Cluster Roots Research Articles

Transcriptomic Response of White Lupin Roots to Short-Term Sucrose Treatment

White lupin (Lupinus albus) has become a model plant for understanding plant adaptations to phosphorus (P) and iron (Fe) deficiency, two major limiting factors for plant productivity. In response to both nutrient deficiencies, white lupin forms cluster roots, bottle-brush-like root structures that aid in P and Fe acquisition from soil. While the cluster root function is well-studied, not much is known about the signaling pathways involved in sensing and responding to a P and Fe deficiency. Sucrose has been identified as a long-distance signal sent in increased concentrations from shoot to root in response to both a P and Fe deficiency. Thus, sucrose plays a dual role both as a signal and as a major source of energy for the root. To unravel the responses to sucrose as a signal, we performed an Illumina paired-end cDNA sequencing of white lupin roots treated with sucrose for 20, 40 or 80 min, compared to untreated controls (0 min). We identified 634 up-regulated and 956 down-regulated genes in response to sucrose. Twenty minutes of sucrose treatment showed the most responses, with the ethylene-activated signaling pathway as the most enriched Gene Ontology (GO) category. The number of up-regulated genes decreased at 40 min and 80 min, and protein dephosphorylation became the most enriched category. Taken together, our findings indicate active responses to sucrose as a signal at 20 min after a sucrose addition, but fewer responses and a potential resetting of signal transduction pathways by the dephosphorylation of proteins at 40 and 80 min.

Bacillus amyloliquefaciens promotes cluster root formation of white lupin under low phosphorus by mediating auxin levels

Abstract White lupin (Lupinus albus L.) produces cluster roots to acquire more phosphorus under phosphorus deficiency. Bacillus amyloliquefaciens SQR9 contributes to plant growth, but whether and how it promotes cluster root formation in white lupin remain unclear. Here, we investigated the roles of SQR9 in cluster root formation under low-phosphorus conditions using a microbial mutant and virus-induced gene silencing (VIGS) in white lupin. SQR9 substantially enhanced cluster root formation under low-phosphorus conditions. The ysnE gene encodes an auxin biosynthesis enzyme in SQR9 and was associated with cluster root formation, as ysnE-defective SQR9 did not trigger cluster root formation. SQR9 inoculation induced the expression of PIN-formed2 (LaPIN2, encoding an auxin transporter) and YUCCA4 (LaYUC4, encoding an auxin biosynthesis enzyme) in white lupin roots. VIGS-mediated knockdown of LaPIN2 and LaYUC4 prevented wild-type SQR9-induced cluster root formation in white lupin. Finally, white lupin LaYUC4-derived auxin and SQR9-derived auxin pools were both transported by LaPIN2, promoting cluster root formation under low phosphorus conditions. Taken together, we propose that B. amyloliquefaciens promotes cluster root formation in white lupin under low-phosphorus conditions by stimulating auxin biosynthesis and transport. Our results provide insights into the interplay between bacteria and root auxin in crop phosphorus use efficiency.

A new condition for Root Clustering in PMI regions

A new condition for Root Clustering in PMI regions

Improving Phosphate Acquisition from Soil via Higher Plants While Approaching Peak Phosphorus Worldwide: A Critical Review of Current Concepts and Misconceptions.

Phosphate (P) is the plant macronutrient with, by far, the lowest solubility in soil. In soils with low P availability, the soil solution concentrations are low, often below 2 [µmol P/L]. Under these conditions, the diffusive P flux, the dominant P transport mechanism to plant roots, is severely restricted. Phosphate is sorbed into various soil solids, Fe/Al oxides, clay minerals and, sometimes overlooked, humic Fe/Al surfaces. The immobilization of P in soil is often the result of the diffusion of P into the internal surfaces of oxides or humic substances. This slow reaction between soil and P further reduces the availability of P in soil, leading to P fixation. The solubilization of soil P by root-released carboxylates is a promising way to increase the acquisition and uptake of P from P-fixing soils. Citrate and, sometimes, oxalate are effective with respect to additional P solubilization or P mobilization, which may help increase the diffusive P flux into the roots by increasing the P solution concentrations in the rhizosphere. The mobilization of humic-associated P by carboxylates may be an effective way to improve soil P solubility. Not only orthophosphate anions are mobilized by root-released carboxylates, but also higher phosphorylated inositol phosphates, as the main part of P esters in soil are mobilized by carboxylates. Because of the rather strong bonding of higher phosphorylated inositol phosphates to the soil solid phase, the mobilization step by carboxylates appears to be essential for plants to acquire inositol-P. The ecological relevance of P mobilization by carboxylates and its effect on the uptake of P by crops and grassland species are, at best, partially understood. Plant species which form cluster roots such as white lupin (Lupinus albus L.) or yellow lupin (Lupinus luteus L.) release high rates of carboxylates, mainly citrate from these root clusters. These plant species acquire fixed or low available P which is accessible to plants at rates which do not satisfy their P demand without P mobilization. And white lupin and yellow lupin make soil P available to other plants in mixed cropping systems or for subsequent plant species in crop rotations. The mobilization of P by carboxylates is probably also important for legume/grass mixtures for forage production. Species such as alfalfa, red clover or white clover release carboxylates. The extent of P mobilization and P uptake from mobilized P by legume/grass mixtures deserves further research. In particular, which plant species mostly benefit from P mobilization by legume-released carboxylates is unknown. Organic farming systems require such legume/grass mixtures for the introduction of nitrogen (N) by forage legumes into their farming system. For this agricultural system, the mobilization of soil P by carboxylates and its impact on P uptake of the mixtures are an important research task.

Combined cellular phenotyping and high-throughput sequencing analysis reveals the symbiotic relationships between different types of macadamia root systems and arbuscular mycorrhizal fungi

Macadamia nuts, scientifically designated as Macadamia integrifolia, are a highly valuable crop that originated in Australia. This study provides a comprehensive examination of the symbiotic relationships between various macadamia root systems and arbuscular mycorrhizal fungi (AMF). The four principal macadamia-producing regions in Yunnan Province were selected for investigation on the basis of meticulous criteria. To determine the AMF infection rate, the roots were stained. Furthermore, high-throughput sequencing was employed to conduct a comprehensive analysis of the fungal diversity in the rhizosphere soil. The findings were definitive, indicating that both normal and cluster roots are capable of establishing a symbiotic relationship with AMF. Secondary forests exhibited significantly elevated fungal diversity relative to normal roots, while cluster roots demonstrated the lowest diversity and notable regional variation, indicating that the environment exerts a considerable influence on inter-root fungi and AMF. The analysis of the fungal community composition revealed that the predominant groups were Ascomycetes and Basidiomycetes. The FUNGuild function prediction clearly indicated distinct differences in the fungal functions of secondary forests, cluster roots, and normal roots. This study provides a scientific foundation for the sustainable development of macadamia nuts and significantly contributes to a deeper comprehension of the intricate interactions between macadamia and AMF, thereby fostering the long-term stable and healthy growth of the macadamia nut industry.

An Explanation of the Name of Baibu ()

The character Bu () of Baibu (), pronounced as BANG (), referred to root of a plant. The original BAND () should be the character Bu (), which had the same meaning with BANG (), ie., root of a plant. Baibu () was actually Baibu (), based on plant features of numerous and clustered roots. The root shape of plant Baibu and Tian Men Dong (, a plant which has the same name with Baibu but looks different) look very similar with the character pattern Bu () in Jia Gu Wen (Chinese character inscription on bones or tortoise shells in the Shang and Zhou Dynasty). The alias of Baibu, Pofucao (), and Baibing () attached to Baibu () in Compendiu of Material Medica (Ben Cao Gang Mu), might be the change of pronunciation phonetically. The Mu () in Beimu () and Zhimu (), the Fu () in Beifu () and the Mo () in Suanmo (), are all the change of pronunciation phonetically, meaning roots of plants.

Phosphorus-Use-Efficiency Gene Identification in Fabaceae and RSL2 Expansion in Lupinus albus Is Associated with Low-Phosphorus Adaptation.

Phosphorus is critical for plant growth but often becomes less accessible due to its precipitation with cations in soil. Fabaceae, a diverse plant family, exhibits robust adaptability and includes species like Lupinus albus, known for its efficient phosphorus utilization via cluster roots. Here, we systematically identified phosphorus-utilization-efficiency (PUE) gene families across 35 Fabaceae species, highlighting significant gene amplification in PUE pathways in Fabaceae. Different PUE pathways exhibited variable amplification, evolution, and retention patterns among various Fabaceae crops. Additionally, the number of homologous genes of the root hair development gene RSL2 in L. albus was far more than that in other Fabaceae species. Multiple copies of the RSL2 gene were amplified and retained in L. albus after whole genome triplication. The gene structure and motifs specifically retained in L. albus were different from homologous genes in other plants. Combining transcriptome analysis under low-phosphorus treatment, it was found that most of the homologous genes of RSL2 in L. albus showed high expression in the cluster roots, suggesting that the RSL2 gene family plays an important role in the adaptation process of L. albus to low-phosphorus environments and the formation of cluster roots.

Pinus pinaster root architecture 2 to 5 years after container rearing and outplanting: tropism loss, root clustering and resilience

Pinus pinaster root architecture 2 to 5 years after container rearing and outplanting: tropism loss, root clustering and resilience

Transcriptomics Provide Insights into Early Responses to Sucrose Signaling in Lupinus albus, a Model Plant for Adaptations to Phosphorus and Iron Deficiency.

Phosphorus (P) and iron (Fe) deficiency are major limiting factors for plant productivity worldwide. White lupin (Lupinus albus L.) has become a model plant for understanding plant adaptations to P and Fe deficiency, because of its ability to form cluster roots, bottle-brush-like root structures play an important role in the uptake of P and Fe from soil. However, little is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose, sent in increased concentrations from the shoot to the root, has been identified as a long-distance signal of both P and Fe deficiency. To unravel the responses to sucrose as a signal, we performed Oxford Nanopore cDNA sequencing of white lupin roots treated with sucrose for 10, 15, or 20 min compared to untreated controls. We identified a set of 17 genes, including 2 bHLH transcription factors, that were up-regulated at all three time points of sucrose treatment. GO (gene ontology) analysis revealed enrichment of auxin and gibberellin responses as early as 10 min after sucrose addition, as well as the emerging of ethylene responses at 20 min of sucrose treatment, indicating a sequential involvement of these hormones in plant responses to sucrose.

Root growth dynamics, nutrient uptake and use efficiency of Grevillea robusta grown under nitrogen and phosphorus deficiency

Root growth, nutrient uptake, and nutrient use efficiency of a plant is influenced by the nutrient availability in its growing environment. The aim of this study was to investigate the root morphology, nutrient uptake and use efficiency of Grevillea robusta grown in nitrogen (N)- and phosphorus (P)-limited conditions. A hydroponic experiment was conducted for three months in a glasshouse with four nutrient treatments; (i) N-deficient, (ii) P-deficient, (iii) N/P-deficient (co-limitation of N and P), and (iv) control (sufficient amounts of N, P, and other nutrients in the growth medium). The composition and the concentration of each nutrient in the control solution were custom-made based on the growth requirement of G. robusta. N and P concentration in nutrient-deficient media were maintained at 2 ppm. The impact of N- or P-deficiency and their co-limitation on cluster root formation, organ-specific dry matter and nutrient accumulation, N and P uptake and their use efficiencies were measured. P-deficient conditions produced the highest number of cluster roots (24 ± 4) which was comparatively lower than those of N- and N/P-deficient conditions indicating that P-deficiency is the primary factor influencing the formation of cluster roots in G. robusta. The use efficiency of N and P in biomass formation was significantly (p < 0.05) enhanced when their uptake was reduced in response to N- and P-limitation. The efficient internal use of P by G. robusta under N- and N/P-deficiency is indicated by the significant increase in P-remobilization efficiency under these nutrient-deficient conditions.

The white lupin trehalase gene LaTRE1 regulates cluster root formation and function under phosphorus deficiency.

Under phosphorus (P) deficiency, white lupin (Lupinus albus L.) forms a specialized root structure, called cluster root (CR), to improve soil exploration and nutrient acquisition. Sugar signaling is thought to play a vital role in the development of CR. Trehalose and its associated metabolites are the essential sugar signal molecules that link growth and development to carbon metabolism in plants; however, their roles in the control of CR are still unclear. Here, we investigated the function of the trehalose metabolism pathway by pharmacological and genetic manipulation of the activity of trehalase in white lupin, the only enzyme that degrades trehalose into glucose. Under P deficiency, validamycin A treatment, which inhibits trehalase, led to the accumulation of trehalose and promoted the formation of CR with enhanced organic acid production, whereas overexpression of the white lupin TREHALASE1 (LaTRE1) led to decreased trehalose levels, lateral rootlet density, and organic acid production. Transcriptomic and virus-induced gene silencing results revealed that LaTRE1 negatively regulates the formation of CRs, at least partially, by the suppression of LaLBD16, whose putative ortholog in Arabidopsis (Arabidopsis thaliana) acts downstream of ARF7- and ARF19-dependent auxin signaling in lateral root formation. Overall, our findings provide an association between the trehalose metabolism gene LaTRE1 and CR formation and function with respect to organic acid production in white lupin under P deficiency.

Attenuated down-regulation of PHOSPHATE TRANSPORTER1 genes as a mechanism for phosphorus sensitivity in phosphorus-efficient Hakea prostrata (Proteaceae)

Background and aimsPhosphorus (P) is an essential plant nutrient and integral for crop yield. However, plants adapted to P-impoverished environments, such as Hakea prostrata (Proteaceae), are often sensitive to P supplies that would be beneficial to other plants. The strategies for phosphate uptake and transport in P-sensitive species have received little attention.MethodsUsing a recently-assembled transcriptome of H. prostrata, we identified 10 putative members of the PHOSPHATE TRANSPORTER1 (PHT1) gene family, which is responsible for inorganic phosphate (Pi) uptake and transport in plants. We examined plant growth, organ P concentrations and the transcript levels for the eight PHT1 members that were expressed in roots of H. prostrata at Pi supplies ranging from P-impoverished to P-excess.Key resultsHakea prostrata plants suppressed cluster root growth above ecologically-relevant Pi supplies, whilst non-cluster root mass ratios were constant. Root P concentrations increased with increasing Pi supply. Of the eight H. prostrata PHT1 genes tested, four had relatively high transcript amounts in young roots suggesting important roles in Pi uptake; however, a maximum five-fold difference in expression between P-impoverished and P-excess conditions indicated a low P-responsiveness for these genes. The HpPHT1;8 and HpPHT1;9 genes were paralogous to Pi-responsive Arabidopsis thaliana PHT1;8 and PHT1;9 orthologues involved in root-to-shoot translocation of P, but only HpPHT1;9 was P responsive.ConclusionsAn attenuated ability of H. prostrata to regulate PHT1 expression in response to Pi supply is likely responsible for its low capacity to control P uptake and contributes to its high P sensitivity.

Do aluminum (Al)-hyperaccumulator and phosphorus (P)-solubilising species assist neighbouring plants sensitive to Al toxicity and P deficiency?

We aimed to evaluate the facilitation effects of an aluminum (Al) hyperaccumulator species bearing cluster roots, Gevuina avellana, on the seedling growth and performance of an Al-intolerant and phosphorus (P)-deficient-sensitive plant, Vaccinium corymbosum. For this, seedlings of G. avellana and V. corymbosum were grown alone or together as follows: i) two G. avellana seedlings, ii) one G. avellana + one V. corymbosum and iii) two V. corymbosum, in soil supplemented with Al (as Al2(SO4)3) and in the control (without Al supplementation). We determined relative growth rate (RGR), photosynthetic rate, chlorophyll concentration, lipid peroxidation and Al and nutrient concentration [Nitrogen (N), P, potassium (K), calcium (Ca), magnesium (Mg), sodium (Na), manganese (Mn), iron (Fe), copper (Cu), zinc (Zn), and sulfur (S)] in leaves and roots of both species. The results showed that, in general, G. avellana did not assist V. corymbosum to enhance its RGR nor reduce its Al uptake. However, G. avellana assisted V. corymbosum in enhanced N acquisition and, consequently, to increase its chlorophyll concentration and photosynthetic rate. Besides, V. corymbosum had lower lipid peroxidation in leaves when grown in the soil with high Al supplementation in association with G. avellana. Our results suggest a facilitating effect of G. avellana to V. corymbosum when grown in soils with high Al concentration, by enhancing chlorophyll concentrations and photosynthetic rate, and decreasing the oxidative damage to lipids.

Comparative effects of humic acid and charcoal on soil, growth, and biomass properties of lupine (Lupinus albus L.)

Recently, charcoal and humic acid application in soils is a burgeoning area of research due to its profound impact on soil properties and crop yields. Charcoal contributes to improved soil structure, enhanced water-holding capacity, and increased carbon sequestration while humic acid, a component of organic matter, enhances nutrient retention and availability, fostering healthier plant growth and long-term soil health. The experiments were conducted on November 20, 2022, at Grdarasha Research Station, College of Agricultural Engineering Sciences, Salahaddin University-Erbil, Iraq. Two organic sources (humic acid and charcoal) were used to improve soil chemical properties, growth, and biomass characteristics of white lupines. Humic acid at the levels of (0, 10, and 15 g m-2), respectively along with 1 kg m-2 of charcoal. Results showed that essential elements and heavy metals in soil were increased and improved with adding humic acid and charcoal, and then well-affected root ability to uptake nutrients. The great values of germination rate, leaf number (LN), and fresh and dry shoot weights were found when charcoal was stirred to the soil (83.33%, 15.67 LN plant-1, 10.91, and 2.24 t ha-1), respectively. While the longest root length was recorded when humic acid applied at rate of 10 g m-2 (24.22 cm), it was true about the enhancement of cluster roots. Despite that, humic acid at the rate of 15 g m-2 caused to improve fresh and dry root and shoot weights, which were compared to control treatment. The final results indicated that by adding humic acid (H), and charcoal (CH) could improve soil chemical properties, and then may affect positively microorganisms, which can promote plant growth by transforming, solubilizing, and mobilizing soil nutrients. As well, lupinus seemed as phytoremediation (uptake) in case of some heavy metals.

Complexity of a root clustering algorithm for holomorphic functions

Complexity of a root clustering algorithm for holomorphic functions

Hierarchical matrix factorization for interpretable collaborative filtering

Hierarchical matrix factorization for interpretable collaborative filtering

Relictithismia kimotsukiensis, a new genus and species of Thismiaceae from southern Japan with discussions on its phylogenetic relationship.

The family Thismiaceae, known as "fairy lanterns" for their urn- or bell-shaped flowers with basally fused tepals, consists of non-photosynthetic flowering monocots mainly in tropical regions, extending into subtropical and temperate areas. Here, we propose a new mycoheterotrophic genus, Relictithismia Suetsugu & Tagane (Thismiaceae), with its monotypic species Relictithismia kimotsukiensis Suetsugu, Yas.Nakam. & Tagane from Kimotsuki Mountains in the Osumi Peninsula, Kagoshima Prefecture, Kyushu Island, southern Japan. Relictithismia resembles Haplothismia Airy Shaw in having a cluster of tuberous roots, a feature previously observed only in this genus within the family Thismiaceae. However, it differs in having solitary flowers (vs. 2-6-flowered pseudo-raceme in Haplothismia), anther thecae largely separated (vs. connate), and the presence of an annulus (vs. absent). Additionally, Relictithismia differs from the geographically overlapping genus Thismia Griff. in its stamen structure and the position of the annulus. In Relictithismia, the stamens lack connectives, and its free filaments arise from the annulus located inside the perianth mouth, while in Thismia, the stamens typically have connate connectives, forming a staminal tube pendulous from the annulus located at the mouth of the floral tube. Our morphological and phylogenetic data indicated that R. kimotsukiensis holds an early-diverging position within the family, situated outside the Old World Thismia clade. This paper offers an extensive description and color photographs of R. kimotsukiensis, complemented by notes on its phylogenetic relationship and evolutionary history.

Adenanthos species (Proteaceae) in phosphorus-impoverished environments use a variety of phosphorus-acquisition strategies and achieve high-phosphorus-use efficiency.

Soils in south-western Australia are severely phosphorus (P) impoverished, and plants in this region have evolved a variety of P-acquisition strategies. Phosphorus acquisition by Adenanthos cygnorum (Proteaceae) is facilitated by P-mobilizing neighbours which allows it to extend its range of habitats. However, we do not know if other Adenanthos species also exhibit a strategy based on facilitation for P acquisition in P-impoverished environments. We collected leaf and soil samples of Adenanthosbarbiger, A. cuneatus, A.meisneri,A. obovatus, A. sericeus and Adenanthos sp. Whicher Range (G.J. Keighery 9736) growing in their natural habitats at different locations within the severely P-limited megadiverse environment of south-western Australia. Hydroponic experiments were conducted to collect the carboxylates exuded by cluster roots. Pot experiments in soil were carried out to measure rhizosheath phosphatase activity. We found no evidence for facilitation of P uptake in any of the studied Adenanthos species. Like most Proteaceae, A. cuneatus, A. meisneri, A. obovatus, A. sericeus and Adenanthos sp. Whicher Range (G.J. Keighery 9736) expressed P-mining strategies, including the formation of cluster roots. Cluster roots of A. obovatus were less effective than those of the other four Adenanthos species. In contrast to what is known for most Proteaceae, we found no cluster roots for A. barbiger. This species probably expressed a post-fire P-acquisition strategy. All Adenanthos species used P highly efficiently for photosynthesis, like other Proteaceae in similar natural habitats. Adenanthos is the first genus of Proteaceae found to express multiple P-acquisition strategies. The diversity of P-acquisition strategies in these Proteaceae, coupled with similarly diverse strategies in Fabaceae and Myrtaceae, demonstrates that caution is needed in making family- or genus-wide extrapolations about the strategies exhibited in severely P-impoverished megadiverse ecosystems.

The LaCLE35 peptide modifies rootlet density and length in cluster roots of white lupin.

White lupin (lupinus albus L.) forms special bottlebrush-like root structures called cluster roots (CR) when phosphorus is low, to remobilise sparingly soluble phosphates in the soil. The molecular mechanisms that control the CR formation remain unknown. Root development in other plants is regulated by CLE (CLAVATA3/ EMBRYO SURROUNDING REGION (ESR)-RELATED) peptides, which provide more precise control mechanisms than common phytohormones. This makes these peptides interesting candidates to be involved in CR formation, where fine tuning to environmental factors is required. In this study we present an analysis of CLE peptides in white lupin. The peptides LaCLE35 (RGVHy PSGANPLHN) and LaCLE55 (RRVHy PSCHy PDPLHN) reduced root growth and altered CR in hydroponically cultured white lupins. We demonstrate that rootlet density and rootlet length were locally, but not systemically, impaired by exogenously applied CLE35. The peptide was identified in the xylem sap. The inhibitory effect of CLE35 on root growth was attributed to arrested cell elongation in root tips. Taken together, CLE peptides affect both rootlet density and rootlet length, which are two critical factors for CR formation, and may be involved in fine tuning this peculiar root structure that is present in a few crops and many Proteaceae species, under low phosphorus availability.

Morphological and physiological responses of 14 macadamia rootstocks to drought stress and a comprehensive evaluation of drought resistance

Morphological and physiological responses of 14 macadamia rootstocks to drought stress and a comprehensive evaluation of drought resistance