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Study area and parcel selectionThe study was conducted in Castro Verde Special Protection Area (SPA), located in southern Portugal (Fig. 1). The climate is Mediterranean, with hot summers (30–35 °C on average in July) and mild winters (averaging 5–8 °C in January), and over 75% of annual rainfall (500–600 mm) concentrated in October–March. The landscape is flat or gently undulating (100–300 m), mainly dominated by open areas used for rainfed pastures (ca. 60%) and annual crops (ca. 25%), and to a less extent by open woodlands (ca. 7%)15.Figure 1(a) Location of the study area within the Castro Verde Special Protected Area (SPA), southern Portugal. (b) Distribution of the 27 sheep (dark grey polygons) and 23 cattle (light grey polygons) grazing parcels and (c) Sampling scheme applied to each parcel surveyed. Bird counts were done at the centroid of the parcel (white dot) whereas vegetation sampling was performed at the indicated 10 points (black dots). The area covered with pastures and annual crops (derived from CORINE land cover 2018—https://land.copernicus.eu/pan-european/corine-land-cover/clc2018) is shown in yellow. The map was done using the version 3.10.0 of QGIS—https://qgis.org/en/site/index.html.Full size imageSince 1995, part of the study area has benefited from a CAP agri-environment aiming to protect the traditional farming system16. This scheme provides financial support to farmers for agricultural practices considered favourable to conservation, including the traditional rotation of cereals and fallows, the maintenance of low stocking rates (usually related with sheep grazing systems), and sowing of crops benefiting grassland birds16. However, in recent years the traditional farming system has been declining, with many farmers converting to specialized livestock systems, mainly, cattle grazing systems, with an increase of stocking rates7,15.Parcel selection started by identifying grasslands grazed by either sheep or cattle, based on parcel-level statistical information from 2010 provided by the Portuguese Ministry of Agriculture7. To minimize potentially confounding effects of adjacent land uses (edge effects) and other non-crop elements within parcels on bird assemblages, we excluded parcels less than 100 m from shrubland or forested areas, with shrub and tree cover  > 5% and with a minimum size of 10 ha. In January 2019 we visited 100 pre-selected parcels which were grazed by either sheep or cattle in 2010 in order to confirm the parcel land use in the agricultural year of 2018/2019, aiming to sample a balanced proportion of 50 sheep and cattle grazed parcels. Additional livestock information for the agricultural year of 2018/2019 was obtained during systematic visits to targeted parcels (see “Grazing Regime” section from Methods). We ended up with 23 cattle parcels and 27 sheep parcels (Fig. 1).Bird and vegetation dataBreeding birds were sampled twice in each parcel during 7–16 April and 1–15 May 2019 respectively, always by the same observer (R.F.R). This was done to take into account species-specific breeding phenology in the area (early and late breeders)17 and minimize bias due to other factors (like weather or disturbance). Sampling was conducted using standardized 10 min point counts18 carried out at the central point of the parcel (Fig. 1). As the open terrain allowed for high visibility, a large detection radius was used, and all birds detected within 100 m of the central point were identified and counted. This radius is roughly similar to the one previously used for characterizing bird populations in the region19. All counts were carried out in the first four hours after sunrise and in the last two hours before sunset, with none in heavy or persistent rain, or in strong wind conditions. To estimate bird species richness and occurrences in each parcel, we pooled the data from the two counts. Species-level analyses focused on the six most common species, which occurred in  > 30% of the parcels (see Supplementary Table S1). In addition to presence/absence, we also estimated population densities, using the count which yielded the highest estimate of density for each species (assuming this is the best indicator of population density, given the potential phenology and detectability biases above mentioned). Bird densities were based on the number of males simultaneously detected and expressed as breeding pairs/10 ha or males/10 ha (in the case of Little Bustard Tetrax tetrax and Common Quail Coturnix coturnix). Categorization to the genus level was made for the Crested and Thekla larks (Galerida cristata and G. theklae) due to difficulties in correctly identifying all individuals of these two very similar species in the field.Vegetation height and cover were measured once in each parcel, between April 22 and May 6. Vegetation height was estimated in a set of ten 3 m radius plots defined inside the 100 m buffer (Fig. 1). In each plot, ten measurements of vegetation height were taken at random locations, for a total of 100 measurements per parcel. Vegetation height was measured using a 50 cm ruler and was defined as the highest point of vegetation projection within 3 cm of the ruler20. All values were estimated to the nearest half centimeter. When no vegetation was present (bare soil, soil litter, rocks or animal dung) the height was set to zero (0) but these measurements were not considered to estimate the mean height of the sward. Vegetation cover was measured inside a 50 × 50 cm quadrat placed at each of the ten grid points, by visual estimation to the nearest 5% of the percentage of the quadrat area covered by vegetation21 (Fig. 1). Vegetation height and cover measurements were averaged within each parcel.Grazing regimeThe number and type of livestock in each parcel as well as the extent of the grazing period since the start of the year (2019) were gathered from interviews (Supplementary Information S1) to land managers during 1–15 May 2019. This information was further validated, and corrected in a few cases, through field checks during regular visits (made at two-week intervals) to the parcels (see “Bird and vegetation data” section from Methods). Three grazing regime indicators were estimated for the whole period (January–May 2019): livestock type (either sheep or cattle), animal density, and grazing pressure. The animal density in each parcel was calculated as the average density (animals per hectare) of any species (regardless of being sheep or cattle) that grazed the parcel during the 5-months period. Stocking Rate translated animal density into livestock unit (LU) per hectare (LU/ha), between January and May, according to the following criteria: one adult bovine = 1 LU; bovine aged  More

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Metabolic profiling of EP and LE root exudates and root periderm samplesHigh performance liquid chromatography (HPLC) analysis of root exudates and root periderm reported the presence of five bioactive NQs. The identified NQs included shikonin (SK), acetylshikonin (AS); isobutyrylshikonin (IBS); β, β-dimethylacrylshikonin (DMAS); and isovalerylshikonin (IVS) (Fig. 1a–d). This suggests that SK and its derivatives accumulate in the rhizosphere of both EP and LE via root exudation. Though all the five NQs were found to be exuded in the rhizosphere however they varied quantitatively among EP and LE species. LE samples had higher SK and its derivatives production compared to EP (Figs. S5–S6). Our results also displayed quantitative variations in SK and its derivatives production among two soil types (Table 1a,b). However, regardless of variation, SK, AS, DMAS, and IVS were consistently present among all the samples.Figure 1Images and chromatograms representing qualitative and quantitative variation of SK and its derivatives production in root periderm extracts. Chromatograms of root extracts of E. plantagenium (EP) and L.erythrorhizon (LE) specimens grown in Peat potting artificial soil (a) EP.PP, (c) LE.PP; and Natural campus soil (b) EP.NC, (d) LE.NC. Resulting peaks correspond to shikonin (SK), acetylshikonin (AS); isobutylshikonin (IBS); β, β-dimethylacrylshikonin (DMAS); and isovalerylshikonin (IVS). Chromatogram for each sample represents a composite sample of 3–4 individual plants. Figure represents only one replicate for each sample while the rest of the two replicates for each sample with standard chromatogram are provided in Fig. S5.Full size imageTable 1 Quantitative analysis of shikonin and its derivatives via HPLC in (a) root periderm; (b) root exudates samples of E. plantagineum (EP) and L.erythrorhizon (LE).Full size tablePacBio sequence reads statistics and taxonomic profilingAfter quality filtering, removal of chimera, chloroplast and mitochondrial sequences, approximately 165,570 high quality sequences (Tags) were obtained. Tags were clustered into 14,429 microbial operational taxonomic units (OTUs) at a 97% sequence similarity cutoff level (Table S2). All OTUs with species annotation are summarized in Table S3. Taxonomic profiling for taxonomic affiliations revealed Proteobacteria, Bacteroidetes, Planctomycetes, Cyanobacteria, Acidobacteria, and Actinobacteria to be the dominant phyla among all the samples (Fig. S7). These 6 phyla accounted for 70.97–96.61% of the total microbial OTUs. The Proteobacterial microbes mainly belonged to Classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria that accounted for 13.94–40.54% of the total microbes (Table S4).Host plant genetics are the drivers for distinct microbiomeTo identify the effects of host plant genetics on microbial acquisition, microbial community composition of bulk soil was compared with root and rhizospher soils of EP and LE. α-diversity estimates revealed a significantly higher observed species richness (Sobs), and shannon diversity for bulk soil (Fig. 3a,b; Table S5). This indicates that bulk soil serves as a reservoir for microbial acquisition in other rhizo-compartments. At different taxonomic levels, microbes associated with Proteobacteria, Planctomycetes, Bacteroidetes and Cyanobacteria were all present in relatively higher abundance in EP and LE rhizo-compartments compared to bulk soil in two different soil types (Fig. 2a; Table S6). Wilcox test also displayed quantitative variation in microbial acquisition at order level. For example, compared to bulk soil, Flavobacteriales, Sphingomonadales, and Verrucomicrobiales had a relatively higher abundance in EP rhizosphere, while Caulobacterales, and Sphingomonadales were significantly higher in LE rhizosphere (Fig. S8, P  More

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P. aeruginosa produces novel glycolipids in response to Pi stressTo determine changes in the membrane lipidome in response to P-stress, the model P. aeruginosa strain PAO1 was grown in minimal medium under high (1 mM) or low Pi (50 µM) conditions (Fig. 1a). The latter condition elicited strong alkaline phosphatase activity, measured through the liberation of para-nitrophenol (pNP) from pNPP (Fig. 1b), this being a strong indication that cells were P-stressed. Analysis of membrane lipid profiles using high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS) revealed the presence of several new lipids under Pi stress conditions (Fig. 1c). Thus, during Pi-replete growth (1 mM phosphate), the lipidome is dominated by two glycerophospholipids: PG (eluted at 6.8 min) and PE (eluted at 12.2 min). During Pi-stress a lipid species with mass to charge ratio (m/z) of 623 and 649 were also found, with MS fragmentation resulting in a 131 m/z peak, a diagnostic ion for the amino-acid containing ornithine lipid. This is consistent with previous reports of ornithine lipids in the P. aeruginosa membrane in response to Pi stress [29, 30].Fig. 1: Lipidomics analysis uncovers novel glycolipid formation in Pseudomonas aeruginosa strain PAO1 in response to phosphorus limitation.a Growth of strain PAO1 WT in minimal medium A containing 1 mM phosphate (+Pi, blue) or 50 µM phosphate (−Pi, black) over 12 h. Data are the average of three independent replicates. b Liberation of para-nitrophenol (pNP) from para-nitrophenol phosphate (pNPP) through alkaline phosphatase activity, under Pi-replete (1 mM, black) and Pi-deplete (50 µM, yellow) conditions. Error bars represent the standard deviation of three independent replicates. c Representative chromatograms in negative ionisation mode of the P. aeruginosa lipidome when grown under phosphorus stress (−Pi, black) compared to growth under phosphorus sufficient conditions (+Pi, orange). PG phosphatidylglycerol, PE phosphatidylethanolamine, OL ornithine lipids. Lower panel: extracted ion chromatograms of three new glycolipid species in P. aeruginosa which are only produced during Pi-limitation (black, 1 mM; orange, 50 µM). MGDG monoglucosyldiacylglycerol, GADG glucuronic acid-diacylglycerol and UGL unconfirmed glycolipid. d Mass spectrometry fragmentation spectra of three glycolipid species present under Pi stress in P. aeruginosa, at retention times of 7.7 (m/z 774.7), 8.7 (m/z 786.7) and 9.8 (m/z 788.6) minutes, respectively. Each spectrum depicts an intact lipid mass with an ammonium (NH4+) adduct exhibiting neutral loss of a head group, yielding diacylglycerol (DAG) (595 m/z). Further fragmentation yields monoacylglycerols (MAG) with C16:0 or C18:1 fatty acyl chains.Full size imageFurther to ornithine lipids, three unknown lipids eluting at 7.7, 8.7 and 9.8 min, were only present under Pi stress conditions (Fig. 1c). Using several rounds of MS fragmentation (MSn), with a quadrupole ion trap MS, fragmentation patterns characteristic of glycolipids were found for all three peaks. For each peak of interest, the most predominant lipid masses of 774.7, 786.8 and 788.6 m/z were analysed by MSn in positive ionisation mode (Fig. 1d). In each case, an initial head group was lost leaving a significant signal of 595.6 m/z, the mass of the glycolipid building block diacylglycerol (DAG). Further fragmentation leads to the loss of either fatty acyl chain from DAG, leaving monoacylglycerols of 313.2 and 339.3 m/z. Two monoacylglycerols with different masses are produced as a result of the original lipid containing 16:0 and 18:1 fatty acids (313.2 and 339.3 m/z monoacylglycerols, respectively). To further elucidate the identity of the peaks, a search for a neutral loss of a polar head group was carried out. Thus, the intact masses of 774.7 and 788.6 m/z in positive ionisation mode leads to the loss of a head group of −179 and −193 m/z, which corresponds to a hexose- and a glucuronate- group, respectively (Fig. 1d), suggesting the occurrence of novel monoglucosyldiacylglycerol (MGDG) and glucuronic acid diacylglycerol (GADG) glycolipids in P. aeruginosa. The third glycolipid peak at 8.7 min remains an unknown lipid with intact mass of 786.8 m/z (hereafter designated as a putative unknown glycolipid, UGL). Together, these data confirm the production of new glycolipids in P. aeruginosa in response to Pi stress.Comparative proteomics uncover the lipid renovation pathway in P. aeruginosa
To determine the proteomic response of P. aeruginosa to phosphorus limitation, and identify the genes involved in glycolipid formation, strain PAO1 was cultivated under high and low Pi conditions for 8 h and the cellular proteome then analysed. A total of 2844 proteins were detected, 175 of which were found to be differentially regulated by Pi availability (Fig. 2a, Table S1). In line with previous transcriptomic studies of strain PAO1 [18], major phosphorus acquisition mechanisms were highly expressed under Pi stress conditions, e.g. the Pi-specific transporter PstSCAB, the two-component regulator PhoBR (Table S1) [31].Fig. 2: Comparative multi-omic analyses for the identification of the PlcP-Agt pathway responsible for glycolipid formation in Pseudomonas aeruginosa strain PAO1.a Volcano plot depicting differentially expressed proteins when comparing Pi-replete and Pi-deplete conditions. Significantly upregulated proteins when under Pi stress are shown in red (left), and those that are significantly upregulated when Pi is sufficient are in green (right). Significance was accepted when the false discovery rate (FDR) was More