Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil.

The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S. viridis. All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S. italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils.

A Comparative Metabolomics Study of Flavonoids in Radish with Different Skin and Flesh Colors (Raphanus sativus L.).

Radish (Raphanus sativus) is an important worldwide vegetable with a wide variety of colors that affect its appearance and nutritional quality. However, the large-scale detection, identification, and quantification of flavonoids in multicolor radish have rarely been studied. To uncover the diversity and accession-specific flavonoids in radish, liquid chromatography electrospray ionization-tandem mass spectrometry was used to analyze the metabolic profiles in the skin and flesh of six colored radish accessions: light-red Manshenhong, dark-red Touxinhong (TXH), purple Zijinling (ZJL), Xinlimei with red flesh (XLMF) and green skin, white Shizhuangbai (SZB), and black radish. In total, 133 flavonoids, including 16 dihydroflavones, 44 flavones, 14 flavonoids, 9 anthocyanins, and 28 flavonols, were characterized. The flavonoid metabolic profiles differed among the different colored radishes. Red and purple radishes contained similar anthocyanin compounds responsible for color pigmentation, including red cyanidin, callistephin, and pelargonin. Purple ZJL was most enriched with cyanidin o-syringic acid and cyanin, whereas callistephin and pelargonin were more abundant in dark-red TXH. Additionally, the black and white radishes shared similar anthocyanin and flavonoid profiles, suggesting that the color of black radishes was not caused by anthocyanin but by other metabolites. The metabolites in colored radishes that differed from SZB were mainly involved in the biosynthesis of plant secondary metabolites, such as flavonoid, flavone, flavonol, isoflavonoid, and phenylpropanoid biosynthesis. This study provides new insights into the differences in metabolite profiles among radishes with different skin and flesh colors. The results will be useful for aiding the cultivation of valuable new radish varieties.

Effects of light irradiation on essential oil biosynthesis in the medicinal plant Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim) Kitag.

Asarum heterotropoides Fr. var. mandshuricum (Maxim) Kitag (Chinese wild ginger) is an important medicinal herb. Essential oil extracted from its roots is the key ingredient and is mainly composed of phenylpropanoid compounds. As a skiophyte plant, light is a crucial factor for A. heterotropoides var. mandshuricum growth and metabolism. To investigate the effects of light irradiation on the essential oil biosynthesis in A. heterotropoides var. mandshuricum, the plants were cultivated in four light irradiation treatments (100, 50, 24 and 12% full sunlight). The photosynthetic capacity, essential oil content and composition, activities of several enzymes and levels of some secondary metabolites involved in the shikimic acid and cinnamic acid pathways were analyzed. The leaf mass per area, average diurnal net photosynthetic rate, and the essential oil content increased significantly with increasing light intensity. Phenylalanine, cinnamic acid, and p-coumaric acid in the cinnamic acid pathway were at their highest levels in plants cultivated in 100% full sunlight. The highest content of shikimic acid in the shikimic acid pathway was obtained in plants grown in 50% sunlight transmittance. The activity of the enzymes 3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase, phenylalanine ammonia lyase, cinnamate-4-hydroxylase and 4-coumarate:CoA ligase increased proportionally with light intensity. Overall, we conclude that high light irradiation promotes high net photosynthetic rate, high activity of enzymes and high amounts of phenylpropanoid precursor metabolites leading to significant biosynthesis of essential oil in A. heterotropoides var. mandshuricum.

Cell Type-Specific Imaging of Calcium Signaling in Arabidopsis thaliana Seedling Roots Using GCaMP3.

Cytoplasmic calcium ([Ca2+]cyt) is a well-characterized second messenger in eukaryotic cells. An elevation in [Ca2+]cyt levels is one of the earliest responses in plant cells after exposure to a range of environmental stimuli. Advances in understanding the role of [Ca2+]cyt in plant development has been facilitated by the use of genetically-encoded reporters such as GCaMP. Most of these studies have relied on promoters such as Cauliflower Mosaic Virus (35S) and Ubiquitin10 (UBQ10) to drive expression of GCaMP in all cell/tissue types. Plant organs such as roots consist of various cell types that likely exhibit unique [Ca2+]cyt responses to exogenous and endogenous signals. However, few studies have addressed this question. Here, we introduce a set of Arabidopsis thaliana lines expressing GCaMP3 in five root cell types including the columella, endodermis, cortex, epidermis, and trichoblasts. We found similarities and differences in the [Ca2+]cyt signature among these root cell types when exposed to adenosine tri-phosphate (ATP), glutamate, aluminum, and salt, which are known to trigger [Ca2+]cyt increases in root cells. These cell type-targeted GCaMP3 lines provide a new resource that should enable more in depth studies that address how a particular environmental stimulus is linked to specific root developmental pathways via [Ca2+]cyt.

Metabolomics Approaches for Analyzing Effects of Geographic and Environmental Factors on the Variation of Root Essential Oils of Ferula assa-foetida L.

Environmental factors shape the production and accumulation processes of plant secondary metabolites in medical and aromatic plants and thus their pharmacological and biological activity. Using an environmental metabolomics approach, we determined chemotypes and specific compounds on the basis of essential oils (EOs) from roots of 10 Iranian Ferula assa-foetida L. populations and related them to geographical, climate, and edaphic data. GC-MS revealed three distinct chemotypes characterized by (I) monoterpenes and Z-1-propenyl sec-butyl disulfide; (II) eudesmane sesquiterpenoids and α-agarofuran; and (III) Z- and E-1-propenyl sec-butyl disulfide. NIRS measurements indicated a similar but less distinct pattern. Structural equation models showed that EO constituents and content were directly influenced by edaphic factors (texture, pH, and iron, potassium, and aluminum content) and temperature and predominantly indirectly by latitude, longitude, and altitude. Predicting EO constituents or chemotypes by geographical, climate, and soil factors can be used in F. assa-foetida to select populations with specific EO characteristics.

Comparative Analysis of Microbial Communities in Fronds and Roots of Three Duckweed Species: Spirodela polyrhiza, Lemna minor, and Lemna aequinoctialis.

The microbial communities inhabiting the fronds of duckweeds have not been investigated in as much detail as those on the roots. We herein examined the microbial communities in three duckweed species using 16S rRNA amplicon sequencing and compared them to those on the roots. The microbial compositions of the fronds were distinct from those of the roots in the three species. Various types of taxonomic bacteria, including rarely cultivated phyla, Acidobacteria, Armatimonadetes, and Verrucomicrobia, were also isolated from the fronds, but at a slightly lower abundance than those from the roots. These results suggest that duckweed fronds are an alternative source for isolating rare and novel microbes, which may otherwise be recalcitrant to cultivation using conventional strategies.

Roots play a key role in drought-tolerance of poplars as suggested by reciprocal grafting between male and female clones.

Drought stress influences the growth of plants and thus grafting has been widely used to improve tolerance to abiotic stresses. Poplars possess sex-specific responses to drought stress, but how male or female rootstock affect the grafted plant is little known. To explore the mechanisms underlying changes in drought tolerance caused by grafting, we investigated the changes in growth, leaf traits, gas exchange and antioxidant enzyme activities of reciprocally grafted seedlings between Populus euramericana cv. "Nanlin895" (NL-895) (female) and Populus deltiodes cv."3412" (NL-3412) (male) under water deficit stress with 30% field capacity for 30 d. Results showed that drought stress affected adversely growth, morphological, and physiological characteristics in all seedlings studied. Grafted seedlings with male roots can effectively alleviated the inhibition of growth induced by drought stress, as shown by higher WUE, activities of SOD, POD and CAT, and lower levels of lipid peroxidation. Male seedlings with female roots were found to be less tolerance to drought than non-grafted male clones and female scions with male roots, but more tolerance than non-grafted female clones. This results suggested that drought tolerance of grafted seedlings is primarily caused by the rootstock, although the scion also affects the grafted plant. Thus, paying attention on the root genotype can provide an important means of improving the drought tolerance of poplars.

Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth.

BACKGROUND: Root systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) are responsible for the formation of Casparian strips. RESULTS: To investigate the function of CASPs in cotton, we identified and characterized 48, 54, 91 and 94 CASPs from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively, at the genome-wide level. However, only 29 common homologous CASP genes were detected in the four Gossypium species. A collinearity analysis revealed that whole genome duplication (WGD) was the primary reason for the expansion of the genes of the CASP family in the four cotton species. However, dispersed duplication could also contribute to the expansion of the GaCASPs gene family in the ancestors of G. arboreum. Phylogenetic analysis was used to cluster a total of 85 CASP genes from G. arboreum and Arabidopsis into six distinct groups, while the genetic structure and motifs of CASPs were conserved in the same group. Most GaCASPs were expressed in diverse tissues, with the exception of that five GaCASPs (Ga08G0113, Ga08G0114, Ga08G0116, Ga08G0117 and Ga08G0118) that were highly expressed in root tissues. Analyses of the tissue and subcellular localization suggested that GaCASP27 genes (Ga08G0117) are membrane protein genes located in the root. In the GaCASP27 silenced plants and the Arabidopsis mutants, the lateral root number significantly increased. Furthermore, GaMYB36, which is related to root development was found to regulate lateral root growth by targeting GaCASP27. CONCLUSIONS: This study provides a fundamental understanding of the CASP gene family in cotton and demonstrates the regulatory role of GaCASP27 on lateral root growth and development.

Medicinal plants used by 'root doctors', local traditional healers in Bié province, Angola.

ETHNOPHARMACOLOGICAL RELEVANCE: This study is one of the first post-civil war efforts to document traditional botanical knowledge in Bié province, central Angola, in a first step to bring more studies on the use of medicinal plant resources in this area so as to bring new insights into Angolan bio-cultural diversity. AIM OF THE STUDY: Examine the variety of plant species used for medical purposes, as well as characterize their social and cultural values. Also, it is aimed to compare their uses in the studied region with those in Sub-Saharan Africa and report new ethnomedicinal uses. MATERIALS AND METHODS: We documented traditional medicinal plant knowledge among professional herbalists in two areas in Bié province through participatory observation, semi-structured interviews and transect walks. Ethnobotanical information was quantified based on Use Reports to (1) rate traditional knowledge; and (2) determine most useful taxa. RESULTS: In total, 10 traditional healers shared information on their knowledge. A total of 87 plant species distributed among 57 genera and 36 botanical families were documented with Fabaceae being the best-represented family with 18 species, followed by Phyllanthaceae (6), Apocynaceae (5), Asteraceae (5), Rubiaceae (5), Lamiaceae (4), and Ochnaceae (3). Most medicinal plants are usually gathered at a distance from human settlements because of the belief in the higher efficacy of 'wild' plants shared by all herbalists. Roots are the most common plant part used (79%), explaining why the consulted herbalists call themselves 'root doctors'. CONCLUSIONS: The culturally most important medicinal species identified in this study, i.e. Securidaca longepedunculata, Garcinia huillensis, Annona stenophylla, Afzelia quanzensis and Strychnos cocculoides, were previously reported for the same use in neighbouring countries and elsewhere in Africa. Our study also indicates that there are several locally valuable species that have not yet been studied for their medical potential, to name a few: Alvesia rosmarinifolia, Diplorhynchus condylocarpon, Eriosema affine, Paropsia brazzaeana, Rhus squalida, Sclerocroton cornutus or Xylopia tomentosa. Moreover, the ethnomedicinal use of 26 species was reported for the first time to sub-Saharan Africa. CLASSIFICATION: Ethnopharmacological field studies.

Phytoremediation ability of naturally growing plant species on the electroplating wastewater-contaminated site.

The presence of heavy metal in soil and water resources has serious impact on human health. The study was designed to examine the phytoremediation ability of plant species that are growing naturally on the Zn-contaminated site. For the study, six plant species and their rhizospheric soil as well as non-rhizospheric soil samples were collected from different parts of the industrial sites for chemical and biological characterization. Visual observations and highest importance value index (IVI) through biodiversity study revealed potential plants as effective ecological tools for the restoration of the contaminated site. Among the plants, almost all were the most efficient in accumulating Fe, Mn, Cu and Zn in its shoots and roots, while Cynodon dactylon, Chloris virgata and Desmostachya bipinnata were found to be stabilizing Cr, Pb and Cd (bioconcentration factor in root = 7.95, 6.28 and 1.98 as well as translocation factor = 0.48, 0.46 and 0.78), respectively. Thus, the results of this study showed that the naturally growing plant species have phytoremediation potential to remediate the electroplating wastewater-contaminated site. These plant species are successful phytoremediators with their efficient metal stabilizing and well-evolved tolerance to heavy metal toxicity.

Comparative anatomy on the vegetative organs of genus Ziziphora L. (Lamiaceae) from Turkey.

The genus Ziziphora L. (Lamiaceae) is represented by five species (nine taxa) in the Turkish Flora. These taxa are Z. clinopodioides Lam. (subsp. elbursensis, subsp. filicaulis, subsp. kurdica, subsp. rigida), Z. capitata L., Z. persica Bunge, Z. tenuior L., Z. taurica Bieb. subsp. taurica, and Z. taurica Bieb. subsp. cleonioides (Boiss.) Davis which to be an endemic taxon for Turkey. They are strongly aromatic herbs which contain rich pulegone and used as herbal teas and spices and for this reason. In this study, comparative anatomy of the genus Ziziphora growing in Turkey is presented for the first time. In anatomical studies, cross sections of vegetative organs such as the root, stem, and leaf (lamina and petiole) were examined. In addition, to exhibit stomatal distribution and anatomy on adaxial and abaxial leaves were taken surface sections of the lamina and calculated stomatal index. Lamina and petiole anatomy were shown to be of great importance in the taxonomy of the Ziziphora taxa. The presence or absence of sclerenchyma in midrib of lamina and petiole, cortex parenchyma layer, mesophyll structure, and epidermal surface were found to be important characters for identification of Ziziphora taxa.

Isolation and Screening of Indigenous Plant Growth-promoting Rhizobacteria from Different Rice Cultivars in Afghanistan Soils.

To develop biofertilizers for rice in Afghanistan, 98 plant growth-promoting rhizobacteria were isolated from rice plants and their morphological and physiological characteristics, such as indole-3-acetic acid production, acetylene reduction, phosphate and potassium solubilization, and siderophore production, were evaluated. The genetic diversity of these bacteria was also analyzed based on 16S rRNA gene sequences. Of 98 bacteria, 89.7% produced IAA, 54.0% exhibited nitrogenase activity, and 40% showed phosphate solubilization and siderophore production. Some isolates assigned to Pseudomonas (brassicacearum, chengduensis, plecoglossicida, resinovorans, and straminea) formed a relationship with rice, and P. resinovorans and P. straminea showed nitrogen fixation. Rhizobium borbori and R. rosettiformans showed a relationship with rice plants and nitrogen fixation. Among the isolates examined, AF134 and AF137 belonging to Enterobacter ludwigii and P. putida produced large amounts of IAA (92.3 µg mL-1) and exhibited high nitrogenase activity (647.4 nmol C2H4 h-1), respectively. In the plant growth test, more than 70% of the inoculated isolates showed significantly increased root and shoot dry weights. Highly diverse bacterial isolates showing promising rice growth-promoting traits were obtained from Afghanistan alkaline soils.

Effects of root and leaf litter identity and diversity on oribatid mite abundance, species richness and community composition.

Habitat heterogeneity is an important driver of aboveground species diversity but few studies have investigated effects on soil communities. Trees shape their surrounding by both leaf litter and roots generating small scale heterogeneity and potentially governing community patterns of soil organisms. To assess the role of vegetation for the soil fauna, we studied whether tree species (Fagus sylvatica L., Acer pseudoplatanus L., Fraxinus excelsior L., Tilia cordata Mill.), markedly differing in leaf litter quality and root associated mycorrhizal symbionts, affect oribatid mite communities by shaping below- and aboveground resources and habitat complexity and availability. Oribatid mite abundance, species richness, community structure and the proportion of litter living and parthenogenetic individuals were analyzed and related to microbial biomass and the amount of remaining litter mass. Although leaf litter species with higher nutritional values decomposed considerably faster, microbial biomass only slightly differed between leaf litter species. Neither root species nor leaf litter species affected abundance, species richness or community structure of oribatid mites. However, root species had an effect on the proportion of parthenogenetic individuals with increased proportions in the presence of beech roots. Overall, the results suggest that identity and diversity of vegetation via leaf litter or roots are of minor importance for structuring oribatid mite communities of a temperate forest ecosystem.

Estimating belowground plant abundance with DNA metabarcoding.

Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2  = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.

Hydrogel-based transparent soils for root phenotyping in vivo.

Root phenotypes are increasingly explored as predictors of crop performance but are still challenging to characterize. Media that mimic field conditions (e.g., soil, sand) are opaque to most forms of radiation, while transparent media do not provide field-relevant growing conditions and phenotypes. We describe here a "transparent soil" formed by the spherification of hydrogels of biopolymers. It is specifically designed to support root growth in the presence of air, water, and nutrients, and allows the time-resolved phenotyping of roots in vivo by both photography and microscopy. The roots developed by soybean plants in this medium are significantly more similar to those developed in real soil than those developed in hydroponic conditions and do not show signs of hypoxia. Lastly, we show that the granular nature and tunable properties of these hydrogel beads can be leveraged to investigate the response of roots to gradients in water availability and soil stiffness.

Seedling traits predict drought-induced mortality linked to diversity loss.

Trait-based approaches are increasingly used to predict ecological consequences of climate change, yet seldom have solid links been established between plant traits and observed climate-driven community changes. Most analyses have focused on aboveground adult plant traits, but in warming and drying climates, root traits may be critical, and seedlings may be the vulnerable stage. Relationships of seedling and root traits to more commonly measured traits and ecological outcomes are poorly known. In an annual grassland where winter drought-induced seedling mortality is driving a long-term decline in native diversity, using a field experiment during the exceptionally dry winter of 2017-2018, we found that seedling mortality was higher and growth of seedlings and adults were lower in unwatered than watered sites. Mortality of unwatered seedlings was higher in species with shorter seedling roots, and also in species with the correlated traits of small seeds, high seedling specific leaf area (SLA), and tall seedlings. Adult traits varied along an axis from short-stature, high SLA and foliar N, and early flowering to the opposite values, and were only weakly correlated with seedling traits and seedling mortality. No evidence was found for adaptive plasticity, such as longer roots or lower SLA in unwatered plants. Among these species, constitutive variation in seedling root length explained most of the variation in survival of a highly vulnerable life stage under winter drought. Selective loss of species with high adult SLA, observed in this community and others under drought stress, may be the byproduct of other correlated traits.

A novel similarity search approach for high-performance thin-layer chromatography (HPTLC) fingerprinting of medicinal plants.

INTRODUCTION: In addition to the development of analytical equipment, another movement has also appeared in the field of computer assisted techniques for metabolite assessment. Although, some studies can be found in the literature there is still not available reliable and user-friendly software which is coupled with a simple chromatography method for developing a database to identify medicinal plants. OBJECTIVES: Developing a novel similarity search approach for high-performance thin-layer chromatography (HPTLC) fingerprinting. METHODS: Combined HPTLC with image analysis approach was used for similarity assessment of 70 standard medicinal plants. Ethyl acetate-ethyl methyl ketone-formic acid 98%-water (50:30:10:10) were chosen among different examined mobile phases. Liebermann-Burchard and anisaldehyde reagents were chosen for HPTLC derivatisation for visualisation. Image analysis based on Cannys' method was used to determine the spot size of each HPTLC image. A similarity search algorithm based on colour (RGB, HSV and Lab) information alone or together with retardation factor (Rf ) and spot size information calculated with the software was built to assess the fingerprinting of medicinal plants. RESULTS: The software was capable of calculating spots size and Rf values. It authenticated unknown samples based on comparing images information, spots size and/or Rf in the built database. Similarity values were 75-96% for the selected plants chromatograms with those of the same plant in the database. It presents better results than principal components analysis (PCA), classification and regression trees (CART) and partial least squares discriminant analysis (PLS-DA). CONCLUSION: The procedure paves the way for constructing a database of HPTLC images of medicinal plants.

Plant hosts control microbial denitrification activity.

In the rhizosphere, complex and dynamic interactions occur between plants and microbial networks that are primarily mediated by root exudation. Plants exude various metabolites that may influence the rhizosphere microbiota. However, few studies have sought to understand the role of root exudation in shaping the functional capacities of the microbiota. In this study, we aimed to determine the impact of plants on the diversity of active microbiota and their ability to denitrify via root exudates. For that purpose, we grew four plant species, Triticum aestivum, Brassica napus, Medicago truncatula and Arabidopsis thaliana separately in the same soil. We extracted RNA from the root-adhering soil and the root tissues, and we analysed the bacterial diversity by using 16S rRNA metabarcoding. We measured denitrification activity and denitrification gene expression (nirK and nirS) from each root-adhering soil sample and the root tissues using gas chromatography and quantitative PCR, respectively. We demonstrated that plant species shape denitrification activity and modulate the diversity of the active microbiota through root exudation. We observed a positive effect of T. aestivum and A. thaliana on denitrification activity and nirK gene expression on the root systems. Together, our results underscore the potential power of host plants in controlling microbial activities.

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa.

Rhizobacteria play an important role in bridging the soil and plant microbiomes and improving the health and growth of plants. In this study, the bacterial community structures and compositions of rhizosphere microbiomes associated with six plant species, representing two orders and three families of wild plants grown in the same field, were evaluated. The six plant species examined harbored a core and similar bacterial communities of the rhizosphere microbiome, which was dominated by members of Rhizobiales, Sphingomonadales, Burkholderiales, and Xanthomonadales of Proteobacteria, Subgroup 4 of Acidobacteria, and Sphingobacteriales of Bacteroidetes. Plant species had a significant effect on the microbial composition and Operational Taxonomic Unit (OTU) abundance of the rhizosphere microbiome. Statistical analysis indicated a significant differential OTU richness (Chao1, p < 0.05) and bacterial diversity (Shannon index, p < 0.0001) of the rhizosphere microbiome at the plant species, genus, or families levels. The paralleled samples from the same plant species in the PCoA and hierarchical cluster analysis demonstrated a clear tendency to group together, although the samples were not strictly separated according to their taxonomic divergence at the family or order level. The CAP analysis revealed a great proportion (44.85%) of the variations on bacterial communities could be attributed to the plant species. The results demonstrated that largely conserved and taxonomically narrow bacterial communities of the rhizosphere microbiome existed around the plant root. The bacterial communities and diversity of the rhizosphere microbiome were significantly related to the plant taxa, at least at the species levels.

Comprehensive Metabolomics Analysis of Mandarins ( Citrus reticulata) as a Tool for Variety, Rootstock, and Grove Discrimination.

The metabolite profile responsible for the quality of mandarin fruit is influenced by preharvest factors including genotype, rootstock, grove location, etc. In this paper, mandarin varieties were discriminated using metabolomics. Additionally, effects on metabolic profiles due to grove location and rootstock differences were also investigated. Results revealed that mandarin varieties could be differentiated using the metabolite profile, while the compositions of flavonoids have the potential for variety differentiation. With regard to fruits of the same variety, grove location might determine the overall profile of metabolites, whereas rootstock possibly affected composition of secondary metabolites. Pathway enrichment analysis demonstrated that biosynthesis pathways of terpenoids and steroids involving limonene and linalool were highly influenced by variety diversity. Moreover, the flavonoid biosynthesis pathway, involving hesperetin, naringenin, eriodictyol, and taxifolin, was indicated to have a close relationship with rootstock differentiation. This study provides useful and important information with depth for breeding and optimizing preharvest practices.