En Tao Wang

Bio: En Tao Wang is an academic researcher from Instituto Politécnico Nacional. The author has contributed to research in topics: Rhizobium leguminosarum & Rhizobia. The author has an hindex of 4, co-authored 7 publications receiving 43 citations.

Defining the Rhizobium leguminosarum Species Complex.

Abstract: Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

Ecology and evolution of rhizobia: Principles and applications

Abstract: Preface -- Chapter 1. Symbiosis between rhizobia and legumes -- Chapter 2. History of rhizobial taxonomy -- Chapter 3. Current Systematics of rhizobia -- Chapter 4. Genomics and evolution of rhizobia -- Chapter 5. Symbiosis genes: diversity and organization -- Chapter 6. Evolution of symbiosis genes: Vertical and horizontal gene transfer -- Chapter 7. Diversity of interactions between rhizobia and legumes -- Chapter 8. Geographical distribution of rhizobia -- Chapter 9. Environmental determinants of biogeography of rhizobia -- Chapter 10. Effects of host plants on biogeography of rhizobia -- Chapter 11. Rhizobial genomics and biogeography -- Chapter 12. Current status of rhizobial inoculants -- Chapter 13. Screening for effective rhizobia -- Chapter 14. Usage of rhizobial inoculants in agriculture -- Chapter 15. Rhizobial activity beyond nitrogen fixation -- Chapter 16. Working on the taxonomy, biodiversity, ecology and evolution of rhizobia -- Index -- Acknowledgments.

Defining the Rhizobium Leguminosarum Species Complex

Abstract: Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

Symbiosis Between Rhizobia and Legumes

Abstract: The term of rhizobia, or root nodule bacteria, is the common collective name for diverse symbiotic nitrogen-fixing soil bacteria that can induce root and/or stem nodules on the legume plants. Although this common name was derived from the genus name Rhizobium (Frank 1889), bacteria distributed in diverse species within different genera, families and classes have been confirmed as microsymbionts of nodules of distinct legume species; therefore, the word “rhizobia” has lost its taxonomic meaning but refers to the symbiotic nitrogen-fixing bacteria associated with nodules of legumes. Inside the nodules, the cells of these bacteria differentiate into bacteroids, which are polymorphic cells with modified cell walls, enclosed by plant cell membrane to form a structure called the symbiosome. This structure provides the conditions that allow the function of nitrogenase, the enzyme that reduces elemental nitrogen to ammonia in the bacteroids. From this association, both the legumes and the rhizobia can benefit: the host plants supply the rhizobia with C4-dicarboxylic acids as carbon and energy source, and the rhizobia offer the plants nitrogen nutrients produced by reducing atmospheric nitrogen and incorporating it into amino acids such as alanine (Poole and Allaway 2000).

History of Rhizobial Taxonomy

Abstract: Biological diversity or biodiversity refers to the wide variety of living things on Earth, including the diversity of ecosystems, diversity of species and diversity of genes. Although studies of biodiversity have a long history, the term “biodiversity” was first used in 1986 by Walter G. Rosen in National Forum on Biodiversity (de Andrade Franco 2013). Ecosystem diversity is the largest scale of biodiversity and concerns systems such as the terrestrial ecosystem, the aquatic ecosystem, agricultural ecosystems, forestry ecosystems, etc., in which the organisms colonise and interact in trophic chains. The diversity of ecosystems can be measured in terms of variation in the complexity of communities, such as trophic levels, niche types/numbers, productivity and biotransformation efficiencies, etc., that depend on both species and genetic diversity (Ives and Carpente 2009). Species diversity is related to the numbers of species represented in the ecosystems or communities and considers both species richness and their relative abundance (species evenness) (Hill 1973). Gene or genetic diversity is usually applied to the biodiversity within species, relating to the total number of genetic characteristics in their chromosomes. This diversity allows microbial populations or species to adapt different environments. A greater gene diversity in a population or species means the existence of more alleles that offer the population and species a greater chance to adapt to variations in the environment and to maintain the population. It has been estimated that about 5.3 × 1031 megabases (Mb) of DNA exist on Earth (Landenmark et al. 2015), which form a huge gene pool for diverse metabolic pathways and for diversification of the species. In conclusion, biodiversity was defined by Wilson (1992) as “… all hereditarily based variation at all levels of organization, from the genes within a single local population, to the species composing all or part of a local community, and finally to the communities themselves that compose the living parts of the multifarious ecosystems of the world”.

Species concept for prokaryotes

Abstract: Trabajo presentado en la 113th General Meeting of the American Society for Microbiology, celebrada en Denver, Estados Unidos, del 18 al 21 de mayo de 2013

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

Abstract: Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

苜蓿中华根瘤菌（Sinorhizobium meliloti）的耐酸性研究

Abstract: 用来自酸性土壤上紫花苜蓿根瘤中分离得到的3株能在pH=4.8的YMA固体培养基上正常生长的根瘤菌进行回接试验和生长曲线测定,结果证明,菌株91532耐酸能力高于其余菌珠,并高于国内外已报道过的苜蓿根瘤菌.91532经16SrRNA分析和扫描电子显微镜分析,鉴定为苜蓿中华根瘤菌（Sinorhizobium meliloti）.pH=4.0的质子通量试验中,与酸敏感菌株相比,91532细胞膜具有较强的阻挡质子能力,细胞具有较高的存活率,耐酸能力具有遗传稳定性.

Rhizobia as a Source of Plant Growth-Promoting Molecules: Potential Applications and Possible Operational Mechanisms

Abstract: The symbiotic interaction between rhizobia and legumes that leads to nodule formation is a complex chemical conversation involving plant release of nod-gene inducing signal molecules and bacterial secretion of lipo-chito-oligossacharide nodulation factors. During this process, the rhizobia and their legume hosts can synthesize and release various phytohormones, such as IAA, lumichrome, riboflavin, lipo-chito-oligossacharide Nod factors, rhizobitoxine, gibberellins, jasmonates, brassinosteroids, ethylene, cytokinins and the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase that can directly or indirectly stimulate plant growth. Whereas these attributes may promote plant adaptation to various edapho-climatic stresses including the limitations in nutrient elements required for plant growth promotion, tapping their full potential requires understanding of the mechanisms involved in their action. In this regard, several N2-fixing rhizobia have been cited for plant growth promotion by solubilizing soil-bound P in the rhizosphere via the synthesis of gluconic acid under the control of pyrroloquinoline quinone (PQQ) genes, just as others are known for the synthesis and release of siderophores for enhanced Fe nutrition in plants, the chelation of heavy metals in the reclamation of contaminated soils, and as biocontrol agents against diseases. Some of these metabolites can enhance plant growth via the suppression of the deleterious effects of other antagonistic molecules, as exemplified by the reduction in the deleterious effect of ethylene by ACC deaminase synthesized by rhizobia. Although symbiotic rhizobia are capable of triggering biological outcomes with direct and indirect effects on plant mineral nutrition, insect pest and disease resistance, a greater understanding of the mechanisms involved remains a challenge in tapping the maximum benefits of the molecules involved. Rather than the effects of individual rhizobial or plant metabolites however, a deeper understanding of their synergistic interactions is may be useful in alleviating the effects of multiple plant stress factors for increased growth and productivity.

Mechanisms in plant growth-promoting rhizobacteria that enhance legume-rhizobial symbioses.

Abstract: Nitrogen fixation is an important biological process in terrestrial ecosystems and for global crop production Legume nodulation and N2 fixation have been improved using nodule-enhancing rhizobacteria (NER) under both regular and stressed conditions The positive effect of NER on legume-rhizobia symbiosis can be facilitated by plant growth-promoting (PGP) mechanisms, some of which remain to be identified NER that produce aminocyclopropane-1-carboxylic acid deaminase and indole acetic acid enhance the legume-rhizobia symbiosis through (i) enhancing the nodule induction, (ii) improving the competitiveness of rhizobia for nodulation, (iii) prolonging functional nodules by suppressing nodule senescence and (iv) upregulating genes associated with legume-rhizobia symbiosis The means by which these processes enhance the legume-rhizobia symbiosis is the focus of this review A better understanding of the mechanisms by which PGP rhizobacteria operate, and how they can be altered, will provide opportunities to enhance legume-rhizobial interactions, to provide new advances in plant growth promotion and N2 fixation