Pseudomonas citri sp. nov., a potential novel plant growth promoting bacterium isolated from rhizosphere soil of citrus.

A novel potential plant growth promoting bacterium, designated OPS13-3T, was isolated from rhizosphere soil of citrus in Aotou Town of Guangzhou, Guangdong Province, PR China. It showed high ability to dissolve insoluble inorganic phosphate and organic phosphorus and to produce 3-indoleacetic acid (IAA) and siderophore. Cells of the novel strain were Gram-stain-negative, rod-shaped, aerobic and motile with polar flagellum. It shared the highest 16S rRNA gene similarity with Pseudomonas mucoides CCUG 74874T (98.7%) and P. bijieensis LMG 31948T (98.7%). Phylogenetic analyses based the 16S rRNA gene and genome sequences revealed that strain OPS13-3T belonged to the genus Pseudomonas, and was most closely related to P. mediterranea ICMP 14184T and P. corrugate ICMP 5819T. The average nucleotide identity (ANI) and DNA-DNA hybridization (dDDH) values between the novel strain and closely relatives with high 16S rRNA gene similarities were 80.8‒87.5% and 24.7‒34.6%, respectively, which were much below the threshold values for species delimitation. The major fatty acids included C16:0, C10:0 3-OH and summed feature 3 (C16:1ω7c and/or C16:1ω6c). It took ubiquinone 9 as the predominant respiratory quinone and the polar lipids contained phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), three unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenetic, phenotypic and chemotaxonomic analyses and genome comparison, strain OPS13-3T should be considered as a novel species of the genus Pseudomonas, for which the name Pseudomonas citri sp. nov. is proposed (type strain OPS13-3T = GDMCC 1.3118T = JCM 35385T).

Linking lipid transfer with reduced arbuscule formation in tomato roots colonized by arbuscular mycorrhizal fungus under low pH stress.

Arbuscules are the core structures of arbuscular mycorrhizae (AM), and arbuscule development is regulated by environmental stress, e.g., low pH. Recent studies indicate that lipid transfer from plants is essential for AM fungal colonization; however, the role of lipid transfer in arbuscule formation and the dynamics of lipid accumulation in arbuscules under low pH stress are far from well understood. In the symbiosis of tomato and Rhizophagus intraradices under contrasting pH conditions (pH 4.5 vs. pH 6.5), we investigated arbuscule formation, nutrient uptake, alkaline phosphatase activity and lipid accumulation; examined the gene expression involved in phosphate transport, lipid biosynthesis and transfer and sugar metabolism; and visualized the lipid dynamics in arbuscules. Low pH greatly inhibited arbuscule formation, in parallel with reduced phospholipid fatty acids accumulation in AM fungus and decreased P uptake. This reduction was supported by the decreased expression of plant genes encoding lipid biosynthesis and transfer. More degenerating arbuscules were observed under low pH conditions, and neutral lipid fatty acids accumulated only in degenerating arbuscules. These data reveal that, under low pH stress, reduced lipid transfer from hosts to AM fungi is responsible for the inhibited arbuscule formation.

Exogenous abscisic acid and root volatiles increase sporulation of Rhizophagus irregularis DAOM 197198 in asymbiotic and pre-symbiotic status.

Several studies have demonstrated asymbiotic growth and development of arbuscular mycorrhizal (AM) fungi, although AM fungi are regarded as obligately symbiotic root-inhabiting fungi. Phytohormones, root exudates, and volatiles are important factors regulating the host-AM fungi interaction. However, the effects of phytohormones, root exudates, and volatiles on asymbiotic (without roots present) or pre-symbiotic (with roots present but no colonization) sporulation of AM fungi are unexplored. In this study, we tested the asymbiotic sporulation of Rhizophagus irregularis DAOM 197198 and further investigated the influences of abscisic acid (ABA), the exudates, and volatiles of tomato hairy roots on asymbiotic or pre-symbiotic sporulation in vitro. Results indicated that mother spores asymbiotically and pre-symbiotically produced daughter spores singly or in pairs. Compared with symbiotically produced spores, pre-symbiotically produced spores were significantly smaller (43.1 µm vs. 89.2 µm in diameter). Exogenous ABA applied to mother spores significantly increased the number of daughter spores, and root volatiles also significantly promoted pre-symbiotic sporulation. Our results provide the first evidence that exogenous ABA can promote AM fungal asymbiotic and pre-symbiotic sporulation, which highlights the potential role of phytohormones in AM fungal propagation.

A comparative analysis of the levels and drivers of regional coordinated development in the Yangtze River Economic Belt and Yellow River Basin, China.

Positioned in the era of the transformation of China's primary social contradictions, this study delves into the new connotations of regional coordinated development(RCD) from the perspective of "factors" coordination within the region and constructs an RCD evaluation system from five subsystems of regional economic coordination(REC), urban-rural coordination(URC), economic and social coordination(EASC), resource and environmental coordination(RAEC), and material and spiritual civilization coordination(MASCC). Then, the Entropy weight-TOPSIS model is used to evaluate the RCD levels of the 19 provinces located in the Yangtze River Economic Belt(YREB) and Yellow River Basin(YRB) from 2010 to 2019, and the two-way fixed-effects model is employed to illustrate the driving mechanisms of various influencing factors on the RCD in YRB and YREB. The results show that:(1)the RCD levels of YRB and YREB show a fluctuating upward trend during 2010 and 2019, however, both regions have low RCD levels, as seen by the mean RCD indices for YREB and YRB, which are only 0.433 and 0.309, respectively. (2) The RCD level of YREB is higher than that of YEB. In 2019, the "coordinated" provinces in YRB and YREB account for 37.50% and 81.82% of the total number of provinces in the basins, respectively, the "uncoordinated" and "low coordinated" provinces all located in YRB. (3) The RCD of YRB and YREB is significantly improved by REC, URC and RAEC, but not significantly positively by MASCC or EASC, and insufficient development of MASCC is the main contradiction limiting the increase in the RCD level of YRB, while the low level of EASC has become the main obstacle limiting the RCD of YREB. (4)Finally, based on the varying impact degrees and directions of different influencing factors on the RCD in YRB and YREB, the recommendations to promote RCD are proposed.

Tomato plant growth promotion and drought tolerance conferred by three arbuscular mycorrhizal fungi is mediated by lipid metabolism.

Arbuscular mycorrhizal fungi (AMF) can promote plant growth and enhance plant drought tolerance with varying effect size among different fungal species. However, the linkage between the variation and the lipid metabolism, which is exclusively derived from plants, has been little explored thus far. Here, we established AM symbiosis between tomato (Solanum lycopersicum) plants and three AMF species (Rhizophagus intraradices, Funneliformis mosseae, Rhizophagus irregularis) under well watered (WW) or drought stressed (DS) conditions in pot experiment. The plant biomass, chlorophyll fluorescence Fv/Fm, shoot P content and mycorrhizal colonization were determined. Meanwhile, fatty acid (FA) profiles and relative expression of genes encoding for nutrition exchange (SlPT4, SlPT5, RAM2, STR/STR2) in roots were also monitored. DS significantly decreased plant biomass while AMF significantly increased it, with three fungal species varying in their growth promoting capacity and drought tolerance capacity. The growth promoting effect of R. irregularis was lower than those of R. intraradices and F. mosseae, and was associated with higher mycorrhizal colonization and more consumption of lipids. However, the drought tolerance capacity of R. irregularis was greater than those of R. intraradices and F. mosseae, and was associated with less decrease in mycorrhizal colonization and lipid content. We also found that AMF mediated plant drought tolerance via regulating both AM specific FAs and non-AM specific FAs in a complementary manner. These data suggest that lipid metabolism in AM plays a crucial role in plant drought tolerance mediated by AMF.

Drought stress reduces arbuscular mycorrhizal colonization of Poncirus trifoliata (L.) roots and plant growth promotion via lipid metabolism.

Drought stress poses increasingly serious threats to agricultural production in the era of global climate change. Arbuscular mycorrhizal (AM) fungi are well-recognized biostimulants promoting plant tolerance to drought stress. Lipids are indispensable for AM fungal colonization, however, the involvement of lipid metabolism in the drought tolerance conferred by AM fungi is largely unknown. In this study, we inoculated Poncirus trifoliata (L.) with Rhizophagus irregularis DAOM197198 under no drought stress, medium drought stress and severe drought stress, with non-inoculation under respective treatments as control. Results indicated that AM fungal inoculation significantly promoted the drought tolerance of P. trifoliata (L.), with the effect size decreasing along with drought severity. Moreover, the effect size was significantly related to arbuscule abundance. Fatty acid profiling showed that the arbuscule abundance was determined by the AM-specific phospholipids (PLs), whose biosynthesis and delivery were inhibited by drought stress as revealed by qRT-PCR of FatM, RAM1 and STR/STR2. More interestingly, AM fungal inoculation increased the lipid allocation to total PLs and the unsaturation rate of total neutral lipids (NLs), probably indicating the involvement of non-AM-specific lipids in the increased drought tolerance. Taken together, our results demonstrate that lipid metabolism in AM mediates the increased drought tolerance conferred by AM fungal inoculation, with AM-specific and non-AM-specific lipids functioning therein in different ways.

Lipids Mediate Arbuscule Development and Senescence in Tomato Roots Colonized by Arbuscular Mycorrhizae Fungus under Drought Stress.

Arbuscular mycorrhizae (AM) symbiosis can enhance plant resistance to drought stress (DS). This study aimed to investigate the DS effects on lipids at different stages of symbiosis and to link lipid profiles to arbuscule dynamics in tomato roots colonized by AM fungi. DS increased mycorrhizal colonization and arbuscule abundance at an early stage but decreased them at a later stage, delayed arbuscule development, and accelerated arbuscule senescence at a later stage. DS decreased the contents of phospholipids (PLs) and saturated neutral lipids (NLs) at the early stage but increased the contents of saturated PLs and unsaturated NLs at the late stage. Specifically, DS inhibited AM-specific PL contents but increased AM-specific NL contents, which was supported by the expression of RAM2, STR/STR2. These data indicate the negative effect of DS on AM symbiosis and arbuscule dynamics with the effect size depending on the symbiosis stage, which highlights the importance of the symbiosis stage under abiotic stress.

Exogenous myristate promotes the colonization of arbuscular mycorrhizal fungi in tomato.

Arbuscular mycorrhizal fungi (AMF) can establish symbiotic associations with the roots of most terrestrial plants, thereby improving the tolerance of the host plants to biotic and abiotic stresses. Although AMF cannot synthesize lipids de novo, they can obtain lipids from the root cells for their growth and development. A recent study reveals that AMF can directly take up myristate (C14:0 lipid) from the environment and produce a large amount of hyphae in asymbiotic status; however, the effect of environmental lipids on AM symbiosis is still unclear. In this study, we inoculated tomato (Solanum lycopersicum) with AMF in an in vitro dual culture system and a sand culture system, and then applied exogenous myristate to the substrate, in order to explore the effect of exogenous lipids on the mycorrhizal colonization of AMF. We investigated the hyphae growth, development, and colonization of AMF, and examined the gene expression involved in phosphate transport, lipid biosynthesis, and transport. Results indicate that exogenous lipids significantly stimulated the growth and branching of hyphae, and significantly increased the number of hyphopodia and mycorrhizal colonization of AMF, with arbuscular abundance and intraradical spores or vesicles being the most promoted. In contrast, exogenous myristate decreased the growth range and host tropism of the germ tubes, and largely inhibited the exchange of nutrition between symbionts. As a result, exogenous myristate did not affect the plant growth. This study suggests that lipids promote mycorrhizal colonization by enhancing the growth and development of AMF hyphae and increasing their contact opportunities with plant roots. To the best of our knowledge, this is the first report that shows that lipids promote the colonization of AMF. Our study highlights the importance of better understanding the roles of environmental lipids in the establishment and maintenance of AM symbiosis and, thus, in agricultural production.

A synthetic community of siderophore-producing bacteria increases soil selenium bioavailability and plant uptake through regulation of the soil microbiome.

Dietary selenium (Se) is an effective strategy to meet Se requirement of human body, and Se biofortification in crops in seleniferous soils with selenobacteria represents an eco-friendly biotechnique. In this study, we tested the effectiveness of siderophore-producing bacterial (SPB) synthetic communities (SynComs) in promoting plant Se uptake in a subtropical seleniferous soil where the fixation of Se by ferric-oxides is severe. The results indicated that SPB SynComs drastically elevated soil bioavailable Se content by up to 68.7 %, and significantly increased plant Se concentration and uptake by up to 83.1 % and 92.2 %, respectively. Seven out of ten SPB isolates in the SynComs were enriched in soils after 120 days of inoculation. Additionally, variation partitioning analysis (VPA) revealed that the contribution of soil bacterial community (up to 42.8 %) to the increased plant Se uptake was much greater than that of soil bioavailable Se (up to 5.1 %), suggesting a direct pathway other than the pathway of mobilizing Se. The relative abundances of some operational taxonomic units (OTUs) showed significantly positive relationship with plant Se status but not with soil Se status, which supports the results of VPA. Network analysis indicates that some inoculated SPB isolates promoted plant Se uptake by regulating the native bacterial taxa. Taken together, this study demonstrates that SPB can be used in Se biofortification in crops, especially in subtropical soils.

Potential functions of the shared bacterial taxa in the citrus leaf midribs determine the symptoms of Huanglongbing.

Instruction: Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress. Methods: With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants. Results: We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas). Disccusion: Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas.

Cooperation of arbuscular mycorrhizal fungi and bacteria to facilitate the host plant growth dependent on soil pH.

Almost all plants grow well in their native soils. We hypothesized that soil microbes promote the growth of their hosts in native soils by the example of soil pH. Here, bahiagrass (Paspalum notatum Flugge) indigenous to subtropical soils was grown in the native soil (the original pH = 4.85) or in pH-adjusted soils with sulfur (pH = 3.14 or 3.34) or calcium hydroxide (pH = 6.85, 8.34, 8.52 or 8.59). Plant growth, soil chemical property, and microbial community composition were characterized to reveal the microbial taxa promoting plant growth in the native soil. Results showed that shoot biomass was the highest in the native soil, while both the decrease and increase in the soil pH reduced the biomass. Compared with other soil chemical properties, soil pH was the top edaphic factor contributing to the differentiation in arbuscular mycorrhizal (AM) fungal and bacterial communities. The top 3 most abundant AM fungal OTUs belonged to Glomus, Claroideoglomus, and Gigaspora, while the top 3 most abundant bacterial OTUs belonged to Clostridiales, Sphingomonas, and Acidothermus, respectively. Regression analyses between microbial abundances and shoot biomass revealed that the most abundant Gigaspora sp. and Sphingomonas sp. were the most promotive fungal and bacterial OTUs, respectively. The application of these two isolates to bahiagrass solely or in combination indicated that Gigaspora sp. was more promotive than Sphingomonas sp. across the soil pH gradient, and they positively interacted to enhance biomass only in the native soil. We demonstrate that microbes cooperate to facilitate host plants to grow well in their native soils with the original pH. Meanwhile, a high-throughput sequencing-guided pipeline to efficiently screen for beneficial microbes is established.

Phenylalanine-mediated changes in the soil bacterial community promote nitrogen cycling and plant growth.

Soil amino acids (AAs) are the most active components of soil N, which can be mineralized or absorbed by bacteria as N and C sources. We hypothesized that exogenous AAs could regulate the bacterial community and affect soil N cycling, and the effect sizes could vary depending on individual AAs. Here, we applied feather (keratin)-based compost rich in AAs to Poncirus trifoliata (L.) to evaluate the regulation of bacterial community by AAs; furthermore, we applied six individual AAs to test their effects. The compost significantly increased soil hydrolysable AA content, ammonia monooxygenase gene abundance, and plant growth and changed bacterial community structure. Redundancy analysis revealed that the effects of AAs on the bacterial community composition were greater than those of soil chemical properties, and phenylalanine (Phe) was the most effective among thirteen individual AAs. When applied individually, Phe caused the greatest increase in N cycling-related enzyme activity and plant growth and most significantly altered the bacterial community structure among the six exogenous AAs. Notably, Phe significantly increased the relative abundances of Burkholderia-Caballeronia-Paraburkholderia, Azospirillum, Cupriavidus, and Achromobacter, whose abundances were significantly positively correlated with plant biomass, and significantly reduced the relative abundances of Arachidicoccus, Pseudopedobacter, Sphingobacterium, and Paenibacillus, whose abundances were significantly negatively correlated with plant biomass. We demonstrate that soil AAs strongly shape the bacterial community. Particularly, Phe enhances N cycling and plant growth by increasing the potentially beneficial bacterial taxa and inhibiting the potentially harmful bacterial taxa, which needs further validation.

A Disturbed Siderophore Transport Inhibits Myxobacterial Predation.

BACKGROUND: Understanding the intrinsic mechanisms of bacterial competition is a fundamental question. Iron is an essential trace nutrient that bacteria compete for. The most prevalent manner for iron scavenging is through the secretion of siderophores. Although tremendous efforts have focused on elucidating the molecular mechanisms of siderophores biosynthesis, export, uptake, and regulation of siderophores, the ecological aspects of siderophore-mediated competition are not well understood. METHODS: We performed predation and bacterial competition assays to investigate the function of siderophore transport on myxobacterial predation. RESULTS: Deletion of msuB, which encodes an iron chelate uptake ABC transporter family permease subunit, led to a reduction in myxobacterial predation and intracellular iron, but iron deficiency was not the predominant reason for the decrease in the predation ability of the ∆msuB mutant. We further confirmed that obstruction of siderophore transport decreased myxobacterial predation by investigating the function of a non-ribosomal peptide synthetase for siderophore biosynthesis, a TonB-dependent receptor, and a siderophore binding protein in M. xanthus. Our results showed that the obstruction of siderophores transport decreased myxobacterial predation ability through the downregulation of lytic enzyme genes, especially outer membrane vesicle (OMV)-specific proteins. CONCLUSIONS: This work provides insight into the mechanism of siderophore-mediated competition in myxobacteria.

Responses of Arbuscular Mycorrhizal Symbiosis to Abiotic Stress: A Lipid-Centric Perspective.

Arbuscular mycorrhizal (AM) fungi are one of the most important soil microbial resources that help host plants cope with various abiotic stresses. Although a tremendous number of studies have revealed the responses of AM fungi to abiotic stress and their beneficial effects transferred to host plants, little work has focused on the role of lipid metabolism in AM fungi under abiotic stress conditions. AM fungi contain a large amount of lipids in their biomass, including phospholipids (PLs) in their hyphal membranes and neutral lipids (NLs) in their storage structures (e.g., vesicles and spores). Recently, lipid transfer from plants to AM fungi has been suggested to be indispensable for the establishment of AM symbiosis, and extraradical hyphae are capable of directly taking up lipids from the environment. This experimental evidence highlights the importance of lipids in AM symbiosis. Moreover, abiotic stress reduces lipid transfer to AM fungi and promotes arbuscule collapse as well as the hydrolysis and conversion of PLs to NLs in collapsed arbuscules. Overall, this knowledge encourages us to rethink the responses of AM symbiosis to abiotic stress from a lipid-centric perspective. The present review provides current and comprehensive knowledge on lipid metabolism in AM fungi, especially in response to various abiotic stresses. A regulatory role of abscisic acid (ABA), which is considered a "stress hormone," in lipid metabolism and in the resulting consequences is also proposed.

Soil Bacterial Function Associated With Stylo (Legume) and Bahiagrass (Grass) Is Affected More Strongly by Soil Chemical Property Than by Bacterial Community Composition.

Soil microbes are driver of nutrient cycling, with microbial function affected by community composition and soil chemical property. Legume and grass are ubiquitous in many ecosystems, however, their differential effects on microbial function are less understood. Here we constructed compartmented rhizobox planted with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum natatum, grass) to compare their influences on bacterial function and to investigate the determinant of bacterial function. Soils in root compartment and in near (0-5 mm from root compartment) or far (10-15 mm from root compartment) rhizosphere were sampled. Soil chemical properties, bacterial community composition and function were characterized. Results indicate that plant species and distance significantly affected bacterial function. The activities of beta-xylosidase, nitrate reductase and phosphomonoesterase were higher in stylo soil than in bahiagrass soil, while leucine-aminopeptidase activity and nosZ abundance were vice versa. Rhizosphere effect was obvious for the activities of beta-glucosidase, beta-xylosidase, chitinase, and the abundances of AOB-amoA, nirS, nosZ. Statistical analysis revealed that soil chemical property was significantly associated with bacterial function, with a higher coefficient than bacterial community composition. These data suggest that stylo and bahiagrass differentially affect bacterial function, which is affected more strongly by soil chemical property than by community composition.

External hyphae of Rhizophagus irregularis DAOM 197198 are less sensitive to low pH than roots in arbuscular mycorrhizae: evidence from axenic culture system.

The growth of plant roots and arbuscular mycorrhizal fungi (AMF) can be inhibited by low pH; however, it is largely unknown which is more sensitive to low pH. This study aimed to compare the physiological and molecular responses of external hyphae (EH) and roots to low pH in terms of growth, development and functioning. We established AM symbiosis in a two-compartmented system (root compartment, RC; hyphal compartment, HC) using AMF and transformed hairy roots and exposed them to pH 6.5 and/or pH 4.5. The results showed that pH 4.5 significantly decreased root cell viability, while EH at pH 6.5 attenuated the effect. In either RC or HC, pH 4.5 reduced biomass, P content, colonization, ALP activity in roots, and ALP activity and polyphosphate accumulation in EH. GintPT expression in EH was inhibited by pH 4.5 in HC but not in RC. The expression of mycorrhiza-responsive LePTs was significantly reduced by the lower colonization due to decreased pH in either RC or HC, while the expression of non-mycorrhiza-responsive LePTs was not affected. Variation partitioning analysis indicated that EH was less sensitive to low pH than roots. The interactions between roots and EH under low pH stress merit further investigation.