollmer 5, Jorge M Vivanco 1,*
Editor: Tobias Isaac Baskin6
PMCID: PMC7269232  PMID: 32492072

Abstract

The role of root exudates has long been recognized for its potential to improve nutrient use efficiency in cropping systems. However, studies addressing the variability of root exudates involved in phosphorus solubilization across plant developmental stages remain scarce. Here, we grew Arabidopsis thaliana seedlings in sterile liquid culture with a low, medium, or high concentration of phosphate and measured the composition of the root exudate at seedling, vegetative, and bolting stages. The exudates changed in response to the incremental addition of phosphorus, starting from the vegetative stage. Specific metabolites decreased in relation to phosphate concentration supplementation at specific stages of development. Some of those metabolites were tested for their phosphate solubilizing activity, and 3-hydroxypropionic acid, malic acid, and nicotinic acid were able to solubilize calcium phosphate from both solid and liquid media. In summary, our data suggest that plants can release distinct compounds to deal with phosphorus deficiency needs influenced by the phosphorus nutritional status at varying developmental stages.

Introduction

Phosphorus is an essential element for plant growth and development [1], and a non-renewable resource [2,3]. Despite the fact that the total amount of phosphorus is high in most agricultural soils, crop yields are often limited by low availability due to the non-soluble form and low mobility of this nutrient [4,5]. It has been estimated that residual phosphorus fertilizer known as ‘phosphorus legacy’ in soil can be sufficient to sustain crop yield for the next century and could alleviate expected phosphorus shortages in the next 50 years [6]. Hence, studies addressing potential solutions to exploit soil phosphorus reserves are needed.

Plants have developed several strategies for acquisition of phosphorus in low nutrient environments mainly by modifying root structure and changing the soil chemical properties in the rhizosphere [7]. These mechanisms include longer root formation and increases of root:shoot ratio allowing the transport of phosphorus from the roots to the shoots [8,9]. Certain plants such as Lupinus sp. can promote the formation of cluster roots to secrete phosphorus solubilizers such as citrate and malate in sufficient quantities to lower the rhizosphere pH, thus enhancing the movement of phosphorus and consequently plant uptake [10,11]. The secretion of phosphorus solubilizers is not restricted to cluster root-forming plants. Several other species such as alfalfa, spinach and radish have also been documented to increase the efflux of organic anions as a result of a lack of phosphorus available in the soil [1214].

Increasing phosphorus solubility can also be achieved by modifying the rhizosphere chemistry. Root-secreted phosphorus solubilizers are capable of increasing solubility of a variety of insoluble phosphorus forms in the soil such as organic phosphorus, inorganic phosphorus like calcium phosphate, and humic substances bonded to phosphorus anions such as Al (III) and Fe (III). They can be classified as protons or OH-/HCO3- equivalents, redox equivalents and di- and tricarboxylic acid anions [13]. The mechanisms used by plants to solubilize phosphorous vary according to the plant species, nutritional status of the plant, and soil and environmental conditions [15]. However, organic acids such as oxalate, citrate, and malate are recurrent in a variety of plant species and thereby are the most studied means used by plants to solubilize phosphorous [13]. Considerably less research has been performed to explore the total root exudate profile and to identify other compounds exerting similar and complementary functions in the rhizosphere.

All plants share a similar need for phosphorus, but this need differs broadly based on the crop type and its developmental stage [16,17]. In general, most crops require early phosphorus supplementation for optimum yield [18]. Nevertheless, higher amounts of phosphorus in later growth stages are required proportional to increases in the biomass of the plant [1922]. Due to the variation of phosphorus demand during the plant’s lifetime, it becomes necessary to fully understand fluctuations of root exudates as a means to solubilize the phosphorus present in the of the soil.

In this study, we tested the effect of three phosphate fertilization levels on root exudate composition of A. thaliana at distinct developmental stages. We hypothesized that phosphate status will promote a shift in the relative concentrations of certain root exudates with inorganic phosphate solubilizing properties and certain metabolites involved in phosphate solubilization will be inhibited under high phosphate concentrations. The results showed that the total exudates changed in response to the addition of phosphate, and that certain metabolites were reduced under increasing phosphorus amendments at varying growth points. As a proof of concept, some of the metabolites that decreased in quantity to the phosphorus addition were tested and four of them were found to solubilize phosphate.

Materials and methods

Plant growth conditions, phosphorus fertilization and collection of root exudates

Arabidopsis thaliana (L.) Heynh wild-type Columbia seeds were obtained from Lehle Seeds (Round Rock, USA) and surface sterilized with Clorox bleach (Sodium Hypochlorite, 8.25%) for 1 min. Seeds were rinsed with distilled water 3 times and plated on different phosphorus levels of Murashige and Skoog (MS) agar (1.5%) (supplemented with 3% sucrose) in square plates. The plates were placed vertically in a growth chamber (Percival Scientific) at 25 ± 2 °C with a photoperiod of 16 h: 8 h, light: dark for germination. The germinated seedlings were grown in three phosphate levels: full strength (100%, 1.25 mM), half (50%, 0.625 mM) and a quarter (25%, 0.3125 mM) in solid MS medium as described above. The three phosphate levels used in this study did not stimulate the plant starvation response, which is generally activated at values below 2 μM phosphorus in the soil solution [23]. Instead, we followed a low and high fertilization regime used commercially in agriculture [24]. phosphate concentration was adjusted with Na2HPO4 and NaH2PO4, and phosphate -free MS medium was used as basal medium. After seven days of growth, the seedlings were transferred to six well plates, each well containing 5 mL of liquid MS with 1% sucrose with one individual seedling per well containing distinct phosphate levels as described above. The seedlings grown in solid MS at the particular phosphate level were placed under the same phosphorus level under liquid M conditions. All the plates were placed on an orbital shaker at 90 rpm under 25 ± 2 °C and lit by cool white fluorescent light (45 μmol m-2 s-1) with a photoperiod of 16 h: 8 h, light: dark. The nutrient solutions were replaced every week by transferring the plants to new six well plates with 5 ml of fresh liquid MS medium under the same phosphate levels as stated above.

Root exudates were collected as follows: 1–3 days after transplanting for seedling stage, 8–10 days after transplanting for vegetative stage, and 15–17 days after transplanting for bolting stage. Prior to the collection of root exudates, plants were removed and washed mildly with sterile water and subsequently placed in new wells containing 5 ml of sterile water for two days. We used sterile distilled water to prevent the interference of exogenously supplemented salts and sucrose present in the Murashige and Skoog media in subsequent GC-MS analyses of the root exudates. The solution in which the plants were floating was collected and considered as the root exudate. The solution of one plate containing six wells with six individual plants was pooled and considered as one replicate. We used three replicates for each stage under three phosphorus levels. The root exudates were filtered through a 0.45 μm (Millipore, MA) to remove root sheathing and root border-like cells and were freeze-dried and stored at -20 °C for further analyses.

Gas Chromatography-Mass Spectrometry (GC-MS) of root exudates

To characterize the chemical composition, root exudates were processed as described by Chaparro et al, [25] and subjected to gas chromatography—mass spectrometry GC-MS analyses at the Genome Center Core Services, University of California Davis. Extracts were briefly dried under nitrogen gas and then methoximated and trimethylsilylated. The derivatives were analyzed by an Agilent 6890 gas chromatograph (Santa Clara, CA) containing a 30-m-long, 0.25-mm inner diameter rtx5Sil-MS column with an additional 10 m integrated guard column. Metabolites were detected using the BinBase algorithm [26] and identified by comparing the retention index and mass spectrum of each analyte against the Fiehn mass spectral library from the West Coast Metabolomics Center, University of California Davis.

Statistical analysis of total root exudate data

To discover the differential expression levels of compounds across the plant’s growth stages and fertilizer levels, R statistical software (R Core Team, 2017) was used to perform principal components analysis (PCA) on all annotated compounds. For each of the following analyses, we performed a PCA by first separating the total root exudate data by plant growth stage. Within each plant growth stage (e.g. bolting), we performed a centered and scaled PCA. By verifying that the first two principal components explained a sufficient amount of the variance in the compound(s) expression levels, we were able to determine which compounds had the highest correlation with these components through the magnitude of the variance. The variances are representative of a compound at each growth stage and at a particular phosphate level. The largest variance represents the highest correlation to the principal components. This method allowed us to determine which compounds explained most of the variance across the fertilizer levels and for each of the plant’s growth stages.

Significant differences between phosphorus amendment and compound counts level per developmental stage were analyzed using a one-way ANOVA. Tukey HSD test was used to identify significance (p < 0.05) among phosphorus treatments.

Qualitative analysis of phosphate solubilizing ability of compounds derived from root exudates

From a list of selected compounds, only 13 of them were diluted in ddH2O at the desired concentration (100 mM) (Table 1). We used the reported concentration of organic acids in the rhizosphere (1 μM to 100 mM) as reference to select the concentration of the compounds tested in this study [2729]. These 13 compounds were qualitatively evaluated for their phosphate solubilizing abilities on National Botanical Research Institute phosphate growth medium (NBRIP) solid medium containing: 10.0 g glucose, 5.0 g Ca3(PO4)2, 0.2 g NaCl, 0.5 g MgSO4·7H2O, 0.5 g (NH4)2SO4, 0.2 g KCl, 0.03 g MnSO4, 0.003 g FeSO4·7H2O, 12 g agarin 1 L water, pH: 7.0–8.0 [30]. All compounds used in this experiment were purchased from Thermo-Fisher Scientific. The specific solution (100 μL) of each compound was placed on NBRIP solid medium. The plates were inoculated at room temperature and let to sit overnight. Phosphate solubilizing ability was visually judged as a clear halo around every drop of solution containing the given compound. Briefly, the test of the relative efficiency of isolated metabolites was carried out by selecting the metabolites that were capable of producing a halo or clear zone in the surrounding medium by the dissociation of inorganic minerals such as calcium phosphate.

Table 1. Five top compounds from root exudates identified by Principal Component Analysis (PCA).

Growth Stage P level (%) Compound name
Seedling N/A N/A
Vegetative 25 Nicotinic acid *
4-hydroxybutyric acid *
3-hydroxypropionic acid *
1-monostearin
1-monopalmitin
Vegetative 50 and 100 Threonine *
Proline *
O-acetylserine *
Leucine *
Alanine *
Bolting 25 Threonic acid
Octadecanol
Malic acid *
Glycine *
Galactinol *
Bolting 50 Scopeletin
phenylacetamine
5-aminovaleric acid *
1-monopalmitin
1-monoheptadecanoyl glyceride NISTT
Bolting 100 Sophorose
Guanine
Glutamic acid *
Adenine
1-Kestose

Compounds are divided by phosphate level and plant developmental stages. Compounds diluted in ddH2O at 100 mM are indicated (*).

Quantitative analysis of phosphorus solubilizing ability of water-soluble compounds (individually and combined)

For quantification, 35 μL of the same concentration previously tested (100 mM) of the 13 compounds were added to 5 mL liquid NBRIP medium resulting in a final concentration of 7mM. The tubes were then placed at a continuous agitation at 150 rpm on a rotary shaker for 72 h. Afterwards, the solution was centrifuged at 6000 rpm for 5 min, and the supernatant was filtered with 0.2 μm filter (Thermo-Fisher Scientific). Liquid NBRIP medium without compound addition was used as control. The concentration of phosphorus in the supernatant was analyzed according to with the protocol of Soltanpour et al. [31] and measured by means of inductive coupled plasma-optical emission spectrometer (ICP-OES) (Perkin Elmer 7300DV) at the Soil, Water and Plant Testing Laboratory of Colorado State University. This experiment and analysis were repeated twice with 3 repetitions.

In order to determine the potential cumulative effect of 3-hydroxypropionic acid, malic acid, nicotinic acid, and glutamic acid, they were combined and the available phosphorus (mg l-1) was determined by OES-ICP. A compound mixture that included the previously tested concentration (7 mM per compound) was assayed in order to compare if the combination of compounds would equal or surpass the effect of a single compound. Briefly, 35 μL (100 mM) of each compound was added to 5 mL liquid NBRIP medium resulting in a final concentration of 7mM. Each compound added to the pool had a concentration of 7 mM. Thus, the combination effect of four compounds were tested in a liquid NBRIP medium.

Statistical analysis for quantitative phosphate release

Significant differences between phosphorus content measured in NBRIP liquid media was analyzed using a one-way ANOVA. Tukey HSD test was used to identify significant treatments in multiple comparisons. P-value were considered significant below 0.05. Assumptions of normality and homogeneity of the data were confirmed prior to the analysis.

Results

Effect of phosphate levels on A. thaliana root exudates at different plant developmental stages

The effect of increasing phosphate at three concentrations on the root exudates of A. thaliana was analyzed at various developmental stages. In total, 456 compounds were detected by GC-MS among the treatments. The data set was reduced to 201 annotated compounds, and only these were kept for statistical analysis. The grouping of the compounds in the plot maintained the same pattern even after subtracting the non-annotated compounds (S1 Fig), suggesting that all of the differentially expressed compounds were indeed annotated by the GC-MS analyses.

The variability in our data, after subtracting the non-annotated compounds, was analyzed using a principal component analysis (PCA) where variability of component 1 (PC1) accounted for 29.8%, while component 2 (PC2) accounted for 21.7%. We determined that the plant’s developmental stage was responsible for the separation of the compounds in three marked groups: seedling, vegetative and bolting (Fig 1A) as previously reported [25,32,33]. When analysis included fertilizer levels segregation was observed in certain developmental stages and phosphate levels (S2 Fig). Overall, phosphate levels did not cause a significant separation on the root exudate patterns at the seedling stage, but the separation was observed in the vegetative and particularly in the bolting phases (Fig 1A). In the vegetative stage, a clear parting was observed at 25% phosphate compared to the 50 and 100% treatments (Fig 1B). In the bolting stage, there was a clear division between the three fertilizer levels, but the 50% level was the most distant rate (Fig 1C).

Fig 1. Root exudate compounds diverge in response to plant developmental stage and fertilization rate.

Fig 1

(A) 201 annotated compounds with proper identification detected using GC-MS was analyzed using a Principal Component Analysis (PCA) graph. PCA show dissimilarity of metabolite expression profiles between plant growth stages where PC1 explained 29.8% and PC2 21.7% of the variability. All phosphorus levels (25%, 50% and 100%) are present in each of the plant growth stages shown; seedling (green), vegetative (blue), and bolting (red). Dotted circle highlight clusters of particular fertilization levels. (B) Plot of PCA for vegetative stage only where PC1 explained 43.6% and PC2 14.6% of the variability. Compounds grouped by phosphorus treatments: 25% P (red) fertilization clusters separates from 50% P (blue) and 100% P (green). (C) Plot of PCA for bolting stage only where PC1 explained 64.3% and PC2 12.9% of the variability. Compounds grouped by phosphorus treatments: 50% phosphorus (green) separated from 25% phosphorus (red) and 100% phosphorus.

Differences in compound-levels in the vegetative and bolting stages due to phosphate fertilization

A separate analysis was performed to determine correlations between different and highly expressed compounds for a specific fertilization level and developmental stage. We focused our analysis on just the 25% phosphate at the vegetative stage, and all three treatments at the bolting stage because these treatments had the highest dissimilarity in the PCA. In addition, the 50% and 100% treatment at the vegetative stage were grouped because they were clustered in the PCA. For each of these treatments, we found the five top compounds that explained the largest proportion of the variance in the principal components (Table 1). In addition, the abundance of the compounds based on phosphate level and growth stage were determined (S3 and S4 Figs). We found some interesting patterns, such as that some compounds decreased expression upon increased fertilization (e.g. 3-hydroxypropionic acid, malic acid, galactinol), while other compounds showed a positive correlation with phosphate amendment (e.g. guanine, glutamic acid, sophorose).

Root-exudate metabolites solubilize calcium phosphate in solid and liquid media

We then tested the ability of some of the selected compounds irrespective of their abundance upon fertilization to solubilize phosphate solubilization. We found that 3-hydroxypropionic acid, malic acid, and nicotinic acid formed a clear halo when tested at a concentration of 100 mM, indicating the ability of this compound to release free phosphate from calcium phosphate (Fig 2). At 100 mM, none of the remaining tested compounds solubilized phosphate detectably.

Fig 2. Qualitative phosphate-solubilization analysis of compounds using a calcium-phosphate based medium (NBRIP).

Fig 2

(A) 3-Hydroxypropionic acid (B) malic acid and (C) nicotinic acid.

The phosphate -solubilizing effect of the selected compounds was further tested using a more sensitive technique (OES-ICP) where the compounds where tested at a final concentration of 7 mM in liquid NBRIP medium. The results showed that in addition to 3-hydroxypropionic acid, malic acid, and nicotinic acid, glutamic acid also had phosphate solubilizing ability. Using this method, glutamate, malate, and nicotinic acid solubilized approximately ten times the amount of phosphorus present in the control (5.34 mg L-1) whereas 3-Hydroxypropionic acid solubilized almost fifteen times more (Fig 3).

Fig 3. Quantitative phosphate-solubilization analyzed by coupled plasma-Optical Emission Spectrometer (ICP-OES) in 13 identified compounds.

Fig 3

Available phosphorus content in NBRIP liquid media after incubation of 72 hours with each of the 13 compounds at 7mM concentration. 3HA+MA+NA+GA treatments is the combination of 3-hydroxypropionic acid (3HA), malic acid (MA), nicotinic acid (NA) and glutamic acid (GA). Each compound added to the pool had 1.75 mM, 7 mM and 28 mM concentration.

Further analysis aimed to test the combined effect of all the four compounds on NBRIP medium at 7 mM concentration of each compound resulting in a twenty times higher available phosphate (101.21 mg L-1) compared to the control (Fig 3).

The plant mediates changes in secretion of solubilizing compounds in response to phosphorus status and developmental stage

We further analyzed the exudation level upon phosphate fertilization of 3-hydroxypropionic acid, malic acid, nicotinic acid, and glutamic acid in the different developmental stages. Depending on the compound, our results showed that the cumulative secretion levels of the compounds increased, decreased or remained statistically similar (p>0.05) as a function of phosphate amendment (Fig 4). At the seedling stage, changes in cumulative secretion of the four solubilizers was not related to phosphate level significantly which agrees with the PCA analysis (Fig 1A). Interestingly, at the vegetative stage, nicotinic acid and 3-hydroxypropionic acid showed higher abundance at the lowest phosphorus level (0.3125 mM) and decreased significantly (p<0.05) for the two higher levels (0.625 and 1.25 mM). Malic and glutamic acid followed a similar pattern; however, their changes were not statistically significant. At the bolting stage, differences of compound cumulative secretion were observed for glutamic acid, malic acid and nicotinic acid, but not for 3-hydroxypropionic acid which did not increase or decrease following an incremental phosphorus level. Cumulative secretion of malic acid was reduced significantly from 0.3125 to 0.625 mM phosphate treatments, and then incremented its cumulative secretion for the highest treatment (1.25 mM). However, secretion levels of malic acid for the two highest phosphate treatments (0.625 and 1.25 mM) were below the value for the lowest rate (0.3125 mM) (Fig 4A). Similarly, cumulative secretion of nicotinic acid increased significantly from 0.3125 to 0.625 mM but dropped for 1.25 mM of phosphate (Fig 4C). Lastly, glutamic acid consistently increased upon higher phosphorus fertilization reaching its peak at 1.25 mM of phosphate (Fig 4B).

Fig 4. Phosphate-solubilizer compounds showing changes in cumulative root secretion levels at three distinct developmental stages (p<0.05) in response to increasing phosphate addition (0.312, 0.625 and 1.25 mM).

Fig 4

Malic acid (A), Glutamic acid (B), Nicotinic acid (C), 3-hydroxypropionic acid (D).

Discussion

For the most part, the influence of phosphorus fertilization on root secretion has been studied at specific developmental stages [34,35], among genotypes of the same plant species [36] or between different species [37]. For instance, Vengavasi et al. [36] found cultivar-dependent differences in root exudation of soybeans grown under phosphorus -sufficient versus phosphorus -deficient conditions. It is worth noting that these plants were sampled at the reproductive stage of growth, a metabolically active stage with higher demand for energy and phosphorus nutrition. In a different study, the authors found differences in root exudation in maize seedlings grown in phosphorus -sufficient and phosphorus -deficient conditions [34]. In contrast, here we studied the interplay of increasing phosphorus fertilization on root exudation at different plant developmental stages (seedling, vegetative and bolting) in A. thaliana.

Our results showed that the root exudate profiles were similar within the seedling stage across all phosphate fertilization treatments (Fig 1A). Thus, we hypothesized that at this growth stage roots did not respond to phosphorus fertilization. A. thaliana is considered a plant that can thrive in marginal soils where optimum nutrient conditions are limited [38], and at early developmental stages the plant does not require high amounts of phosphorus as a mechanism to cope with poor soil conditions [39]. In fact, it has been shown that the reserves of phosphorus in the seeds of several plants, including Brassicaceae species, can support seedling growth in a medium lacking phosphorus for at least four weeks after germination [4042,39].

In contrast, maize, a monocotyledonous plant, possesses two genes induced by phosphate starvation in its genomes compared to five in eudicots such as A. thaliana [43,44]; suggesting a difference in phosphate responsiveness between these two plant groups. In addition, signs of phosphorus scarcity in eudicots (e.g. A. thaliana) is often observed at later stages of growth [45]. In the vegetative stage, the root exudates at 50% and 100% phosphate showed greater visual similarity in the PCA than the exudates at 25% evincing an initial sensing from the plant in response to its phosphorus demand. At the bolting stage, the three levels of phosphate fertilization had distinct root exudation patterns. These results may suggest that as the plant ages the demand for phosphorus increases, as evidenced by the differential root exudation profiles [46]. This result is in accordance with Tawaraya et al. [47], who showed that phosphorus content increased in shoot and root-dried soybean tissues as the plant developed, and that root exudate content, collected on day 1, 5, 10 and 15 of growth, increased for phosphate -depleted compared to phosphate -sufficient treatments.

Our results suggest that plants in the vegetative stage sense only the 25% phosphate treatment as being low, whereas plants at bolting stage sense both 25% and 50% phosphate as low. This pattern of incremental phosphorus requirement during progression in plant development is common in annual plants such as A. thaliana [39]. For instance, Brassica napus L. requires an incremental supply of phosphorus at flowering onset, which is critical for protein and oil synthesis, and the development of seeds [48,49]. It is worth noting that the intermediate phosphate rate (50%) at bolting stage was largely separated (in the PCA plot) compared to 25% and 100% treatments, indicating a higher dissimilarity in root exudation composition. This could be due to the fact that the functions of plant metabolites are diverse and are not restricted only to nutrient acquisition. For instance, root exudates can be substrates, chemotactic or signaling molecules that regulate plant root and microbial interactions [50]. Such plant modulation can be specific to developmental stages [51].

The PCA data allowed for the visual determination of changes in root exudation composition between plant developmental stages and phosphate fertilization levels. We then developed a list of compounds based on those differences observed in the PCA in response to phosphorus nutrient status; and four of those compounds (i.e. 3-hydroxypropionic acid, nicotinic acid, glutamic acid and malic acid) were confirmed as phosphate solubilizers. Three (3-hydroxypropionic acid, nicotinic acid, and malic acid) out of the four compounds were significantly more abundant at the lowest phosphate rate and reduced in concentration as the amendments was elevated.

Our findings agree with a variety of studies evaluating the exudation of organic acids (e.g. malic acid) in various plant species under various phosphate availabilities [52,13]. Malic acid is a primary compound released by roots under phosphorus deficiency, but often not the most effective [52]. In contrast, nicotinic acid and glutamic acid are less abundant than malic acid or oxalic acid in plant species [46,53]. 3-Hydroxypropionic acid has not been previously associated with phosphate solubilization, however it has been described as a natural product of a plant endophytic fungus [54,55]. Further, the knowledge of the secretion of these compounds throughout plant phenology is scarce mainly because these studies are often performed in hydroponic systems limiting the root exudate collection to early stages of plant development for a variety of plant crops [52,56]. In our study, we observed that the cumulative secretion of malic acid significantly increased during low phosphate availability, but it was limited at the bolting stage. 3-Hydroypropionic acid and nicotinic acid followed the same pattern, however they were significantly secreted above control level only in the vegetative stage. Conversely, glutamic acid and nicotinic acid increased in abundance at bolting stage when phosphate levels increased. Interestingly, nicotinic acid changed cumulative secretion depending on the developmental stage. It has been reported that nicotinic acid induced flowering in Lemna plants [57], and that nicotinic acid can alleviate abiotic plant stresses by increasing hormone levels such as indole-3-acetic acid and gibberellic acid [58].

Based on these observations we hypothesize that plant developmental stage modulates root exudation to deal with phosphorus deficiency by three potential mechanisms: (1) Plants secrete synergistic phosphate-solubilizing compounds in stages of high phosphorus demand. In this study nicotinic acid, a moderate phosphate -solubilizer, was released in combination with 3-hydroxypropionic acid, a stronger phosphorus-solubilizer. This agrees with a recent study showing synergistic association of citrate and phytase to improve acquisition of plant unavailable phosphorus in tobacco in the vegetative stage [59]. However, this study was performed under soil conditions and not using liquid NBRIP media. (2) Plants prevent the degradation of phosphate-solubilizing compounds such as malic acid, rapidly degraded by soil microbes [60], by releasing a different compound such as 3-hydroxypropionic acid preceding a growth stage of high phosphorus demand. It has been shown that certain plants, such as lupin, can release compounds that inhibit microbial activity to reduce organic acid degradation prior to the release of organic acids. [61]. Lastly, (3) plants secrete specific compounds to mediate either direct nutrient solubilization or the proliferation of distinct microbial taxa (with phosphate solubilizing activity) at specific growth stages (e.g. vegetative, bolting). In support of this hypothesis, root exudates can promote the activity of symbiotic microbes, such as phosphate solubilizing bacteria and siderophore-releasing bacteria and exert mobilization of non-available plant nutrients in soils at a single growth stage [6264].

It has been estimated that organic acids constitute 5 to 10% of the total organic carbon in the soil solution. The concentration of organic anions measured in the soil solution usually ranges from 100 nM to more than 580 μM in the rhizosphere of cluster roots [65]. However, millimolar concentrations of organic anions are likely required in the soil solution to effectively increase soluble phosphate concentration especially in calcareous soils [66, 67]. Strom et al. [66] tested three organic acids (citrate, malic and oxalate) and a wide range of concentrations (1 mM to 100 mM) to evaluate its effects on the mobilization of phosphorus in calcareous soil. The results showed that the phosphorus mobilization of the tested compounds had a low efficiency and its effect varied depending on the type of organic acid, compound concentration, and pH. Further, due to the low phosphorus mobilization efficiency of those compounds it is still argued if the benefit of releasing large amounts of organic acids into the soil will exceed the cost of carbon lost by the plant, which can be seen as an unnecessary trade-off [66]. However, low efficiency organic acids can be particularly important in phosphate mobilization for calcareous soils with a limited phosphorus availability for plants. Finally, our evidence supports the above-mentioned hypothesis, that plants release a combination of compounds with different phosphorus-solubilizing efficiencies, at specific stages of growth, to deal with particular phosphorus needs.

Lastly, root exudates from liquid culture systems allow the determination of exudation rates unaltered by the soil matrix or microbial decomposition if performed under sterile conditions as we did in this study [56]. However, the quality and quantity of the root exudate profile may be impacted by the nutrient solution culture method (also known as hydroponic methods) [68]. Soil-hydroponic hybrids methods for root exudation collection are not exempt of potential physical/physiological perturbances. Thus, sterile nutrient solution culture methods remain especially important to assess temporal dynamics of root exudates.

In summary, the significance of these findings relies on the potential of customizing specific metabolites to be utilized as soil amendments under the most limiting phosphorus conditions and most demanding stage of plant growth. The role of secondary metabolites in phytoremediation efforts has been previously investigated [69] as well as the use of customized synthetic bacteria communities to modify plant phosphate accumulation [70,71]. However, the use of customized metabolites for phosphorus acquisition remains unexplored.

Conclusions

The data collected indicate that root exudate patterns change as a response to the supply levels of phosphorus, and this change was accentuated as the plant reached maturity, when phosphate demands are higher. 3-Hydroxypropionic acid and nicotinic acid accumulated significantly at the vegetative stage under lower phosphate supplementation and was found to solubilize phosphate under both solid and liquid medium. This study sheds light on the influence of plant nutrient status and plant phenological growth stages driving the composition of plant root exudates. Future research should focus on understanding the effects of metabolites at a particular developmental stage of growth under phosphorus depleted soil, as well as to test the potential of these phosphate-solubilizing compounds in making phosphorus available for plants grown in soils saturated in unavailable phosphorus forms.

Supporting information

S1 Fig. Root exudate compounds diverge in response to plant developmental stage and phosphate fertilization rate.

(A) 456 compounds detected using GC-MS are plotted on the graph. PCA show dissimilarity among group of metabolites in the seedling stage at different fertilization levels: 25% (light green), 50% (light blue), 100% (green); vegetative stage: 25% (purple), 50% (pink), 100% (blue); and bolting stage: 25% (brown), 50% (olive), 100% (orange). (B) Data reduced to 201 annotated compounds with proper identification. PCA of compounds grouped by phosphate treatments in the seedling stage: 25% (light green), 50% (light blue), 100% (green); vegetative stage: 25% (purple), 50% (pink), 100% (blue); bolting stage: 25% (brown), 50% (olive), 100% (orange). The dotted circle indicates a cohesive group at a given fertilization level.

(DOCX)

S2 Fig. Root exudate compounds grouped by repetitions of fertilizer level.

Treatments within plant developmental stages differ from one another, particularly the vegetative and bolting growth stages. Ellipses circle three repetitions of same fertilizer level. Color code correspond to seedling: 25% (light green), 50% (light blue), 100% (green); vegetative: 25% (purple), 50% (pink), 100% (blue); bolting: 25% (brown), 50% (olive), 100% (orange).

(DOCX)

S3 Fig. Top 10 compounds showing changes in cumulative secretion levels in the vegetative developmental stage (p<0.05) in response to increasing phosphate addition (0.312, 0.625 and 1.25 mM).

Selected compounds based on PCA from vegetative 25% phosphate (A), and vegetative 50% and 100% phosphate (B).

(DOCX)

S4 Fig. Top 15 compounds showing changes in cumulative secretion levels in the bolting developmental stage (p<0.05) in response to increasing phosphate addition (0.312, 0.625 and 1.25 mM).

Selected compounds from bolting 25% phosphate (A), bolting 50% P (B) and bolting 100% (C).

(DOCX)

Acknowledgments

We thank Dr. James Self, manager of the Soil, Water and Plant testing laboratory at Colorado State University for their invaluable advice regarding phosphorous chemical analysis.

Data Availability

All relevant data are within the paper and its Supporting Information files.

Funding Statement

J. Y. was supported by National Postdoctoral Program for Innovative Talents (BX201600075) and Natural Science Foundation of Jiangsu Province (BK20170724), Y. H. was supported by China Scholarship Council (No. 201709505007). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Decision Letter 0

Tobias Isaac Baskin

13 Mar 2020

PONE-D-20-04662

Phosphorus assimilation effects by root exuded compounds across plant developmental stages

PLOS ONE

Dear Dr. Vivanco,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Generally both reviewers liked your paper and neither suggested or required new experiments. However both of them made comments about the presentation and language. Reviewer 1 brings up some fairly substantial conceptual points. Please consider these and revise your text accordingly . Reviewer 2 has a large number of small but interesting comments and suggestions. The more of these that you can attend to, the better your paper will be. 

In addition, I read parts of your paper and have a few comments of my own. 

Line 1. Title. Your title is difficult to parse. Please rewrite. For example: “On the role of root exudates on the assimilation of phosphorus in young and old roots”. 

Line 26, and elsewhere. Please spell out phosphorus everywhere in the text. Do not use “P”. I am aware that many authors use this abbreviation. However repeated use is a poor argument for validity. In fact, abbreviations and acronyms make a text difficult to read. Abbreviations rarely occur in newspapers or fiction. Any time a reader encounters a symbol (P is a symbol for phosphorus), they must translate that symbol into words. Translation takes mental energy away from comprehension. Translation slows down the reader and gives nothing in return. It is one thing to have to write about a chemical with a name that is 38 syllables long. In that case, the name is just as difficult to read as the acronym. However phosphorus is a good word of the English language. In fact, phosphorus literally means ‘carrier of light’. Rather beautiful. Spell it out. 

Line 26. “… have not been conducted…” This wording implies that you have read every paper ever published. Use less extreme wording, such as “…rarely if ever…”

Line 29. You are using the word ‘metabolome’, to refer to root exudates. This is misleading and confusing. The word metabolome refers to all of the metabolites in the cell or organism. However here, you are not measuring the metabolome. Instead you are measuring exudates. These compounds number about a dozen, far less than the threshold for ‘omics’.  Please remove the word ‘metabolome’ throughout the paper and instead talk about ‘total exudates’ or the equivalent.  For example, the sentence staring at line 29 can read: “The composition of root exudates changed in response…”

Lines 29 and 34. You write ‘in vitro’ conditions. What does this mean? Instead say what the conditions are. By the way, typically in vitro implies isolated components, cells or cell fragments. I have never seen in vitro used for whole organisms. Also you write ‘solid’ and ‘liquid media conditions’. Again, be specific, say what the solid and liquid media are. 

Line 31. What does ‘respond negatively’ mean? If you mean decreased in quantity, just say so. 

Line 66. Based on long-established rules for scientific nomenclature, the word “Arabidopsis” (Capital A, italic font) means the genus. No matter how many illiterate molecular biologists make this mistake, rules of taxonomic nomenclature remain in force until the international committee decrees otherwise. Longstanding practice allows “arabidopsis” (lower case a, Roman font) as the common name of our friendly lab weed; however, many journals will auto-correct this by adding a capital and italics. I am not sure about PLoS One. Thus, either use ‘arabidopsis’ and hope the journal lets it stand, or use A. thaliana(italics) (but Arabidopsis thalianaat first mention). 

Line 83. This should read “Arabidopsis thalianaL. (Heynh) wild-type Columbia seed…” It is customary in the Material and Methods to give the full Latin binomial along with the taxonomic authority. And unless you sequenced your Columbia line, you should drop the “0”.

Line 84, and elsewhere. Do not use circle-R, or TM, or other commercial symbols. Those marks exist to protect consumers (not manufacturers) from fraud. Thus if you sell a product that you say contains X circle-R, you are defrauding the consumer if you substitute something cheaper for X. There is no such issue here. In fact you are not selling anyone anything (you are paying). 

Line 98. I don’t understand the meaning of the word ‘power’ here. 

You embedded the figure legends into the results text but not the figures. I think this is awkward. Please put the figure legends with the figures, preferably at the end of the text. Also for the principal component analyses, please simply call your x and y axes “PC1” and “PC2” and put the percentages of explained variance in the figure legend. 

In figure 3A, the names of some compounds are capitalized but others are not. And “control” is in all caps. This is bizarre. I suggest that none of them should be capitalized, but whatever you do please do the same for all. And note that if you choose to capitalize the first letter, this should be done even for those compounds that start with a number (e.g., “5-Aminovaleric acid”). Also, please put the name of the horizontal axis below, next to the numbers (or put the numbers above, next to the name; the point is, the numbers and the name belong together. 

Also please remember that the abbreviation for liter is L (not l). And to always put a space between the number and the unit (except when the unit is the degree sign or the percent sign). 

In Figure 4, there are problems with the y-axes. Many of them have huge numbers. But no units. I think peak area is arbitrary so you could use 1, 2, 3. If it is needed to compare the quantity between states, then you could have the smallest numbers be 1, 2, 3 and the other states relative to that. Also many of the graphs do not start at zero. But some of them do. This is misleading. They should all start at zero. The names of the axes could be in a larger font. 

We would appreciate receiving your revised manuscript by Apr 27 2020 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Tobias Isaac Baskin

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Two minor and three major critics

minor:

1. Root exudates depending on plant develpment were reported by Keerthisinghe et al. 1998, Plant Cell Environ., 21, 467- 478 and by Neumann et al., 1999, Planta, 208, 373- 382.

2. L 278 ff. Misleading since P and carboxylate concetrations must be clearly separated.

major:

1. Misleading: P starvation response 50 µM P. Cultivation in non buffered systems, agar or solution means that a solution threshald is only valid for a special volume. In soil P is buffered and P starvation values are below 2 µM P , see Föhse te al., 1988, Plant Soil, 110, 101- 109.

2. Decisive for the solubilizing ability of root exudates is the relation between soil solid P and the quatity of exudates (see in detail Gerke, 2015, cited in the ms). Solution concentrations are not an appropriate measure of exudate efficiency. Mesurement of pH changes as a central factor of P mobilization from Ca-P forms?

3. The relevance of the results with respect to P solubilization is questionable since the P form is rather unrepresentative and the exudate quantity is rather high.

Reviewer #2: General comments:

The manuscript “Phosphorus assimilation effects by root exuded compounds across plant developmental stages” characterises root exudates across growth stages and P-levels for Arabidopsis. Interesting contrasts were found. The authors select some important exuded compounds and go on to test their ability at solubilising P in soil-analogues individually and together. This was a well written manuscript, with well thought out experiments, executed well leading to interesting results. I really enjoyed reading this manuscript, I learnt a lot that is relevant to my work, and appreciated the work that went into it. I have some general comments that I think would improve the presentation and some of the discussion.

1) I think in the materials and methods the presentation of the PCA is sometimes over complicated, and could be made simpler. My detailed comments below would address this.

2) The presentation of the PCA results could be improved. I think showing all the data with no groupings used on the PC-axis (with different colours and marker styles and legends!) would make it much clearer an. This could come at the expense of some of the plots where treatments are grouped. Also make it clear if a PCA is done per grouping or not. Again, many of my detailed comments try and address this.

3) The discussion would be improved by quickly pointing out the agricultural/ecological significance (or lack of) of the results. For example 7mM of acids order of magnitude more than what is found in the rhizosphere. See the Eva Oburger papers I referenced. Hence the solubilisation seen here might not appear in the field. One of our group's papers found that P solubilisation by a single root exuding citrate at a realistic rate actually made no difference to P uptake by the root https://doi.org/10.1007/s11104-019-04376-4 (dont feel you have to reference this). It also might be worth pointing out how similar NBRIP media is to soil, solubilisation in this media might not be the same as soil. Also see my detailed comment regarding your proposed mechanism number 1.

Sorry, I have a lot of detailed comments, however many of them are pointing out the same thing and many are complimentary. I hope they aren’t too hard to deal with.

Detailed comments:

L25: roots->root

Abstract is clear and well written.

The paragraph starting line 67 doesn’t segway smoothly into that starting on 73 because root exudates have been shown to be less important for good P conditions (not to say that the paragraph on L67 isnt useful introductory information). Calling back to the ‘legacy P’ argument here would make it smoother.

L90: ‘gradient’ isn’t the best word here. It makes it seem like the growth media each plant is grown in has a gradient of P conditions in it. Is ‘The low P conditions used in this study….’ Better?

L129: ‘…which compounds had the highest correlation with these components through the magnitude of the variance’. ‘correlation’ is unclear here. Do you mean which two original basis vectors (compounds) explained the most variance? This would be an easier way of explaining it.

L133: ‘The largest…’ Is it not that these compounds explain the most variance? Its best to write these in terms of what percent of the original variance they explain (before dimension reduction).

L134: differential isn’t the right word here.

I think the end of this paragraph can be explained in a simpler way by saying: “We determined which compounds explained the most variance for each P level and growth stage. The contrasts in these ‘most principle compounds’ over growth stage and P level indicated differences in exudation depending on these factors” Or something like this.

L144: This needs more explanation this is quite a large range, how did you ‘adjust’ the concentrations? The reader needs to know how this is done to interpret the results. Did you take concentrations from these references to calibrate your values? Due to the variability in reported exudate concentration due to sampling technique (https://doi.org/10.1016/j.rhisph.2018.06.004) ‘exudate concentration’ is relative to the study. Probably needs a mention in the discussion.

Side note: Could be worth mentioning that you didn’t adjust the concentrations for the PCA, when I first read it I thought you had.

L152: What concentrations did you add to test the P solubilising ability of the compounds? Were they comparable to rhizospshere concentrations? Knowing this puts this into an ecological context for the reader. Is the visual inspection for solubility standard? Add a reference if so. Otherwise explain the reasoning.

Table 1: were they diluted to 100mM before PCA? Would this effect PCA? (see my side note above). 100mM is a really high concentration for most root exudates in the rhizosphere no? I know for most organic acids and amino acids I would expect micro molar concentrations in the rhizosphere, see https://doi.org/10.1016/j.envexpbot.2012.11.007

L171: again this a high concentration for the rhizosphere, I would expect a discussion on the ecological relevance later.

L181: I think ‘cumulative’ effect is better than ‘additive’. Additive makes it seem like you could add up the effects individually to determine to summed effect.

L200: unclear what ‘distribution’ means here. After looking at FigS1 we see it’s the groupings after plotting on the first two principle components. This needs to be made clearer. I think the author means the separation of growth stage and P treatment by PCA persists after throwing away the non-annotated compounds. Which implies the non-annotated compounds explained little of the variance, which I believe justifies the author’s conclusion. Were the principle components determined twice i.e. before and after throwing away the non-annotated compounds? FigS1 could use a legend saying what the other colours are.

Fig 1A also needs a legend.

In Fig 1A did you group by developmental stage, do PCA then plot? If this is the case, the % variance explained by the PCs reported in line 203 isnt correct.

Same goes for Fig 1B but by P level? The different percent of variance explained by components suggests this is the case. Need legend for Fig 1B also.

I would use colours to indicate developmental stage and stars/dots/crosses to indicate P-levels (or vice versa). This and a legend would make fig 1 a lot easier to understand.

Fig 1A caption is wrong “201 annotated compounds with proper identification detected using GC-MS are plotted on the Principal Component Analysis (PCA) graph”. The compounds aren’t plotted. The compounds are the 201-axis, the dimension is then reduced to 2-axis with PCA and the locations of the growth stages are plotted.

L205: “We determined that the plant’s developmental stage was responsible for

the separation of the compounds in three marked groups” to convince the reader that its not P level you would need to not group by anything and plot all the data with stars/dots/crosses and colors.

All these figures desperately need legends (Fig1, S1, S2) and clearly state if there is a PCA per grouping.

L230: explained the most variance.

L231: ‘correlation’ isn’t really defined here. Its more that the compounds which point in the most similar direction to the two principle components, I would get rid of the bit after the comment.

Change this sentence to: For each of these treatments, we found the five top compounds that explained the largest proportion of the variance.

Figs S3-S4 are really intresting! Great results

Same goes for Fig 2 and 3A

L254: does the 1.75 7 and 28 mM mean that the sum of the concentrations or each have that concentration? Fig 3 caption makes this clear but also make it clear in the manuscript.

L255: The 1.75M is really interesting, 7mM of them mixed does worse than 7mM of any individually

Again, really interesting results with Fig 4, very hard to interpret though there is lots going on.

L300: …’where optimum conditions are scare’ -> where nutrients are scarce ??

L304: These papers might be useful for this discussion on maize need for P early on with respect to yield: https://doi.org/10.1007/s11104-011-0814-y. https://www.nrcresearchpress.com/doi/pdfplus/10.4141/P00-093) Take them or leave them

L309: ‘similarity’ do you mean they grouped close together in the PSA? To talk about similarity you would need to use a norm between the treatments.

L323: I think your mention of other functions of exudates is a good explanation and something other authors overlook.

346: that ‘the’ shouldn’t be there

L351: new paragraph

L352: mechanism 1. Your results suggest there is no synergy (in fact the opposite) in terms of P solubilisation by root exudates, see my comment about L255, at least for the 4 acids you picked out. But this doesn’t disprove your mechanism: I think I read somewhere that certain exudates solubilise P from certain soil surfaces, Al oxides, Fe oxides etc (possibly a paper by Gerke about citrate and malate?) Maybe this is why they exude a mixture of acids? Did the soil-analogue you used have this variability in mineral surfaces which soil has?

Nonetheless, I think this deserves some more discussion.

L357. I like point 2, I had never heard of this before.

I don’t think Table S1 is mentioned in the manuscript

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PLoS One. 2020 Jun 3;15(6):e0234216. doi: 10.1371/journal.pone.0234216.r002

Author response to Decision Letter 0


6 Apr 2020

Reviewers responses:

Line 1. Title. Your title is difficult to parse. Please rewrite. For example: “On the role of root exudates on the assimilation of phosphorus in young and old roots”.

RESPONSE: Thank you. As suggested, the title was rewritten and now it reads as follow: ‘Role of root exudates on assimilation of phosphorus in young and old Arabidopsis thaliana plants

Line 26, and elsewhere. Please spell out phosphorus everywhere in the text. Do not use “P”. I am aware that many authors use this abbreviation. However repeated use is a poor argument for validity. In fact, abbreviations and acronyms make a text difficult to read. Abbreviations rarely occur in newspapers or fiction. Any time a reader encounters a symbol (P is a symbol for phosphorus), they must translate that symbol into words. Translation takes mental energy away from comprehension. Translation slows down the reader and gives nothing in return. It is one thing to have to write about a chemical with a name that is 38 syllables long. In that case, the name is just as difficult to read as the acronym. However phosphorus is a good word of the English language. In fact, phosphorus literally means ‘carrier of light’. Rather beautiful. Spell it out.

RESPONSE: Thanks for the suggestion and wonderful comments particularly related to “carrier of light”. The abbreviation for phosphorus was changed for the full word throughout the manuscript.

Line 26. “… have not been conducted…” This wording implies that you have read every paper ever published. Use less extreme wording, such as “…rarely if ever…”

RESPONSE: Thanks for the suggestion. We have changed ‘have not been conducted’ for ‘remain scarce’.

Line 29. You are using the word ‘metabolome’, to refer to root exudates. This is misleading and confusing. The word metabolome refers to all of the metabolites in the cell or organism. However here, you are not measuring the metabolome. Instead you are measuring exudates. These compounds number about a dozen, far less than the threshold for ‘omics’. Please remove the word ‘metabolome’ throughout the paper and instead talk about ‘total exudates’ or the equivalent. For example, the sentence staring at line 29 can read: “The composition of root exudates changed in response…”

RESPONSE: Thanks. We agreed with the editor. We replaced the word metabolome for total root exudates and/or total exudate profile throughout the manuscript.

Lines 29 and 34. You write ‘in vitro’ conditions. What does this mean? Instead say what the conditions are. By the way, typically in vitro implies isolated components, cells or cell fragments. I have never seen in vitro used for whole organisms. Also you write ‘solid’ and ‘liquid media conditions’. Again, be specific, say what the solid and liquid media are.

RESPONSE:

Thank you for the recommendation. To make the distinction, we have replaced the word in vitro for ‘sterile nutrient solution’.

The type of media described as solid and liquid is a microbiological growth medium for screening phosphate solubilizing microorganisms known as NBRIP (National Botanical Research Institute’s phosphate) growth media. This information appears in the material and methods. In line 29-34 (now 36) we have specified the type of liquid and solid media and it reads now as: “solid and liquid NBRIP media conditions”.

Line 31. What does ‘respond negatively’ mean? If you mean decreased in quantity, just say so.

RESPONSE: Thank you. Changes were made accordingly and now the sentence reads as follows: ‘It was found that specific metabolites decreased in quantity related to phosphorus supplementation at specific stages of development.’

Line 66. Based on long-established rules for scientific nomenclature, the word “Arabidopsis” (Capital A, italic font) means the genus. No matter how many illiterate molecular biologists make this mistake, rules of taxonomic nomenclature remain in force until the international committee decrees otherwise. Longstanding practice allows “arabidopsis” (lower case a, Roman font) as the common name of our friendly lab weed; however, many journals will auto-correct this by adding a capital and italics. I am not sure about PLoS One. Thus, either use ‘arabidopsis’ and hope the journal lets it stand, or use A. thaliana(italics) (but Arabidopsis thalianaat first mention).

RESPONSE: Thanks for the observation. Arabidopsis thaliana was first mentioned in the abstract and ‘Arabidopsis’ word was replaced by A. thaliana throughout the manuscript.

Line 83. This should read “Arabidopsis thalianaL. (Heynh) wild-type Columbia seed…” It is customary in the Material and Methods to give the full Latin binomial along with the taxonomic authority. And unless you sequenced your Columbia line, you should drop the “0”.

RESPONSE: Thanks for the observation. The sentence was modified and now it reads as follows: ‘A. thaliana (L.) Heynh wild-type Columbia seeds’.

Line 84, and elsewhere. Do not use circle-R, or TM, or other commercial symbols. Those marks exist to protect consumers (not manufacturers) from fraud. Thus if you sell a product that you say contains X circle-R, you are defrauding the consumer if you substitute something cheaper for X. There is no such issue here. In fact you are not selling anyone anything (you are paying).

RESPONSE: Thank you. Changes were made accordingly.

Line 98. I don’t understand the meaning of the word ‘power’ here.

RESPONSE: Thank you. The word power is not necessary. It was deleted.

You embedded the figure legends into the results text but not the figures. I think this is awkward. Please put the figure legends with the figures, preferably at the end of the text. Also for the principal component analyses, please simply call your x and y axes “PC1” and “PC2” and put the percentages of explained variance in the figure legend.

RESPONSE: As suggested, figures and legends are together in a separate file uploaded right after the text.

All principal component analyses have been modified and the explained variance is now shown in the legend.

In figure 3A, the names of some compounds are capitalized but others are not. And “control” is in all caps. This is bizarre. I suggest that none of them should be capitalized, but whatever you do please do the same for all. And note that if you choose to capitalize the first letter, this should be done even for those compounds that start with a number (e.g., “5-Aminovaleric acid”). Also, please put the name of the horizontal axis below, next to the numbers (or put the numbers above, next to the name; the point is, the numbers and the name belong together.

Also please remember that the abbreviation for liter is L (not l). And to always put a space between the number and the unit (except when the unit is the degree sign or the percent sign).

RESPONSE: Thanks for the observation. The first letters of all compounds have been capitalized, and the horizontal axis is now next to the numbers. The abbreviation L and the space between the number and the unit was also modified as suggested.

In Figure 4, there are problems with the y-axes. Many of them have huge numbers. But no units. I think peak area is arbitrary so you could use 1, 2, 3. If it is needed to compare the quantity between states, then you could have the smallest numbers be 1, 2, 3 and the other states relative to that. Also many of the graphs do not start at zero. But some of them do. This is misleading. They should all start at zero. The names of the axes could be in a larger font.

RESPONSE: Thank you for the observation. The y-axis values show the magnitude of the cumulative secretion level of the compound per each stage. Those values are different based on the compounds. Thus, standardizing the values for all compounds will make some compounds hard to asses due to low levels. This set of plots aimed to provide to the reader with a visual aid to see significant differences by compound between the phosphorous treatments.

We think keeping the peak area unit as it is will help the reader to determine the degree of change (of the compound) in response to P amendment as well as to locate the compound that was the most affected by phosphorus amendment.

With respect to graphs not starting at zero: the compounds with statistical significance are properly labeled which will help the reader to see which of those secretion levels are highly responsive to phosphorus addition. We do not think this is misleading and we would rather keep it as it is.

Reviewer #1: Two minor and three major critics

minor:

1. Root exudates depending on plant develpment were reported by Keerthisinghe et al. 1998, Plant Cell Environ., 21, 467- 478 and by Neumann et al., 1999, Planta, 208, 373- 382.

RESPONSE: We appreciate your valuable comments. Both papers are very relevant for our work, and we have included references about that work in our manuscript. We modified the abstract to state that: ‘However, studies addressing the variability of roots exudates involved in phosphorus solubilization across plant developmental stages remain scarce’. Instead of saying that these studies ‘have not been conducted’. Having said this, in contrast with Keerthisinghe et al. (1998) and Neumann et al., (1999), our study showed effects of P supply on non-proteoid plant-roots such as Arabidopsis.

Neumann et al., (1999) support our findings showing that phosphorus mobilizing compounds such as citric acid was predominantly restricted to mature root clusters in the later stages of P deficiency. However, they conclude that this mechanism is ‘predominantly confined to proteoid-roots’ which is not the case for Arabidopsis as shown in our study. We have incorporated this to the discussion section.

2. L 278 ff. Misleading since P and carboxylate concetrations must be clearly separated.

RESPONSE: Thank you for the observation. We have rewritten this sentence to better describe how cumulative secretion of different carboxylates vary depending on the treatment (phosphorus level) and to make the distinction between phosphorus and carboxylates. Now the sentence reads as follows: ‘Cumulative secretion of malic acid was reduced significantly from 0.3125 to 0.625 mM phosphorus treatments, and then incremented its cumulative secretion for the highest phosphorus treatment (1.25 mM). However, secretion levels of malic acid for the two highest phosphorus treatments (0.625 and 1.25 mM) were below the value for the lowest phosphorus rate (0.3125 mM) (Fig 4A).’

major:

1. Misleading: P starvation response 50 µM P. Cultivation in non buffered systems, agar or solution means that a solution threshald is only valid for a special volume. In soil P is buffered and P starvation values are below 2 µM P , see Föhse te al., 1988, Plant Soil, 110, 101- 109.

RESPONSE: Thank you for the clarification. As per your suggestion, we clarified that plant starvation response to phosphorus is activated at values below 2 µM P. We have added Föhse et al., (1988) reference to the manuscript and the sentence now reads as follows: ‘The three phosphorus levels used in this study did not induce the plant starvation response, which is generally activated at values below 2 μM of phosphorus in the soil solution [23].

2. Decisive for the solubilizing ability of root exudates is the relation between soil solid P and the quatity of exudates (see in detail Gerke, 2015, cited in the ms). Solution concentrations are not an appropriate measure of exudate efficiency. Mesurement of pH changes as a central factor of P mobilization from Ca-P forms?

RESPONSE: We appreciate your valuable comment. We are aware that a combination of factors including carboxylate efflux, the accumulation of carboxylate in the rhizosphere and the chemistry of phosphorus mobilization in the soil phase affect the solubilization ability of root exudates (Gerke, 2015). We acknowledge that we did not take into account these variables, because our study was entirely done in liquid culture to test solubilization ability of the selected compounds, not necessarily efficiency which would require the measurement of abovementioned factors. However, we have added a paragraph in the discussion section that address pros and cons of root exudate studies in liquid conditions (our study).

The paragraph added reads as follows: ‘Lastly, root exudates from liquid culture systems allow the determination of exudation rates unaltered by the soil matrix or microbial decomposition if performed under sterile conditions as we did in this study (Oburger and Jones, 2015). However, the quality and quantity of the root exudate profile may be impacted by the nutrient solution culture method (also known as hydroponic methods) (Oburger et al., 2013). Soil-hydroponic hybrids methods for root exudation collection are not exempt of potential physical/physiological perturbances. Thus, sterile nutrient solution culture methods remain especially important to assess temporal dynamics of root exudates.’

3. The relevance of the results with respect to P solubilization is questionable since the P form is rather unrepresentative and the exudate quantity is rather high.

RESPONSE: Thank you for your observation. It would be helpful if the reviewer elaborates on his comment. Why are the P form is unrepresentative? Is it because calcium phosphate is not necessarily predominant in all agricultural soils? Calcareous soils constitute over one-third of the world’s land area. Why you consider the root exudate quantity as high, relative to what? Root exudates concentration varies a lot across P levels, developmental stage and on a per compounds basis in our study.

Reviewer #2: General comments:

The manuscript “Phosphorus assimilation effects by root exuded compounds across plant developmental stages” characterises root exudates across growth stages and P-levels for Arabidopsis. Interesting contrasts were found. The authors select some important exuded compounds and go on to test their ability at solubilising P in soil-analogues individually and together. This was a well written manuscript, with well thought out experiments, executed well leading to interesting results. I really enjoyed reading this manuscript, I learnt a lot that is relevant to my work, and appreciated the work that went into it. I have some general comments that I think would improve the presentation and some of the discussion.

1) I think in the materials and methods the presentation of the PCA is sometimes over complicated, and could be made simpler. My detailed comments below would address this.

RESPONSE: Thanks for the valuable observations. Detail corrections regarding the PCA plots have been addressed in each of your comments below.

2) The presentation of the PCA results could be improved. I think showing all the data with no groupings used on the PC-axis (with different colours and marker styles and legends!) would make it much clearer an. This could come at the expense of some of the plots where treatments are grouped. Also make it clear if a PCA is done per grouping or not. Again, many of my detailed comments try and address this.

RESPONSE: Thanks for the valuable observations. Detail corrections regarding the PCA plots have been made and addressed in each of your comments below.

3) The discussion would be improved by quickly pointing out the agricultural/ecological significance (or lack of) of the results. For example 7mM of acids order of magnitude more than what is found in the rhizosphere. See the Eva Oburger papers I referenced. Hence the solubilisation seen here might not appear in the field. One of our group's papers found that P solubilisation by a single root exuding citrate at a realistic rate actually made no difference to P uptake by the root https://doi.org/10.1007/s11104-019-04376-4 (dont feel you have to reference this). It also might be worth pointing out how similar NBRIP media is to soil, solubilisation in this media might not be the same as soil. Also see my detailed comment regarding your proposed mechanism number 1.

RESPONSE: Thank you for the observations. We have added a paragraph that discusses the relevance and ecological significance of organic acids as phosphorus mobilizers and the relevance of the root exudate analysis in liquid cultures.

The new paragraph reads as follows: ‘It has been estimated that organic acids constitute 5 to 10 % of the total organic carbon in the soil solution. The concentration of organic anions measured in the soil solution usually range from 100 nM to more than 580 uM in the rhizosphere of cluster roots (Jones, 1998). However, millimolar concentrations of organic anions are likely required in the soil solution to effectively increase soluble P concentration especially in calcareous soils (Strom et al. 2005; Ryan and Jones, 2001). Strom et al. (2005) tested three organic acids (citrate, malic and oxalate) and a wide range of concentrations (1 mM to 100 mM) to evaluate its effects on the mobilization of phosphorus in calcareous soil. The results showed that the phosphorus mobilization of the tested compounds had a low efficiency and its effect varied depending on the type of organic acid, compound concentration, and pH. Further, due to the low phosphorus mobilization efficiency of those compounds it is still argued if the benefit of releasing large amounts of organic acids into the soil will exceed the cost of carbon lost by the plant, which can be seen as an unnecessary trade-off (Strom et al. 2005). However, low efficiency organic acids can be particularly important in phosphorus mobilization for calcareous soils with a limited phosphorus availability for plants. Finally, our evidence supports the above-mentioned hypothesis, that plants release a combination of compounds with different phosphorus-solubilizing efficiencies, at specific stages of growth, to deal with particular phosphorous needs.’

Sorry, I have a lot of detailed comments, however many of them are pointing out the same thing and many are complimentary. I hope they aren’t too hard to deal with.

Detailed comments:

L25: roots->root

RESPONSE: Thank you. Please see correction in line 28.

Abstract is clear and well written.

The paragraph starting line 67 doesn’t segway smoothly into that starting on 73 because root exudates have been shown to be less important for good P conditions (not to say that the paragraph on L67 isnt useful introductory information). Calling back to the ‘legacy P’ argument here would make it smoother.

RESPONSE: Thank you for the observation. We considered your suggestion and have improved the transitioning sentence between the two paragraphs. Now it reads as follows: ‘Due to the variation of phosphorus demand during the plant’s lifetime, it becomes necessary to fully understand fluctuations of root exudates as a means to solubilize the phosphorous present in the P legacy of the soil.’

L90: ‘gradient’ isn’t the best word here. It makes it seem like the growth media each plant is grown in has a gradient of P conditions in it. Is ‘The low P conditions used in this study….’ Better?

RESPONSE: The authors used gradient to refer to the three concentrations of phosphorous used in the study. For clarity, we changed it to: ‘The three phosphorus levels used in this study did not stimulate the plant starvation response, which is generally activated around 2 μM of P [23].’

L129: ‘…which compounds had the highest correlation with these components through the magnitude of the variance’. ‘correlation’ is unclear here. Do you mean which two original basis vectors (compounds) explained the most variance? This would be an easier way of explaining it.

RESPONSE: Thank you for the observation. No, in this sentence (now line 140) we refer to the magnitude of the loadings of the compound (variance of the compound secretion level) not to the PCA explained variance. We elaborate on the meaning in more detail in the two following sentences in the manuscript.

L133: ‘The largest…’ Is it not that these compounds explain the most variance? Its best to write these in terms of what percent of the original variance they explain (before dimension reduction).

RESPONSE: Here we refer to the variance of the individual compounds based on the secretion level (loadings). Compounds with the largest loadings drive the PCA variance and therefore were selected for further testing. Please see line 131 to 146 for more detail.

L134: differential isn’t the right word here.

I think the end of this paragraph can be explained in a simpler way by saying: “We determined which compounds explained the most variance for each P level and growth stage. The contrasts in these ‘most principle compounds’ over growth stage and P level indicated differences in exudation depending on these factors” Or something like this.

RESPONSE: Thank for your suggestion. We have modified the sentence for clarity and now it reads as follows: ‘this method allowed us to determine which compounds explained most of the variance across the fertilizer levels and for each of the plant’s growth stages.’

L144: This needs more explanation this is quite a large range, how did you ‘adjust’ the concentrations? The reader needs to know how this is done to interpret the results. Did you take concentrations from these references to calibrate your values? Due to the variability in reported exudate concentration due to sampling technique (https://doi.org/10.1016/j.rhisph.2018.06.004) ‘exudate concentration’ is relative to the study. Probably needs a mention in the discussion.

Side note: Could be worth mentioning that you didn’t adjust the concentrations for the PCA, when I first read it I thought you had.

RESPONSE: Thanks for your observations. As stated in the text, we used a range of concentrations reported in the literature as a reference to select the concentration of the compounds tested in this study. The word ‘adjust’ has been replaced by the word ‘select’ for clarity.

As you well pointed out, the range of concentrations of this compound is wide. We cited 3 papers that support that the concentrations used in our experiments are present in the rhizosphere (Jones, 1998; Veneklaas et al., 2003 and Ström et al., 2005). In addition, we have added a paragraph in the discussion where we elaborate on the concentrations of compounds selected for this study (please see previous answer to your comment) and included the paper that you suggested: Oburger and Jones, 2018.

L152: What concentrations did you add to test the P solubilising ability of the compounds? Were they comparable to rhizospshere concentrations? Knowing this puts this into an ecological context for the reader. Is the visual inspection for solubility standard? Add a reference if so. Otherwise explain the reasoning.

RESPONSE: Thank you for the comments. We direct the reviewer to the methodology sub-section (149-160) where the rationale for selecting the concentrations to test P solubilization and the actual concentrations are stated; as well as the paper showing the efficacy of the qualitative technique used in our study. Please see reference number 30 in the reference list (Nautiyal et al., 1999. FEMS microbiology Letters, 170(1), 265-270).

Table 1: were they diluted to 100mM before PCA? Would this effect PCA? (see my side note above). 100mM is a really high concentration for most root exudates in the rhizosphere no? I know for most organic acids and amino acids I would expect micro molar concentrations in the rhizosphere, see https://doi.org/10.1016/j.envexpbot.2012.11.007

RESPONSE: Thanks for the observation. Indeed, PCA show total root exudates as a response to phosphorus levels. We agree, 100 mM is in the higher end of the concentrations. This concentration was used only in the qualitative experiment (Petri dish). Several lower concentrations were used as well, and we decided to use 100 mM for this qualitative analysis which aimed to provide an initial visual tool to narrow down a long list of compounds that could solubilize P. Please note that we reduced this concentration to 7 mM and the compounds still showed phosphorus solubilization.

L171: again this a high concentration for the rhizosphere, I would expect a discussion on the ecological relevance later.

RESPONSE: This question was addressed above.

L181: I think ‘cumulative’ effect is better than ‘additive’. Additive makes it seem like you could add up the effects individually to determine to summed effect.

RESPONSE: Thank you. We replaced the word additive for the word ‘cumulative’ to better describe the meaning.

L200: unclear what ‘distribution’ means here. After looking at FigS1 we see it’s the groupings after plotting on the first two principle components. This needs to be made clearer. I think the author means the separation of growth stage and P treatment by PCA persists after throwing away the non-annotated compounds. Which implies the non-annotated compounds explained little of the variance, which I believe justifies the author’s conclusion. Were the principle components determined twice i.e. before and after throwing away the non-annotated compounds? FigS1 could use a legend saying what the other colours are.

RESPONSE: Thank you. For clarity, the word distribution has been replaced by the word “grouping”. In addition to indicating that the PCA was conducted with the data after removal of the non-annotated compounds, we have modified this sentence and now it reads as follow: ‘The variability in our data after subtracting the non-annotated compounds was analyzed using a principal component analysis (PCA) where variability of component 1 (PC1) accounted for 29.8%, while component 2 (PC2) accounted for 21.7%.’

PCA from figure 1 is identical than supplementary figure 1. Both depict the overall dissimilarity of compound groups across phosphorus levels and growth stages. Both figures show detailed information in the legend now.

Fig 1A also needs a legend.

RESPONSE: Thank you. Figure 1A has now a legend with the suggested information.

In Fig 1A did you group by developmental stage, do PCA then plot? If this is the case, the % variance explained by the PCs reported in line 203 isnt correct.

RESPONSE: Thank you for the comment. For figure 1 as well as for supplementary figure 1, no grouping was performed before constructing the PCA. The complete data set from three developmental stages and 3 levels were plotted and analyzed at the same time without previous modification. As suggested, the explained variance of figure 1A was added to the legend. For more detail, please see line 132-144.

Same goes for Fig 1B but by P level? The different percent of variance explained by components suggests this is the case. Need legend for Fig 1B also.

RESPONSE: In figure 1A, we present the three plant stages and three phosphorus levels (all data). Figure 1B presents data for three phosphorus levels within the vegetative stage only, and figure 1C presents the three phosphorus levels within the vegetative stage only. The explained variance for each PCA has been added to the figure legend.

I would use colours to indicate developmental stage and stars/dots/crosses to indicate P-levels (or vice versa). This and a legend would make fig 1 a lot easier to understand.

Fig 1A caption is wrong “201 annotated compounds with proper identification detected using GC-MS are plotted on the Principal Component Analysis (PCA) graph”. The compounds aren’t plotted. The compounds are the 201-axis, the dimension is then reduced to 2-axis with PCA and the locations of the growth stages are plotted.

RESPONSE: Thank you for the clarification. Your observation is technically correct. We have replaced the word plotted. Now, the sentence reads as follows: ‘201 annotated compounds with proper identification detected using GC-MS were analyzed using a Principal Component Analysis (PCA) graph.’

With respect to editing the colors. The phosphorus levels and growth stages are color-coded, and the information related to each treatment is explained in the legend. We would rather keep the graphs as they are currently.

L205: “We determined that the plant’s developmental stage was responsible for

the separation of the compounds in three marked groups” to convince the reader that its not P level you would need to not group by anything and plot all the data with stars/dots/crosses and colors.

All these figures desperately need legends (Fig1, S1, S2) and clearly state if there is a PCA per grouping.

RESPONSE: Thank you. This comment was addressed in the previous answers.

L230: explained the most variance.

RESPONSE: Thank you. Following your suggestion, we have corrected this sentence and now it reads as follows: ‘For each of these treatments, we found the five top compounds that explained the largest proportion of the variance in the principal components (Table 1).’

L231: ‘correlation’ isn’t really defined here. Its more that the compounds which point in the most similar direction to the two principle components, I would get rid of the bit after the comment.

Change this sentence to: For each of these treatments, we found the five top compounds that explained the largest proportion of the variance.

RESPONSE: Thanks. We added this suggestion in the previous response.

Figs S3-S4 are really intresting! Great results

Same goes for Fig 2 and 3A

RESPONSE: Thank you.

L254: does the 1.75 7 and 28 mM mean that the sum of the concentrations or each have that concentration? Fig 3 caption makes this clear but also make it clear in the manuscript.

RESPONSE: Good observation. Each compound added to the pool had 1.75 mM, 7 mM and 28 mM concentration. We have added this detail in the manuscript. As explained in the methodology section line 189-195: ‘In order to determine the potential cumulative effect of 3-hydroxypropionic acid, malic acid, nicotinic acid, and glutamic acid they were combined and the available phosphorus (mg l-1) was determined by OES-ICP. A phosphorus gradient that included the previous tested concentration (7 mM per compound), a higher (28 mM per compound) and a lower (1.75 mM per compound) concentration was tested in order to compare if the combination of compounds would equal or surpass the effect of a single compound. Each compound added to the pool had 1.75 mM, 7 mM and 28 mM concentration. Thus, the combination effect of four compounds were tested in a liquid NBRIP medium.’

L255: The 1.75M is really interesting, 7mM of them mixed does worse than 7mM of any individually

Again, really interesting results with Fig 4, very hard to interpret though there is lots going on.

RESPONSE: Each compound has a different molarity; therefore we cannot say that the 4 compounds at 1.75 mM add up to 7mM. We conclude that 1) compounds in combination have an additive effect, and that 2) the addition of one does not inhibit the effect of the other.

L300: …’where optimum conditions are scare’ -> where nutrients are scarce ??

RESPONSE: Thank you. We have corrected this sentence and now it read as follows: ‘Thus, we hypothesized that at this growth stage roots did not respond to phosphorus fertilization. A. thaliana is considered a plant that can thrive in marginal soils where optimum nutrient conditions are limited.’

L304: These papers might be useful for this discussion on maize need for P early on with respect to yield: https://doi.org/10.1007/s11104-011-0814-y. https://www.nrcresearchpress.com/doi/pdfplus/10.4141/P00-093) Take them or leave them

RESPONSE: Thank you for the recommendation. As suggested, those two relevant papers were included one in the introduction section (Grant et al., 1999) and the second in the discussion section (Nadeem et al., 2011).

L309: ‘similarity’ do you mean they grouped close together in the PSA? To talk about similarity you would need to use a norm between the treatments.

RESPONSE: Thanks for the observation. We are referring to visual similarity. We have corrected by adding: ‘In the vegetative stage, the root exudates at 50% and 100% phosphorus showed greater visual similarity in the PCA than the exudates at 25% phosphorus, evidencing an initial sensing from the plant in response to its phosphorus demand.’

L323: I think your mention of other functions of exudates is a good explanation and something other authors overlook.

RESPONSE: Thank you.

346: that ‘the’ shouldn’t be there

RESPONSE: Thank you; ‘the’ was removed.

L351: new paragraph

RESPONSE: Thank you.

L352: mechanism 1. Your results suggest there is no synergy (in fact the opposite) in terms of P solubilisation by root exudates, see my comment about L255, at least for the 4 acids you picked out. But this doesn’t disprove your mechanism: I think I read somewhere that certain exudates solubilise P from certain soil surfaces, Al oxides, Fe oxides etc (possibly a paper by Gerke about citrate and malate?) Maybe this is why they exude a mixture of acids? Did the soil-analogue you used have this variability in mineral surfaces which soil has?

Nonetheless, I think this deserves some more discussion.

RESPONSE: We addressed this question in comment L255 above.

L357. I like point 2, I had never heard of this before.

RESPONSE: Thank you.

I don’t think Table S1 is mentioned in the manuscript

RESPONSE: Table S1 show data that is already presented in supplementary figure 3 and 4 in more detail. Therefore, is was deleted it.

Attachment

Submitted filename: Reviewers responses-0406.docx

Decision Letter 1

Tobias Isaac Baskin

8 May 2020

PONE-D-20-04662R1

Role of root exudates on assimilation of phosphorus in young and old Arabidopsis thaliana plants

PLOS ONE

Dear Dr. Vivanco,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

We are almost there. 

First I apologize for the length of time this step has taken. In addition the reviewers being late, there was a peculiar piece of administrative weirdness that I had to resolve before sending you the decision. That’s all set now. 

As you can see, reviewer 1 is totally satisfied and reviewer 2 raises only a couple of minor points. In fact, reviewer 2 has a very long comment about the ‘additive’ effect but in the revised manuscript, you have downplayed this, so I think most of the comment is moot. You may consider it as you see fit. However, reviewer 2 writes:

“I note the paper “Does the combination of citrate and phytase exudation in Nicotiana tabacum promote the acquisition of endogenous soil organic phosphorus?” which you cite for the synergy of exudates for P solubilisation is an experiment done in soil not NRIB.” Clearly this needs your attention. 

and writes:

“I think when describing the method for the cumulative experiment, you should make it clear whether the mixtures were all  added to 5 mL of liquid NBRIP so that the same amount of P is the same as the individual experiment. Currently it is unclear.”  And this too should be fixed. 

I also read the paper carefully. I uploaded the pdf with my edits. Most of these are places where your English is non-idiomatic or other small problems of style. I also added a few comments in places where I simply could not understand what you meant or where there was some other small problem. Where I understood, I offered a solution. I am not going to repeat them here but please go through them carefully as you revise. 

Two of these comments though I want to bring up here for emphasis. 

This first is the difference between phosphorus and phosphate. You use ‘phosphorus’ almost everywhere but I think this obscures an important difference. In experiments, you are fertilizing the plants with phosphate. I think it is sloppy to talk about adding “1 mM phosphorus” to the plants when you added 1 mM phosphate. Plants take up phosphate, not phosphorus. Likewise, your compounds act to dissolve phosphate. They do not free elemental phosphorus. It seems misleading to describe them as phosphorus-solubilizing compounds. Instead, phosphorus is more of a concept. It is reasonable to write about ‘phosphorus deficiency’ or like that. In some places, the choice is a bit arbitrary. In my edits, I changed ‘phosphorus’ to ‘phosphate’ where the sense was the specific chemical involved, which actually it usually was. 

The second comment concerns figure 3B where you check the solubilizing activity of combinations of the key compounds. The problem here is that you test the single compounds at 7 mM (Fig. 3A). But you test the combinations at that concentration, and also at lower and higher concentrations. I do not see how the higher and lower combinations can be interpreted without also showing values for the single compounds at each concentration. Without that data, I suggest adding the 7 mM combined results as the last bar of figure 3 A and deleting the data for the other combinations (unless you happen to have data for single compounds at the alternate concentrations). By the way, given that the combination solubilized about the same amount of phosphate as did 3-hydroxyproprionate alone, I don’t see how you can even think about an additive effect.

When you submit your revised ms, please do NOT use track changes for any of my edits on the text that you accept with no change. Instead, track only those places where you either do not use my edit at all or you modify it in some way. Also track any changes you make in response to reviewer two. 

All of this should be very straightforward and I expect the next round should go very much faster. 

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Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. The journal requires you to say something but you do not need to go thru all the small things. Just comment on anything where there is some disagreement, etc. 

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Tobias Isaac Baskin

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

**********

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The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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Reviewer #1: I Don't Know

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: The Ms should now be published in the present form.

One answer to the question the authors made:

Ca- phosphates may account for a high proportion of P in calcareous soils. However even in these soils as well as in other soils often P adsorbed to Fe/Al- surfaces is the oprincipal form of available P. This may be the case because in many soils P desorption from the soil solid phase is konetically and not thermodynamically controlled (see Gerke, 2015 and reference there).

Reviewer #2: Comments to the authors and editor:

Thank you for considering my comments so thoughtfully in the response. I believe the authors have answered the vast majority of my comments, I only have one outstanding query regarding the following in the response document:

'''

L255: The 1.75M is really interesting, 7mM of them mixed does worse than 7mM of any

individually

Again, really interesting results with Fig 4, very hard to interpret though there is lots going on.

RESPONSE: Each compound has a different molarity; therefore we cannot say that the 4 compounds at

1.75 mM add up to 7mM. We conclude that 1) compounds in combination have an additive effect, and

that 2) the addition of one does not inhibit the effect of the other.

'''

I think concluding there is an ‘additive effect’ is a bit miss leading. Here is the standard definition of an additive affect https://www.dictionary.com/browse/additive-effect. The sum of 7mM individually is much more than 7mM combined (I use the 7mmol case now so there is no issues with the molarity. Both cases has 7mM of each.) thus it is not an additive system. This is of course because in the individual cases are done in separate assays and they solubilise the lightly-bound P pool 4 times, while the combined is done in one assay. I think if you want to convince the reader that they are ‘additive’ (and later ‘synergize’ L348 in the discussion) you need to define exactly what it means for the current system to be additive or synergize. Possibly the current experiments and media aren’t suitable to make this conclusion. As I mentioned before, I suspect the compounds ‘synergise’ (I define this to mean to do better than the sum of its parts) when the media has a range of minerals that buffer P and are attacked more efficiently by certain exudates. For example (this is entirely hypothetical) assume the soil is made up of 50% Al-oxide and 50% Fe-oxide and nicotinic acid solubilises P from Al-oxide very effectively but badly from Fe-oxide and malic acid vice-versa. In this case the two compounds would certainly synergise. As I mentioned before I think there is papers about this but I cannot remember, the other reviewer Prof Gerke is likely to know about this and can point you in the right direction. I note the paper “Does the combination of citrate and phytase exudation in Nicotiana tabacum promote the acquisition of endogenous soil organic phosphorus?” which you cite for the synergy of exudates for P solubilisation is an experiment done in soil not NRIB.

I do not think more experiments or analysis is needed as this is a minor result in the overall paper, but a more careful discussion of this is needed in liight of the results.

I do agree with conclusion that the addition of one does not inhibit the other which is a good result in itself.

Detailed comments:

L187 (on tracked document): Should ‘A phosphorus gradient’ here instead be a ‘compound gradient’?

I think when describing the method for the cumulative experiment, you should make it clear whether the mixtures were all added to 5 mL of liquid NBRIP so that the same amount of P is the same as the individual experiment. Currently it is unclear.

I would like to point out to the editor that when responding to one of my comments they also partly answered one of reviewer one’s, this wasn’t clear in the authors response. In particular, reviewers one’s comment:

‘The relevance of the results with respect to P solubilization is questionable since the P form is rather unrepresentative and the exudate quantity is rather high’

Is partly answered by the author’s response to one of my comments in the same vain:

We have added a paragraph that discusses the relevance and ecological significance of organic acids as phosphorus mobilizers and the relevance of the root exudate analysis in liquid cultures. The new paragraph reads as follows: ‘It has been estimated that organic acids constitute 5 to 10 % of the total organic carbon in the soil solution. The concentration of organic anions measured in the soil solution usually range from 100 nM to more than 580 uM in the rhizosphere of cluster roots (Jones, 1998). However, millimolar concentrations of organic anions are likely required in the soil solution to effectively increase soluble P concentration especially in calcareous soils (Strom et al. 2005; Ryan and Jones, 2001). Strom et al. (2005) tested three organic acids (citrate, malic and oxalate) and a wide range of concentrations (1 mM to 100 mM) to evaluate its effects on the mobilization of phosphorus in calcareous soil. The results showed that the phosphorus mobilization of the tested compounds had a low efficiency and its effect varied depending on the type of organic acid, compound concentration, and pH. Further, due to the low phosphorus mobilization efficiency of those compounds it is still argued if the benefit of releasing large amounts of organic acids into the soil will exceed the cost of carbon lost by the plant, which can be seen as an unnecessary trade-off (Strom et al. 2005). However, low efficiency organic acids can be particularly important in phosphorus mobilization for calcareous soils with a limited phosphorus availability for plants. Finally, our evidence supports the above-mentioned hypothesis, that plants release a combination of compounds with different phosphorus-solubilizing efficiencies, at specific stages of growth, to deal with particular phosphorous needs.

**********

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Attachment

Submitted filename: PONE-D-20-04662_R1TBedts.pdf

PLoS One. 2020 Jun 3;15(6):e0234216. doi: 10.1371/journal.pone.0234216.r004

Author response to Decision Letter 1


19 May 2020

Reviewers responses

Editor comments:

The second comment concerns figure 3B where you check the solubilizing activity of combinations of the key compounds. The problem here is that you test the single compounds at 7 mM (Fig. 3A). But you test the combinations at that concentration, and also at lower and higher concentrations. I do not see how the higher and lower combinations can be interpreted without also showing values for the single compounds at each concentration. Without that data, I suggest adding the 7 mM combined results as the last bar of figure 3 A and deleting the data for the other combinations (unless you happen to have data for single compounds at the alternate concentrations). By the way, given that the combination solubilized about the same amount of phosphate as did 3-hydroxyproprionate alone, I don’t see how you can even think about an additive effect.

RESPONSE: We agree with the editor. Following your recommendation, the 7 mM combined results from figure 3B was added to figure 3A. Figure 3B was removed. Legend of figure 3 was modified accordingly. Results and methods section were also updated accordingly.

Reviewer #2:

Thank you for considering my comments so thoughtfully in the response. I believe the authors have answered the vast majority of my comments, I only have one outstanding query regarding the following in the response document:

'''

L255: The 1.75M is really interesting, 7mM of them mixed does worse than 7mM of any

individually

Again, really interesting results with Fig 4, very hard to interpret though there is lots going on.

RESPONSE: Each compound has a different molarity; therefore we cannot say that the 4 compounds at

1.75 mM add up to 7mM. We conclude that 1) compounds in combination have an additive effect, and

that 2) the addition of one does not inhibit the effect of the other.

'''

I think concluding there is an ‘additive effect’ is a bit miss leading. Here is the standard definition of an additive affect https://www.dictionary.com/browse/additive-effect. The sum of 7mM individually is much more than 7mM combined (I use the 7mmol case now so there is no issues with the molarity. Both cases has 7mM of each.) thus it is not an additive system. This is of course because in the individual cases are done in separate assays and they solubilise the lightly-bound P pool 4 times, while the combined is done in one assay. I think if you want to convince the reader that they are ‘additive’ (and later ‘synergize’ L348 in the discussion) you need to define exactly what it means for the current system to be additive or synergize. Possibly the current experiments and media aren’t suitable to make this conclusion. As I mentioned before, I suspect the compounds ‘synergise’ (I define this to mean to do better than the sum of its parts) when the media has a range of minerals that buffer P and are attacked more efficiently by certain exudates. For example (this is entirely hypothetical) assume the soil is made up of 50% Al-oxide and 50% Fe-oxide and nicotinic acid solubilises P from Al-oxide very effectively but badly from Fe-oxide and malic acid vice-versa. In this case the two compounds would certainly synergise. As I mentioned before I think there is papers about this but I cannot remember, the other reviewer Prof Gerke is likely to know about this and can point you in the right direction. I note the paper “Does the combination of citrate and phytase exudation in Nicotiana tabacum promote the acquisition of endogenous soil organic phosphorus?” which you cite for the synergy of exudates for P solubilisation is an experiment done in soil not NRIB.

I do not think more experiments or analysis is needed as this is a minor result in the overall paper, but a more careful discussion of this is needed in liight of the results.

I do agree with conclusion that the addition of one does not inhibit the other which is a good result in itself.

RESPONSE: We appreciate your follow-up comments. Due to a similar concern by the editor we have modified Figure 3 and made changes to the methods and results sections to address in the best way possible your comment. Please see below:

1. We incorporated the 7 mM combination from figure 3B as the last column of figure 3A. We removed figure 3B. We agreed that not having single data for every compound with different concentrations, including 1.75 and 28 mM, make difficult to assess the effects. The result (line: 245-254) and method sections (line: 186-193) were modified accordingly to reflect these changes.

2. With respect to the citation: we were not able to find a similar result under the same conditions used in our study (NBRIP media). We kept the citation because we believe this paper is relevant for our discussion. However, to address your concern, we have clearly stated that the conditions from that finding are different that ours. Now it reads as follow: ‘However, this study was performed under soil conditions and not using liquid NBRIP media”. In addition, it is clearly stated in this paragraph that these are hypotheses that will warrant experimental testing.

Detailed comments:

L187 (on tracked document): Should ‘A phosphorus gradient’ here instead be a ‘compound gradient’?

RESPONSE: Good observation. The word gradient was replaced by ‘compound mixture’. Now the sentence read as follow:

‘A compound mixture that included the previous tested concentration (7 mM per compound) was tested in order to compare if the combination of compounds would equal or surpass the effect of a single compound’

I think when describing the method for the cumulative experiment, you should make it clear whether the mixtures were all added to 5 mL of liquid NBRIP so that the same amount of P is the same as the individual experiment. Currently it is unclear.

RESPONSE: Thank you. We added this information to the result section. Now it reads as follow:

‘…. Briefly, 35 μL (100 mM) of each compound was added to 5 mL liquid NBRIP medium resulting in a final concentration of 7mM. Each compound added to the pool had 7 mM.’

Attachment

Submitted filename: Reviewersresponses-0518.docx

Decision Letter 2

Tobias Isaac Baskin

21 May 2020

Role of root exudates on assimilation of phosphorus in young and old Arabidopsis thaliana plants

PONE-D-20-04662R2

Dear Dr. Vivanco,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Tobias Isaac Baskin

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Tobias Isaac Baskin

22 May 2020

PONE-D-20-04662R2

Role of root exudates on assimilation of phosphorus in young and old Arabidopsis thaliana plants

Dear Dr. Vivanco:

I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

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With kind regards,

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on behalf of

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Fig. Root exudate compounds diverge in response to plant developmental stage and phosphate fertilization rate.

    (A) 456 compounds detected using GC-MS are plotted on the graph. PCA show dissimilarity among group of metabolites in the seedling stage at different fertilization levels: 25% (light green), 50% (light blue), 100% (green); vegetative stage: 25% (purple), 50% (pink), 100% (blue); and bolting stage: 25% (brown), 50% (olive), 100% (orange). (B) Data reduced to 201 annotated compounds with proper identification. PCA of compounds grouped by phosphate treatments in the seedling stage: 25% (light green), 50% (light blue), 100% (green); vegetative stage: 25% (purple), 50% (pink), 100% (blue); bolting stage: 25% (brown), 50% (olive), 100% (orange). The dotted circle indicates a cohesive group at a given fertilization level.

    (DOCX)

    S2 Fig. Root exudate compounds grouped by repetitions of fertilizer level.

    Treatments within plant developmental stages differ from one another, particularly the vegetative and bolting growth stages. Ellipses circle three repetitions of same fertilizer level. Color code correspond to seedling: 25% (light green), 50% (light blue), 100% (green); vegetative: 25% (purple), 50% (pink), 100% (blue); bolting: 25% (brown), 50% (olive), 100% (orange).

    (DOCX)

    S3 Fig. Top 10 compounds showing changes in cumulative secretion levels in the vegetative developmental stage (p<0.05) in response to increasing phosphate addition (0.312, 0.625 and 1.25 mM).

    Selected compounds based on PCA from vegetative 25% phosphate (A), and vegetative 50% and 100% phosphate (B).

    (DOCX)

    S4 Fig. Top 15 compounds showing changes in cumulative secretion levels in the bolting developmental stage (p<0.05) in response to increasing phosphate addition (0.312, 0.625 and 1.25 mM).

    Selected compounds from bolting 25% phosphate (A), bolting 50% P (B) and bolting 100% (C).

    (DOCX)

    Attachment

    Submitted filename: Reviewers responses-0406.docx

    Attachment

    Submitted filename: PONE-D-20-04662_R1TBedts.pdf

    Attachment

    Submitted filename: Reviewersresponses-0518.docx

    Data Availability Statement

    All relevant data are within the paper and its Supporting Information files.


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