A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota.

Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.

Metagenome-Assembled Genome of Acidibrevibacterium fodinaquatile FLA01 from Fumarole Sediments from the Los Azufres Geothermal Field.

The Los Azufres geothermal field contains diverse microbial communities inhabiting thermal springs whose bacterial genomic diversity is being analyzed. Here, we describe a metagenome-assembled genome of Acidibrevibacterium fodinaquatile FLA01 obtained from fumarole sediment sequencing data. The genome contained genes for carbon fixation, osmotic shock, and heavy metal resistance.

Bacterial Diversity Profiling of Desert Sand from Tierra Caliente, Mexico, Based on 16S rRNA Gene Amplicon Sequencing.

Tierra Caliente is an arid region in Mexico, representing a reservoir of understudied xerophilic bacteria. Here, we report the bacterial amplicon sequencing characterization of desert sand collected from the Zicuirán-Infiernillo Biosphere Reserve within Tierra Caliente. Bacteria known to be resistant to desiccation and high radiation were detected.

Metagenome Assembly and Metagenome-Assembled Genome of "Candidatus Aramenus sulfurataquae" from Thermal Sediments from the Los Azufres Volcanic Complex.

A plethora of hot springs are found at the Los Azufres volcanic complex in Mexico, and studies are needed to determine their microbial genomic diversity. Here, we report a metagenome of hot spring sediments and a metagenome-assembled genome of "Candidatus Aramenus sulfurataquae." This study reveals novel genomic sequences of Sulfolobales archaea.

The Convergent Effect of International Collaboration between Young Leaders of Two Global Societies: Strengthening Microbiology Education and Training Practices Worldwide.

There has never been a more critical time than the present for young microbiologists to engage in continuous postgraduate education. Next-generation microbiologists need to integrate several scientific disciplines in the early stages of their careers to keep up with the ever-changing nature of microbiology (advent of high-throughput sequencing platforms, bioinformatics, complex omic, culture and systems-biology approaches) and to ensure timely response to the current global health and biodiversity threats. Here we propose that international collaboration of young experts would help to address the challenges in microbiology training and serve as a communication bridge between senior and early career scientists. To establish a one-of-a-kind collaboration, the Trainee Association (TAE) of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and the Young Leaders Circle (YLC) of the American Society for Microbiology (ASM) have joined forces to adequately represent the interests of young members within the two largest societies in the field of microbiology. Through this partnership, both societies aim to promote continuous education for young scientists and the general public. Additionally, we intend to identify shared objectives and introduce joint activities that could lead to a beneficial exchange process for a long-lasting relationship. This partnership further contributes to advancing both the quality and quantity of education.

En la actualidad es crítico que los jóvenes microbiólogos se involucren en estudios de posgrado y formación continua. La próxima generación de microbiólogos necesita integrar varias disciplinas científicas durante las primeras etapas de sus carreras para mantenerse al día con la naturaleza siempre cambiante de la microbiología (por ejemplo, con el advenimiento de las plataformas de secuenciación masiva, de las herramientas bioinformáticas, de las técnicas ómicas avanzadas, de cultivo y de biología de sistemas), y para asegurar una respuesta oportuna ante las amenazas mundiales actuales para la salud y la biodiversidad. Se propone que la colaboración internacional de jóvenes expertos ayudará a enfrentar los desafíos de la formación en microbiología y servirá como un puente de comunicación entre científicos experimentados y en etapas tempranas de sus carreras. Para establecer una colaboración única, la Asociación de Pasantes (TAE) de la Sociedad Europea de Microbiología Clínica y Enfermedades Infecciosas (ESCMID) y el Círculo de Jóvenes Líderes (YLC) de la Sociedad Americana de Microbiología (ASM) han conjuntado esfuerzos para representar adecuadamente los intereses de los jóvenes integrantes de las dos sociedades más numerosas en la disciplina de la microbiología. A través de esta colaboración, ambas sociedades tienen como objetivo promover la formación continua de jóvenes científicos y del público en general. Además, se tiene la intención de identificar objetivos compartidos y proponer actividades conjuntas que propicien un proceso de intercambio beneficioso para mantener una relación duradera. Esta colaboración contribuye a mejorar tanto la calidad como la cantidad de la educación.

Genome Sequence of Rhizobium jaguaris CCGE525T, a Strain Isolated from Calliandra grandiflora Nodules from a Rain Forest in Mexico.

We present the genome sequence of Rhizobium jaguaris CCGE525T, a nitrogen-fixing bacterium isolated from nodules of Calliandra grandiflora. CCGE525T belongs to Rhizobium tropici group A, represents the symbiovar calliandrae, and forms nitrogen-fixing nodules in Phaseolus vulgaris. Genome-based metrics and phylogenomic approaches support Rhizobium jaguaris as a novel species.

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus.

We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, a nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus. Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island.

Species in Wolbachia? Proposal for the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxteri', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylori', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitum' for the different species within Wolbachia supergroups.

Wolbachia are highly extended bacterial endosymbionts that infect arthropods and filarial nematodes and produce contrasting phenotypes on their hosts. Wolbachia taxonomy has been understudied. Currently, Wolbachia strains are classified into phylogenetic supergroups. Here we applied phylogenomic analyses to study Wolbachia evolutionary relationships and examined metrics derived from their genome sequences such as average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, and synteny to shed light on the taxonomy of these bacteria. Draft genome sequences of strains wDacA and wDacB obtained from the carmine cochineal insect Dactylopius coccus were included. Although all analyses indicated that each Wolbachia supergroup represents a distinct evolutionary lineage, we found that some of the analyzed supergroups showed enough internal heterogeneity to be considered as assemblages of more than one species. Thus, supergroups would represent supraspecific groupings. Consequently, Wolbachia pipientis nomen species would apply only to strains of supergroup B and we propose the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxterii', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylorii', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitis' for other supergroups.

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. Spiroplasma's 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.

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.

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.

Draft Genome Sequence of Commensalibacter papalotli MX01, a Symbiont Identified from the Guts of Overwintering Monarch Butterflies.

We report the draft genome sequence of Commensalibacter papalotli strain MX01, isolated from the intestines of an overwintering monarch butterfly. The 2,332,652-bp AT-biased genome of C. papalotli MX01 is the smallest genome for a member of the Acetobacteraceae family and provides the first evidence of plasmids in Commensalibacter.

Draft Genome Sequence of the Sulfolobales Archaeon AZ1, Obtained through Metagenomic Analysis of a Mexican Hot Spring.

The Sulfolobales archaea have been found inhabiting acidic hot springs all over the world. Here, we report the 1.798-Mbp draft genome sequence of the thermoacidophilic Sulfolobales archaeon AZ1, reconstructed from the metagenome of a Mexican hot spring. Sequence-based comparisons revealed that the Sulfolobales archaeon AZ1 represents a novel candidate genus.

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

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).

Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a mexican hot spring.

The consensus genome sequence of a new member of the family Fuselloviridae designated as SMF1 (Sulfolobales Mexican fusellovirus 1) is presented. The complete circular genome was recovered from a metagenomic study of a Mexican hot spring. SMF1 exhibits an exceptional coding strand bias and a reduced set of fuselloviral core genes.

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 a novel archaeal rudivirus recovered from a mexican hot spring.

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.

Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02.

Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico.