Luis E. Servín-Garcidueñas

Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics

Phylogenomic analyses showed two major superclades within the family Rhizobiaceae that corresponded to the Rhizobium/Agrobacterium and Shinella/Ensifer groups. Within the Rhizobium/Agrobacterium group, four highly supported clades were evident that could correspond to distinct genera. The Shinella/Ensifer group encompassed not only the genera Shinella and Ensifer but also a separate clade containing the type strain of Rhizobium giardinii. Ensifer adhaerens (Casida A(T)) was an outlier within its group, separated from the rest of the Ensifer strains. The phylogenomic analysis presented provided support for the revival of Allorhizobium as a bona fide genus within the Rhizobiaceae, the distinctiveness of Agrobacterium and the recently proposed Neorhizobium genus, and suggested that R. giardinii may be transferred to a novel genus. Genomics has provided data for defining bacterial-species limits from estimates of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH). ANI reference values are becoming the gold standard in rhizobial taxonomy and are being used to recognize novel rhizobial lineages and species that seem to be biologically coherent, as shown in this study.

Gut and root microbiota commonalities.

ABSTRACT Animal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.

Genome Sequence of a Novel Archaeal Rudivirus Recovered from a Mexican Hot Spring

ABSTRACT We report the consensus genome sequence of a novel GC-rich rudivirus, designated SMR1 (Sulfolobales Mexican rudivirus 1), assembled from a high-throughput sequenced environmental sample from a hot spring in Los Azufres National Park in western Mexico.

Complete Mitochondrial and Plastid Genomes of the Green Microalga Trebouxiophyceae sp. Strain MX-AZ01 Isolated from a Highly Acidic Geothermal Lake

ABSTRACT We report the complete organelle genome sequences of Trebouxiophyceae sp. strain MX-AZ01, an acidophilic green microalga isolated from a geothermal field in Mexico. This eukaryote has the remarkable ability to thrive in a particular shallow lake with emerging hot springs at the bottom, extremely low pH, and toxic heavy metal concentrations. Trebouxiophyceae sp. MX-AZ01 represents one of few described photosynthetic eukaryotes living in such a hostile environment. The organelle genomes of Trebouxiophyceae sp. MX-AZ01 are remarkable. The plastid genome sequence currently presents the highest G+C content for a trebouxiophyte. The mitochondrial genome sequence is the largest reported to date for the Trebouxiophyceae class of green algae. The analysis of the genome sequences presented here provides insight into the evolution of organelle genomes of trebouxiophytes and green algae.

Molecular evolution of cytochrome bd oxidases across proteobacterial genomes.

This work is aimed to resolve the complex molecular evolution of cytochrome bd ubiquinol oxidase, a nearly ubiquitous bacterial enzyme that is involved in redox balance and bioenergetics. Previous studies have created an unclear picture of bd oxidases phylogenesis without considering the existence of diverse types of bd oxidases. Integrated approaches of genomic and protein analysis focused on proteobacteria have generated a molecular classification of diverse types of bd oxidases, which produces a new scenario for interpreting their evolution. A duplication of the original gene cluster of bd oxidase might have occurred in the ancestors of extant α-proteobacteria of the Rhodospirillales order, such as Acidocella, from which the bd-I type of the oxidase might have diffused to other proteobacterial lineages. In contrast, the Cyanide-Insensitive Oxidase type may have differentiated into recognizable subtypes after another gene cluster duplication. These subtypes are widespread in the genomes of α-, β-, and γ-proteobacteria, with occasional instances of lateral gene transfer. In resolving the evolutionary pattern of proteobacterial bd oxidases, this work sheds new light on the basal taxa of α-proteobacteria from which the γ-proteobacterial lineage probably emerged.

Arthropod–Spiroplasma relationship in the genomic era

The genus Spiroplasma comprises wall-less, low-GC bacteria that establish pathogenic, mutualistic and commensal symbiotic associations with arthropods and plants. This review focuses on the symbiotic relationships between Spiroplasma bacteria and arthropod hosts in the context of the available genomic sequences. Spiroplasma genomes are reduced and some contain highly repetitive plectrovirus-related sequences. Spiroplasmas diversity in viral invasion susceptibility, virulence factors, substrate utilization, genome dynamics and symbiotic associations with arthropods make this bacterial genus a biological model that provides insights about the evolutionary traits that shape bacterial symbiotic relationships with eukaryotes.

Complete mitochondrial genome recovered from the gut metagenome of overwintering monarch butterflies, Danaus plexippus (L.) (Lepidoptera: Nymphalidae, Danainae)

Abstract We present a 15,314 bp mitochondrial genome (mitogenome) sequence from monarch butterflies overwintering in Mexico. The complete mitogenome was generated by next generation sequencing techniques and was reconstructed by iterative assembly of reads from a metagenomic study of pooled butterfly gut DNA. The mitogenome codes for 13 putative protein coding genes, 22 tRNA genes, the large and small rRNA genes, and contains the A + T-rich sequence corresponding to the control region. The consensus sequence presented here has a depth of coverage of 142-fold and only three putative single nucleotide polymorphisms could be detected. The recovered D. plexippus mitogenome represents the second analyzed for the subfamily Danainae and accordingly, the closest available sequenced mitogenome was found to be the one corresponding to Euploea mulciber (Lepidoptera: Nymphalidae, Danainae).

Phylogenetic evidence of the transfer of nodZ and nolL genes from Bradyrhizobium to other rhizobia

Nod factor modifications mediated by nodZ and nolL gene products (fucosylation and acetylation of fucose residues, respectively) were probably later acquisitions in the nodulation process. Novel phylogenetic analyses suggest that nodZ and nolL genes were transferred from Bradyrhizobium to other nodule bacteria. These bradyrhizobial genes are highly diverse while rhizobial, sinorhizobial and mesorhizobial nodZ and nolL genes are represented by few branches among those from bradyrhizobia. These genes in novel rhizobial backgrounds may have favored efficient nodulation in legume hosts commonly associated with Bradyrhizobium strains.

Genome Sequence of Rhizobium sp. Strain CCGE510, a Symbiont Isolated from Nodules of the Endangered Wild Bean Phaseolus albescens

We present the genome sequence of Rhizobium sp. strain CCGE510, a nitrogen fixing bacterium taxonomically affiliated with the R. leguminosarum-R. etli group, isolated from wild Phaseolus albescens nodules grown in native pine forests in western Mexico. P. albescens is an endangered bean species phylogenetically related to P. vulgaris. In spite of the close host relatedness, Rhizobium sp. CCGE510 does not establish an efficient symbiosis with P. vulgaris. This is the first genome of a Rhizobium symbiont from a Phaseolus species other than P. vulgaris, and it will provide valuable new insights about symbiont-host specificity.

Symbiont shift towards Rhizobium nodulation in a group of phylogenetically related Phaseolus species

Bean plants from the Phaseolus genus are widely consumed and represent a nitrogen source for human nutrition. They provide biological fertilization by establishing root nodule symbiosis with nitrogen-fixing bacteria. To establish a successful interaction, bean plants and their symbiotic bacteria need to synchronize a proper molecular crosstalk. Within the Phaseolus genus, P. vulgaris has been the prominent species to study nodulation with Rhizobium symbionts. However the Phaseolus genus comprises diverse species whose symbionts have not been analyzed. Here we identified and studied nodule bacteria from representative Phaseolus species not previously analyzed and from all the described wild species related to P. vulgaris. We found Bradyrhizobium in nodules from most species representing all Phaseolus clades except in five phylogenetically related species from the P. vulgaris clade. Therefore we propose that Bradyrhizobium nodulation is common in Phaseolus and that there was a symbiont preference shift to Rhizobium nodulation in few related species. This work sets the basis to further study the genetic basis of this symbiont substitution.