The Ralstonia solanacearum species complex has long been recognized as a group of phenotypically diverse strains that can be subdivided into four phylotypes. Using a polyphasic taxonomic approach on an extensive set of strains, this study provides evidence for a taxonomic and nomenclatural revision of members of this complex. Data obtained from phylogenetic analysis of 16S-23S rRNA ITS gene sequences, 16S-23S rRNA intergenic spacer (ITS) region sequences and partial endoglucanase (egl) gene sequences and DNA-DNA hybridizations demonstrate that the R. solanacearum species complex comprises three genospecies. One of these includes the type strain of Ralstonia solanacearum and consists of strains of R. solanacearum phylotype II only. The second genospecies includes the type strain of Ralstonia syzygii and contains only phylotype IV strains. This genospecies is subdivided into three distinct groups, namely R. syzygii, the causal agent of Sumatra disease on clove trees in Indonesia, R. solanacearum phylotype IV strains isolated from different host plants mostly from Indonesia, and strains of the blood disease bacterium (BDB), the causal agent of the banana blood disease, a bacterial wilt disease in Indonesia that affects bananas and plantains. The last genospecies is composed of R. solanacearum strains that belong to phylotypes I and III. As these genospecies are also supported by phenotypic data that allow the differentiation of the three genospecies, the following taxonomic proposals are made: emendation of the descriptions of Ralstonia solanacearum and Ralstonia syzygii and descriptions of Ralstonia syzygii subsp. nov. (type strain R 001(T) = LMG 10661(T) = DSM 7385(T)) for the current R. syzygii strains, Ralstonia syzygii subsp. indonesiensis subsp. nov. (type strain UQRS 464(T) = LMG 27703(T) = DSM 27478(T)) for the current R. solanacearum phylotype IV strains, Ralstonia syzygii subsp. celebesensis subsp. nov. (type strain UQRS 627(T) = LMG 27706(T) = DSM 27477(T)) for the BDB strains and Ralstonia pseudosolanacearum sp. nov. (type strain UQRS 461(T) = LMG 9673(T) = NCPPB 1029(T)) for the strains of R. solanacearum phylotypes I and III.

Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov.

Ralstonia solanacearum is a soil-borne beta-proteobacterium that causes bacterial wilt disease in many food crops and is a major problem for agriculture in intertropical regions. R. solanacearum is a heterogeneous species, both phenotypically and genetically, and is considered as a species complex. Pathogenicity of R. solanacearum relies on the Type III secretion system that injects Type III effector (T3E) proteins into plant cells. T3E collectively perturb host cell processes and modulate plant immunity to enable bacterial infection. We provide the catalogue of T3E in the R. solanacearum species complex, as well as candidates in newly sequenced strains. 94 T3E orthologous groups were defined on phylogenetic bases and ordered using a uniform nomenclature. This curated T3E catalog is available on a public website and a bioinformatic pipeline has been designed to rapidly predict T3E genes in newly sequenced strains. Systematical analyses were performed to detect lateral T3E gene transfer events and identify T3E genes under positive selection. Our analyses also pinpoint the RipF translocon proteins as major discriminating determinants among the phylogenetic lineages. Establishment of T3E repertoires in strains representatives of the R. solanacearum biodiversity allowed determining a set of 22 T3E present in all the strains but provided no clues on host specificity determinants. The definition of a standardized nomenclature and the optimization of predictive tools will pave the way to understanding how variation of these repertoires is correlated to the diversification of this species complex and how they contribute to the different strain pathotypes.

https://epub.ub.uni-muenchen.de/23009/1/1471-2164-14-859.pdf

Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

Summary
Healthy soils that contain an active microbiome and food web are critical to sustainably produce food for a growing global human population. Many studies have focussed on the role of microbial species diversity and the presence of key functional groups as important controls on the many functions that a sustainable food system relies on.
Here, we synthesise recent ecological empirical evidence and theory to propose that the interactions between organisms in the soil food web are the critical determinant of soil function.
We propose the Rhizosphere Interactions for Sustainable Agriculture Model, in which crop roots recruit small, modular, highly connected soil rhizosphere networks from large, static, relatively unconnected and diverse bulk soil networks. We argue that conventional agricultural management disrupts the connections between rhizosphere and bulk soil networks.
Synthesis. We identify future research directions for optimising ecological connections between roots and rhizosphere microbial and faunal networks, and between rhizosphere networks and bulk soil networks in agricultural production systems. Knowledge on these connections can be applied in agricultural systems to sustainability produce food for a growing global population.

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Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere

Root exudates play an important role in ecosystem response to climate change, but the functional consequences of drought‐induced changes in the quality of root exudates are unknown. Here, we addressed this knowledge gap in a unique experimental approach. We subjected two common grassland species that differ widely in their growth strategies and root systems, the grass Holcus lanatus and the forb Rumex acetosa, to 2 wk of drought. We collected root exudates and soils at the end of the drought and after 2 wk of recovery and readded all root exudates to all soils in a fully reciprocal set‐up to measure root‐exudate‐induced respiration. We found that soil treatment was unimportant for determining root‐exudate‐induced respiration. By contrast, root exudates collected from plants that had experienced drought clearly triggered more soil respiration than exudates from undroughted plants. Importantly, this increased respiration compensated for the lower rates of root exudation in droughted plants. Our findings reveal a novel mechanism through which drought can continue to affect ecosystem carbon cycling, and a potential plant strategy to facilitate regrowth through stimulating microbial activity. These findings have important implications for understanding plant and ecosystem response to drought.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.16001

Changes in root-exudate-induced respiration reveal a novel mechanism through which drought affects ecosystem carbon cycling.

Root functional traits explain root exudation rate and composition across a range of grassland species

Identification of benzoic acid and 3-phenylpropanoic acid in tobacco root exudates and their role in the growth of rhizosphere microorganisms

Ralstonia solanacearum strain FQY_4 was isolated from a bacterial wilt nursery, which is used for breeding crops for Ralstonia resistance in China. Here, we report the complete genome sequence of FQY_4 and its comparison with other published R. solanacearum genomes, especially with the strains GMI1000 and Y45 in the same group.

https://journals.asm.org/doi/pdf/10.1128/genomeA.00125-13

Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance.

Tobacco bacterial wilt caused by Ralstonia solanacearum is a serious disease affecting tobacco cultivation in southwest China. The response surface methodology was employed to evaluate the optimal conditions of tobacco bacterial wilt, and green fluorescent protein gene (gfp) labelling was applied to monitor the location and survival dynamics of R. solanacearum (Rs::gfp) on tobacco roots and in soil under these optimal conditions. The results showed that the highest wilt incidence was 91.13%, which occurred when the population reached 6.6 × 106 CFU/g soil, the temperature was 30.55 °C, and the humidity was >81.42%. The Rs::gfp densely colonized the root tips and root hairs, and cells of Rs::gfp were observed intermittently in the elongation zone or at the point of the emerging lateral roots. The Rs::gfp number in the rhizosphere soil was 10.75-, 73.13- and 74.86-times higher than that in the bulk soil at 10, 15 and 20 days after transplantation, respectively. Increased colonization by Rs::gfp was related to the population of the pathogen, the environmental temperature and the humidity in the soil. These three conditions determined whether R. solanacearum would induce tobacco wilt. This is the first study to investigate factors affecting the virulence of a tobacco wilt bacterial pathogen, which is important for conducting field diagnosis and biocontrol of tobacco bacterial wilt.

Factors affecting the virulence of Ralstonia solanacearum and its colonization on tobacco roots

The invention discloses a comprehensive preventing and controlling method for tobacco bacterial wilt. Following treatments are performed to soil before tobacco plantation: 1) soil pretreatment: in the last October and November after tobacco harvest, uniformly spreading quick lime of 90 to 100kg per Mu on the surface of the soil; 2) planting green manure crops on the soil and performing green manuring treatment in the next February to March; 3) soil reprocessing treatment: uniformly spreading quick lime of 90 to 100kg per Mu on the surface of the soil once again after green manuring; 4) performing deep plowing to the soil; 5) applying organic fertilizer. By use of the comprehensive preventing and controlling method, the morbidity of bacterial wilt is effectively reduced; tobacco production and output value are increased; pathogenic bacteria concentration in the soil is reduced so that pathogenic bacteria infection to root is reduced; transformation from diseased soil ecosystem to healthy and sustainable development direction is facilitated so that a good preventing and controlling effect on tobacco bacterial wilt in heavy diseased areas is achieved; the problem of limited preventing and controlling effects on bacterial wilt caused by existing single measure is solved.

Comprehensive preventing and controlling method for tobacco bacterial wilt

The invention discloses a method for water-soluble root fertilizer application to flue-cured tobaccos. The weight ratio of the formula of basic fertilizers N, P2O5 and K2O is 8:9:14, the weight ratio of topdressing formula of N, P2O5 and K2O is 1:1:2, the basic topdressing application amount of N is 5 kg/mu, wherein the topdressing proportion is 60%; the topdressing fertilizer is applied to soil in three times; when the flue-cured tobaccos are transplanted, N is applied as root fixing water for the first time according to a concentration of 0.5 kg/mu after being diluted by 100 folds by water; in 20 days after the flue-cured tobaccos are transplanted, according to a concentration of 1.0 kg/mu, N is applied for the second time; in 35 days after the flue-cured tobaccos are transplanted, according to concentration of 1.5 kg/mu, N is diluted by water by 10 folds and then applied into the soil at the positions which are 15 cm away from the flue-cured tobaccos. By fertilization in the method, the fertilizer efficiency can be effectively brought into play, the flue-cured tobacco growth is promoted, the dry matter accumulation quantity and energy of the flue-cured tobaccos can be increased by 4.91-16.71%, the tobacco yield is increased by 5.62-14.92%, and the yield is increased by 5.03-14.34%.

Liu Yanxia

Papers

Identification of benzoic acid and 3-phenylpropanoic acid in tobacco root exudates and their role in the growth of rhizosphere microorganisms

Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance.

Factors affecting the virulence of Ralstonia solanacearum and its colonization on tobacco roots

Comprehensive preventing and controlling method for tobacco bacterial wilt

Method for water-soluble root fertilizer application to flue-cured tobaccos