The structure and function of the global citrus rhizosphere microbiome

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health

Display of Cell Surface Sites for Fibronectin Assembly Is Modulated by Cell Adherence to 1F3 and C-Terminal Modules of Fibronectin

BACKGROUND: Fibronectin-null cells assemble soluble fibronectin shortly after adherence to a substrate coated with intact fibronectin but not when adherent to the cell-binding domain of fibronectin (modules (7)F3-(10)F3). Interactions of adherent cells with regions of adsorbed fibronectin other than modules (7)F3-(10)F3, therefore, are required for early display of the cell surface sites that initiate and direct fibronectin assembly. METHODOLOGY/PRINCIPAL FINDINGS: To identify these regions, coatings of proteolytically derived or recombinant pieces of fibronectin containing modules in addition to (7)F3-(10)F3 were tested for effects on fibronectin assembly by adherent fibronectin-null fibroblasts. Pieces as large as one comprising modules (2)F3-(14)F3, which include the heparin-binding and cell adhesion domains, were not effective in supporting fibronectin assembly. Addition of module (1)F3 or the C-terminal modules to modules (2)F3-(14)F3 resulted in some activity, and addition of both (1)F3 and the C-terminal modules resulted in a construct, (1)F3-C, that best mimicked the activity of a coating of intact fibronectin. Constructs (1)F3-C V0, (1)F3-C V64, and (1)F3-C Delta(V(15)F3(10)F1) were all able to support fibronectin assembly, suggesting that (1)F3 through (11)F1 and/or (12)F1 were important for activity. Coatings in which the active parts of (1)F3-C were present in different proteins were much less active than intact (1)F3-C. CONCLUSIONS: These results suggest that (1)F3 acts together with C-terminal modules to induce display of fibronectin assembly sites on adherent cells

Mitochondrial genome of Diaphorencyrtus aligarhensis (Hymenoptera: Chalcidoidea: Encyrtidae) and phylogenetic analysis

Diaphorencyrtus aligarhensis is an important natural enemy of the psyllid Diaphorina citri Kuwayama, a vector of the huanglongbing (HLB). Here, we sequenced and annotated the mitochondrial genome (mitogenome) of D. aligarhensis. This mitogenome was 16,264 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). All 13 PCGs were initiated by the ATN (ATG, ATT, ATA, and ATC) codon. All PCGs terminate with the stop codon TAA except for cox2 and nad1 which end with the incomplete codon T−. Phylogenetic analysis showed that D. aligarhensis got together with the same family species Encyrtus infelix, and Encyrtidae had a close relationship with Agaonidae

Modeling Citrus Huanglongbing transmission within an orchard and its optimal control

Citrus Huanglongbing (HLB) is the most devastating citrus disease worldwide. In this paper, a deterministic dynamical model is proposed to explore the transmission dynamics of HLB between citrus tree and Asian citrus psyllid (ACP). Using the theory of dynamical system, the dynamics of the model are rigorously analyzed. The results show that the disease-free equilibrium is globally asymptotically stable when the basic reproduction number \mathscr{R}_0 < 1, and when \mathscr{R}_0 > 1 the system is uniformly persistent. Applying the global sensitivity analysis of $\mathscr{R}_0$, some parameters that have the greatest impact on HLB transmission dynamics are obtained. Furthermore, the optimal control theory is applied to the model to study the corresponding optimal control problem. Both analytical and numerical results show that: (1) the infected ACP plays a decisive role in the transmission of HLB in citrus trees, and eliminating the ACP will be helpful to curtail the spread of HLB; (2) optimal control strategy is superior to the constant control strategy in decreasing the prevalence of the diseased citrus trees, and the cost of implementing optimal control is much lower than that of the constant control strategy; and (3) spraying insecticides is more effective than other control strategies in reducing the number of ACP in the early phase of the transmission of HLB. These theoretical and numerical results may be helpful in making public policies to control HLB in orchards more effectively

The complete mitochondrial genome of click beetle Agrypnus sp. (Coleoptera: Elateridae) and phylogenetic analysis

Larvae of click beetles are the most important soil-dwelling agricultural pests and are abundant throughout the world. Agrypnus sp. belongs to the subfamily Agrypninae of Elateridae. Here, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Agrypnus sp., the new representative of the mitogenome of the subfamily. This mitogenome was 16,056 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). Gene order was conserved and identical to most other previously sequenced Elateridae. The nucleotide composition biases towards A and T, which together made up 70.8% of the entirety. Phylogenetic analysis based on 13 PCGs sequences showed that Agrypnus sp. got together with the same subfamily species Pyrophorus divergens, Pyrearinus termitilluminans, Ignelater luminosus, and Hapsodrilus ignifer with high support value

Antioxidant and Anticancer Activities of Essential Oil from Gannan Navel Orange Peel

China is one of the leading producers of citrus in the world. Gannan in Jiangxi Province is the top navel orange producing area in China. In the present study, an essential oil was prepared by cold pressing of Gannan navel orange peel followed by molecular distillation. Its chemical composition was analyzed by GC-MS. Twenty four constituents were identified, representing 97.9% of the total oil. The predominant constituent was limonene (74.6%). The anticancer activities of this orange essential oil, as well as some of its major constituents, were investigated by MTT assay. This essential oil showed a positive effect on the inhibition of the proliferation of a human lung cancer cell line A549 and prostate cancer cell line 22RV-1. Some of the oil constituents displayed high anticancer potential and deserve further study

Chemical composition and antimicrobial activity of Gannan navel orange (Citrus sinensis Osbeck cv. Newhall) peel essential oils

The present investigation reported the chemical composition of cold pressed Gannan navel orange peel essential oil (EO) and its molecular distillation fraction (light phase EO), and examined their antimicrobial activity against spoiling and pathogenic microorganisms. Gas chromatography‐mass spectrometry analysis identified 27 and 20 different chemical constituents in cold pressed EO and light phase EO, respectively. Limonene was the major constituent, accounting for 85.32% of cold pressed EO and 60.44% of light phase EO. Both EOs and some of their constituents showed good antimicrobial activity. Compared to cold pressed EO, light phase EO exhibited the better antimicrobial activity under weak acidic and neutral conditions. The light phase EO presented a higher antimicrobial activity after thermo‐treatment at 60–100°C for 20 min than cold pressed EO. These results demonstrated that light phase EO had a potential to be used as a novel antimicrobial agent for food preservation and food processing

Comparative Transcriptome and sRNAome Analyses Reveal the Regulatory Mechanisms of Fruit Ripening in a Spontaneous Early-Ripening Navel Orange Mutant and Its Wild Type

A complex molecular regulatory network plays an important role in the development and ripening of fruits and leads to significant differences in apparent characteristics. Comparative transcriptome and sRNAome analyses were performed to reveal the regulatory mechanisms of fruit ripening in a spontaneous early-ripening navel orange mutant (&lsquo;Ganqi 4&rsquo;, Citrus sinensis L. Osbeck) and its wild type (&lsquo;Newhall&rsquo; navel orange) in this study. At the transcript level, a total of 10792 genes were found to be differentially expressed between MT and WT at the four fruit development stages by RNA-Seq. Additionally, a total of 441 differentially expressed miRNAs were found in the four periods, and some of them belong to 15 families. An integrative analysis of the transcriptome and sRNAome data revealed some factors that regulate the mechanisms of formation of early-ripening traits. First, secondary metabolic materials, especially endogenous hormones, carotenoids, cellulose and pectin, obviously changed during fruit ripening in MT and WT. Second, we found a large number of differentially expressed genes (PP2C, SnRK, JAZ, ARF, PG, and PE) involved in plant hormone signal transduction and starch and sucrose metabolism, which suggests the importance of these metabolic pathways during fruit ripening. Third, the expression patterns of several key miRNAs and their target genes during citrus fruit development and ripening stages were examined. csi-miR156, csi-miR160, csi-miR397, csi-miR3954, and miRN106 suppressed specific transcription factors (SPLs, ARFs, NACs, LACs, and TCPs) that are thought to be important regulators involved in citrus fruit development and ripening. In the present study, we analyzed ripening-related regulatory factors from multiple perspectives and provide new insights into the molecular mechanisms that operate in the early-ripening navel orange mutant &lsquo;Ganqi 4&rsquo;

Effects of Postharvest Time, Heat Treatment, pH and Filtration on the Limonin Content in Newhall Navel Orange (Citrus sinensis Osbeck cv. Newhall) Juice

Delayed bitterness causes severe economic loss in citrus juice industry worldwide, which is mostly due to the formation of limonoid compounds, especially limonin, in juice. In this study, effects of postharvest time of fruits, heat treatment, pH and filtration of juice on limonin content in Newhall navel orange (Citrus sinensis Osbeck cv. Newhall) juice were investigated. Our research indicated for the first time that: (1) limonin content in juice would gradually increase to a maximal level and then remained almost constant thereafter as storage time going on, whereas the maximum constant value (MCV) of limonin content in juice significantly (p &lt; 0.05) decreased with the increment of postharvest time of fruits being juiced; (2) heat treatment and acidification of juice only speeded up the formation of limonin to the maximal level while without changing the MCV of limonin content; (3) the juice after filtration exhibited much lower MCV of limonin content compared with the unfiltered one. These experimental observations might not only provide useful information for the development of new debitterness method for navel orange juice, but also strongly support the acid-promoted delayed bitterness mechanism, suggesting the formation of delayed bitterness might primary due to the acid-promoted rather than the enzyme-catalyzed lactonization of limonoate A-ring lactone (LARL) to produce limonin in juice of navel orange

Isolation and Structure-Activity Relationship of Subergorgic Acid and Synthesis of Its Derivatives as Antifouling Agent

In this study, as part of our continuous search for environmentally-friendly antifoulants from natural resources, subergorgic acid (SA) was identified from the gorgonian coral Subergorgia suberosa, demonstrating non-toxic, significant inhibitory effects (EC50 1.25 &#956;g/mL, LC50 &gt; 25 &#956;g/mL) against the settlement of Balanus amphitrite. To further explore the bioactive functional groups of SA and synthesize more potent antifouling compounds based on the lead SA, the structure-activity relationships of SA were studied, followed by rational design and synthesis of two series of SA derivatives (one being benzyl esters of SA and another being SA derivatives containing methylene chains of various lengths). Our results indicated that (1) both the double bond and ketone carbonyl are essential elements responsible for the antifouling effect of SA, while the acid group is not absolutely necessary for maintaining the antifouling effect; (2) all benzyl esters of SA displayed good antifouling effects (EC50 ranged from 0.30 to 2.50 &#956;g/mL) with the most potent compound being 5 (EC50 0.30 &#956;g/mL, LC50 &gt; 25 &#956;g/mL), which was over four-fold more potent than SA; and (3) the introduction of a methylene chain into SA reduces the antifouling potency while the length of the methylene chain may differently influence the antifouling effect, depending on the functional group at the opposite site of the methylene chain. Not only has this study successfully revealed the bioactive functional groups of SA, contributing to the mechanism of SA against the settlement of B. amphitrite, but it has also resulted in the identification of a more potent compound 5, which might represent a non-toxic, high-efficiency antifoulant