Specificity of root microbiomes in native‐grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization

Plants recruit microbial communities from the soil in which they germinate. Our understanding of the recruitment process and the factors affecting it is still limited for most microbial taxa. We analysed several factors potentially affecting root microbiome structure – the importance of geographic location of natural populations, the microbiome of native seeds as putative source of colonization and the effect of a plant's response to UVB exposure on root colonization of highly abundant species. The microbiome of Nicotiana attenuata seeds was determined by a culture‐dependent and culture‐independent approach, and the root microbiome of natural N. attenuata populations from five different locations was analysed using 454‐pyrosequencing. To specifically address the influence of UVB light on root colonization by Deinococcus, a genus abundant and consistently present in N. attenuata roots, transgenic lines impaired in UVB perception (irUVR8) and response (irCHAL) were investigated in a microcosm experiment with/without UVB supplementation using a synthetic bacterial community. The seed microbiome analysis indicated that N. attenuata seeds are sterile. Alpha and beta diversities of native root bacterial communities differed significantly between soil and root, while location had only a significant effect on the fungal but not the bacterial root communities. With UVB supplementation, root colonization of Deinococcus increased in wild type, but decreased in irUVR8 and irCHAL plants compared to nontreated plants. Our results suggest that N. attenuata recruits a core root microbiome exclusively from soil, with fungal root colonization being less selective than bacterial colonization. Root colonization by Deinococcus depends on the plant's response to UVB.     

Allelic variation for broad‐spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population

Quantitative trait loci (QTL) that confer broad‐spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub‐Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar‐specific QTL. The most promising BSR QTL (qXO‐2‐1, qXO‐4‐1 and qXO‐11‐2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes.     

Infection Process of Burkholderia glumae Before Booting Stage of Rice

Burkholderia glumae is a well‐known pathogen for causing bacterial panicle blight of rice. In this study, the infection process of B. glumae in rice plants at different growing stages was tracked by means of real‐time fluorescence quantitative PCR. Burkholderia glumae tended to colonize at the growing point of rice plants, and the biomass of population was 10⁴ to 10⁸ CFU/g. The most intensive colonization was detected in the upmost leaf in the two‐leaf period. However, after the two‐leaf period, the population of pathogens decreased significantly, and they successfully recovered in the booting stage and broke out in panicles. We also illustrated the incubation location of B. glumae by presenting the infection pattern in the seedling and tillering stage of rice. Under fluorescent microscopy, the gfp‐labelled pathogens were first found in the vascular bundle of lateral roots, taproots and injured cells, then they were observed in the root hairs, epidermal cells and main root cap. The pathogens in the vascular bundle laterally dispersed towards the epidermal cells. By spray application of a bacterial suspension, the pathogens landed on the leaf sheaths and leaves, colonized in the epidermal hairs and leaf hairs, or invaded into the cells through the stomas. At the same time, the pathogens from the vascular bundle of the roots spread into the vascular bundle of leaf sheaths and leaves, which caused the leaves to curl and wilt, beginning from the tip.     

Relationships between intra‐specific variation in seed size and recruitment in four species in two contrasting habitats

Large seeds contain more stored resources, and seedlings germinating from large seeds generally cope better with environmental stresses such as shading, competition and thick litter layers, than seedlings germinating from small seeds. A pattern with small‐seeded species being associated with open habitats and large‐seeded species being associated with closed (shaded) habitats has been suggested and supported by comparative studies. However, few studies have assessed the intra‐specific relationship between seed size and recruitment, comparing plant communities differing in canopy cover. Here, seeds from four plant species commonly occurring in ecotones between open and closed habitats (Convallaria majalis, Frangula alnus, Prunus padus and Prunus spinosa) were weighed and sown individually (3200 seeds per species) in open and closed‐canopy sites, and seedling emergence and survival recorded over 3 years. Our results show a generally positive, albeit weak, relationship between seed size and recruitment. In only one of the species, C. majalis, was there an association between closed canopy habitat and a positive seed size effect on recruitment. We conclude that there is a weak selection gradient favouring larger seeds, but that this selection gradient is not clearly related to habitat.     

Landscape‐scale Variation in Pathogen‐suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica

Bacteria in the genus Streptomyces are ubiquitous in soil and are well‐known for their production of diverse secondary metabolites, including antibiotics that can inhibit soil‐borne plant pathogens and suppress disease. Pathogen‐suppressive soil bacteria have the potential to influence plant community composition and diversity, but remain relatively unexplored in tropical forest soils. To estimate the potential for disease suppression among Streptomyces communities in tropical dry forests, we cultured soil‐borne Streptomyces from plots in two forests in northwestern Costa Rica (Santa Rosa and Palo Verde) and quantified antibiotic‐mediated pathogen inhibition against three plant pathogens. The potential for pathogen inhibition and disease suppression by Streptomyces was highly variable across the landscape. Densities of pathogen‐suppressive Streptomyces varied by over ten‐fold and were correlated with soil nutrients across the plots. In particular, Streptomyces communities became more pathogen‐suppressive as labile soil P decreased. Inhibitor densities were significantly higher in Santa Rosa than Palo Verde, which may be related to differences in soil texture and/or plant community composition between the two forests. Our findings suggest potential differences in the degree and specificity of antibiotic‐mediated disease suppression in tropical dry forest soils of Costa Rica, and highlight the need for further studies on the drivers of pathogen‐suppressive phenotypes as well as the consequences of spatially variable pathogen inhibition for plant community composition in tropical forest ecosystems.     

The roles of the shikimate pathway genes,aroA and aroB,in virulence,growth and UV tolerance of Burkholderia glumae strain 411gr‐6

Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, which is a growing disease problem for rice growers worldwide. In our previous study, some B. glumae strains showed pigmentation phenotypes producing at least two (yellow–green and purple) pigment compounds in casein–peptone–glucose agar medium. The B. glumae strains LSUPB114 and LSUPB116 are pigment‐deficient mutant derivatives of the virulent and pigment‐proficient strain 411gr‐6, having mini‐Tn5gus insertions in aroA encoding 3‐phosphoshikimate 1‐carboxyvinyltransferase and aroB encoding 3‐dehydroquinate synthase, respectively. Both enzymes are known to be involved in the shikimate pathway, which leads to the synthesis of aromatic amino acids. Here, we demonstrate that aroA and aroB are required for normal virulence in rice and onion, growth in M9 minimal medium and tolerance to UV light, but are dispensable for the production of the phytotoxin toxoflavin. These results suggest that the shikimate pathway is involved in bacterial pathogenesis by B. glumae without a significant role in the production of toxoflavin, a major virulence factor of this pathogen.     

2,6‐Dimethoxy‐1,4‐Benzoquinone Enhances Resistance Against the Rice Blast Fungus Magnaporthe oryzae

We investigated the effect of 2,6‐dimethoxy‐1,4‐benzoquinone (DMBQ) on induced resistance to Magnaporthe oryzae in rice. DMBQ concentrations greater than 50 μg/ml inhibited spore germination and appressorium formation in M. oryzae. When rice leaves pretreated with 10 μg/ml DMBQ, which did not show antifungal activity against spore germination and appressorium formation of M. oryzae, were inoculated with M. oryzae spores 5 days after DMBQ pretreatment, blast lesion formation was inhibited compared with control leaves pretreated with distilled water. In addition, infection‐inhibiting activity against M. oryzae was significantly enhanced in rice leaf sheaths pretreated with 10 μg/ml DMBQ. H₂O₂ generation was observed in rice leaves pretreated with DMBQ, and PAL, POX, CHS and PR10a were significantly expressed in these leaves. These results suggested that DMBQ can protect rice from blast disease caused by M. oryzae.     

Conventional farming impairs Rhizoctonia solani disease suppression by disrupting soil food web

Intensive farming in agriculture raises questions in relation to environmental sustainability and the widespread use of agrochemicals. In the present work, we compare the impact of organic and intensive farming, in connection to the soil suppressiveness against the soilborne pathogen Rhizoctonia solani. Three farms were considered in the study: two practicing organic cultivation (for 10 and 20 years, respectively), and one applying conventional cultivation. Soil suppressiveness was assessed in a greenhouse bioassay with lettuce (Lactuca sativa). Soil microbiome was characterized by combining BIOLOG EcoPlates^? with high‐throughput sequencing of bacterial and eukaryotic rRNA gene markers. Suppressiveness towards R. solani was higher in organic than in conventional farming soil, but this property was lost after soil sterilization. Functional biodiversity was significantly higher in the two organic soils, and this parameter was predictive of the suppressiveness towards R. solani. According to our analyses, the overall microbial taxonomic diversity was unlinked to suppressiveness. A correlation analysis, carried out at the genus level for the most abundant bacterial and eukaryotic microbial taxa, showed that 58.7% of the genera had a statistically significant correlation with suppressiveness. In particular, the genera Flavisolibacter, Massilia, Pseudomonas, Ramlibacter, Rhizophus and the oligochaete worms belonging to the Enchytraeidae family positively correlated with the disease suppression.     

Long‐term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro‐ecosystems across the globe

Long‐term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long‐term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long‐term N and NPK fertilization on soil bacterial diversity and community composition using meta‐analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long‐term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long‐term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro‐ecosystems worldwide.     

Oryza sativa Lysine‐Histidine‐type Transporter 1 functions in root uptake and root‐to‐shoot allocation of amino acids in rice

In agricultural soils, amino acids can represent vital nitrogen (N) sources for crop growth and yield. However, the molecular mechanisms underlying amino acid uptake and allocation are poorly understood in crop plants. This study shows that rice (Oryza sativa L.) roots can acquire aspartate at soil concentration, and that japonica subspecies take up this acidic amino acid 1.5‐fold more efficiently than indica subspecies. Genetic association analyses with 68 representative japonica or indica germplasms identified rice Lysine‐Histidine‐type Transporter 1 (OsLHT1) as a candidate gene associated with the aspartate uptake trait. When expressed in yeast, OsLHT1 supported cell growth on a broad spectrum of amino acids, and effectively transported aspartate, asparagine and glutamate. OsLHT1 is localized throughout the rice root, including root hairs, epidermis, cortex and stele, and to the leaf vasculature. Knockout of OsLHT1 in japonica resulted in reduced root uptake of amino acids. Furthermore, in ¹⁵N‐amino acid‐fed mutants versus wild‐type, a higher percentage of ¹⁵N remained in roots instead of being allocated to the shoot. ¹⁵N‐ammonium uptake and subsequently the delivery of root‐synthesized amino acids to Oslht1 shoots were also significantly decreased, which was accompanied by reduced shoot growth. These results together provide evidence that OsLHT1 functions in both root uptake and root to shoot allocation of a broad spectrum of amino acids in rice.     

Long‐term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome

Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run‐off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short‐ and long‐term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short‐term exposure to high‐salinity levels. By comparison, long‐term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long‐term acclimation to high‐salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy‐based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.     

Characterization of culturable bacterial endophytes of switchgrass (Panicum virgatum L.) and their capacity to influence plant growth

Switchgrass (Panicum virgatum L.) is a perennial warm season grass that is native to the plains of North America and is widely grown as a forage, bioenergy or groundcover crop. Despite its importance, a bottleneck in switchgrass production is poor seedling vigor, which as a perennial crop represents an important time for management. Herein, data identify a suite of culturable bacterial microflora extracted from switchgrass, and show their capability to influence host plant growth and development. A total of 307 bacterial isolates were cultured and isolated from surface sterilized switchgrass biomass and sequence identified into 76 strains (subspecies classification), 36 species and 5 phyla. Approximately 58% of bacterial strains, when reintroduced into surface‐sterilized switchgrass seeds, were documented to increase lamina length (cm from base to tip after 60 days growth) relative to uninoculated controls. Ecologically, Phylum Firmicutes was the most abundant bacterial classification and encompassed 75% of all isolates. Although the culturable bacterial community studies herein represent an unknown and assumedly minor proportion of the total microbiome, by focusing on culturable bacteria, we delineate functional feedback between the presence of isolated bacteria and switchgrass seedling growth.     

Bacillus subtilis QST 713 Confers Protection to Tomato Plants Against Pseudomonas syringae pv tomato and Induces Plant Defence‐related Genes

Bacterial speck, caused by Pseudomonas syringae pv. tomato (Pst), is an economically important disease of tomato, resulting in yield loss of marketable fruit. Management of bacterial speck is a challenge in commercial production fields due to the limited efficacy of current disease management strategies, as the pathogen acquires resistance to antibiotics and fixed copper bactericides and host resistance has not proven durable. Therefore, it is essential to develop alternative disease management strategies, like biological control. In this study, the efficacy of the commercially available biocontrol agent Bacillus subtilis QST 713 along with copper hydroxide was tested against Pst under greenhouse conditions. QST 713 reduced significantly disease severity and incidence compared to control and the copper hydroxide treatment; subsequently, the Pst population was lower in the QST 713‐treated plants compared to control. In parallel, QST 713 and copper hydroxide increased plant height compared to control and mock plants. Furthermore, the quantitative PCR analysis of PR1a, PR1b and Pin2 expression suggests a positive role for Pin2 in the plant protective activity of QST 713, as Pin2 expression was significantly higher in the QST 713‐treated plants challenged with Pst compared to the control Pst‐inoculated plants.