Genotypic and Phenotypic Characterization of Pseudomonas atacamensis EMP42 a PGPR Strain Obtained from the Rhizosphere of Echinocactus platyacanthus (Sweet Barrel).

Plant growth-promoting rhizobacteria (PGPR) are a group of bacteria that associate with the rhizosphere of plants; one of the most abundant bacterial genera in this ecological niche is Pseudomonas, which is constantly expanding due to the emergence of new species such as Pseudomonas atacamensis, whose discovery in 2019 has led to the characterization of several strains from different environments but taxonomically related. The objective of this work was to phenotypically and molecularly characterize P. atacamensis strain EMP42, isolated from the rhizosphere of Echinocactus platyacanthus. The strain EMP42 is able to use different substrates and reduce oxidative stress in plants. It is capable of improving growth parameters such as the number of inflorescences and the height of the aerial body of Arabidopsis thaliana, as well as the germination and seedling survival of the cacti Echinocactus platyacanthus and Astrophytum capricorne. The genetic structure of P. atacamensis EMP42 consists of a closed chromosome of 6.14 Mbp, and 61.1% GC content. It has 5572 genes, including those associated with PGPR activities, such as the trpABCDE, SAP, phoABPRU and acsABC genes, among others, and three ncRNA loci, nine regulatory regions, five complete rRNA operons and three CRISPR-Cas loci, showing phylogenomic similarities with the reference strain P. atacamensis B21-026. Therefore, this study contributes to the understanding of genomic diversity within P. atacamensis and, particularly, highlights the potential application of strain EMP42 as a PGPR.

Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas.

BACKGROUND: Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS: The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS: The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.

Chronic consumption of sweeteners in mice and its effect on the immune system and the small intestine microbiota / Consumo crónico de edulcorantes en ratones y su efecto sobre el sistema inmunitario y la microbiota del intestino delgado

Introduction: Sweeteners are additives used in different foods. They can be natural (sucrose and stevia) or artificial (sucralose). Currently, they are routinely consumed in multiple products and their effects on the mucosa of the small intestine and its microbiota are still controversial. Objective: To relate the consumption of sweeteners and their effect on the immune system and the microbiota of the small intestine in CD1 mice. Materials and methods: We used 54 three-week-old CD1 mice divided into three groups in the experiments: 1) A group of three weeks without treatment, 2) a group treated for six weeks, and 3) a group treated for 12 weeks using sucrose, sucralose, and stevia. We obtained CD19+ B lymphocytes, IgA+ antibodies, transforming growth factor-beta (TGF-b), and interleukins 12 and 17 (IL-12 and -17) from Peyer's patches and lamina propria cells while DNA was obtained from intestinal solids to identify bacterial species. Results: After 12 weeks, sucrose and sucralose consumption caused a reduction in bacterial communities with an increase in CD19+, a decrease in IgA+ and TGF-b, and an increase in IL-12 and -17 in the Peyer's patches while in the lamina propria there was an increase in all parameters. In contrast, stevia led to an improvement in bacterial diversity and percentage of CD19+ lymphocytes with minimal increase in IgA+, TGF-b, and IL-12, and a decrease in IL-17. Conclusion: Sucrose and sucralose caused negative alterations in bacterial diversity and immune parameters after 12 weeks; in contrast, stevia was beneficial for the intestinal mucosa.

Introducción. Los edulcorantes son aditivos que se consumen en los alimentos. Pueden ser naturales (sacarosa y estevia) o artificiales (sucralosa). Actualmente, se consumen rutinariamente en múltiples productos, y sus efectos en la mucosa y la microbiota del intestino delgado aún son controversiales Objetivo. Relacionar el consumo de edulcorantes y su efecto en el sistema inmunitario y la microbiota del intestino delgado en ratones CD1. Materiales y métodos. Se utilizaron 54 ratones CD1 de tres semanas de edad divididos en tres grupos: un grupo de tres semanas sin tratamiento, un grupo tratado durante seis semanas y un grupo tratado durante 12 semanas. Se les administró sacarosa, sucralosa y estevia. A partir del intestino delgado, se obtuvieron linfocitos B CD19+ y células IgA+, TGF-ß (Transforming Growth Factor-beta) o el factor de crecimiento transformador beta (TGF-beta), IL-12 e IL-17 de las placas de Peyer y de la lámina propia. De los sólidos intestinales se obtuvo el ADN para identificar las especies bacterianas. Resultados. Después del consumo de sacarosa y sucralosa durante 12 semanas, se redujeron las comunidades bacterianas, la IgA+ y el TGF-beta, se aumentó el CD19+, y además, se incrementaron la IL-12 y la IL-17 en las placas de Peyer; en la lámina propia, aumentaron todos estos valores. En cambio, con la estevia mejoraron la diversidad bacteriana y el porcentaje de linfocitos CD19+, y hubo poco incremento de IgA+, TGF-b e IL-17, pero con disminución de la IL-17. Conclusión. La sacarosa y la sucralosa alteraron negativamente la diversidad bacteriana y los parámetros inmunitarios después de 12 semanas, en contraste con la estevia que resultó benéfica para la mucosa intestinal.

Consumo crónico de edulcorantes en ratones y su efecto sobre el sistema inmunitario y la microbiota del intestino delgado / Chronic consumption of sweeteners in mice and its effect on the immune system and the small intestine microbiota

Resumen Introducción. Los edulcorantes son aditivos que se consumen en los alimentos. Pueden ser naturales (sacarosa y estevia) o artificiales (sucralosa). Actualmente, se consumen rutinariamente en múltiples productos, y sus efectos en la mucosa y la microbiota del intestino delgado aún son controversiales. Objetivo. Relacionar el consumo de edulcorantes y su efecto en el sistema inmunitario y la microbiota del intestino delgado en ratones CD1. Materiales y métodos. Se utilizaron 54 ratones CD1 de tres semanas de edad divididos en tres grupos: un grupo de tres semanas sin tratamiento, un grupo tratado durante seis semanas y un grupo tratado durante 12 semanas. Se les administró sacarosa, sucralosa y estevia. A partir del intestino delgado, se obtuvieron linfocitos B CD19+ y células IgA+, TGF-ß (Transforming Growth Factor-beta) o el factor de crecimiento transformador beta (TGF-beta), IL-12 e IL-17 de las placas de Peyer y de la lámina propia. De los sólidos intestinales se obtuvo el ADN para identificar las especies bacterianas. Resultados. Después del consumo de sacarosa y sucralosa durante 12 semanas, se redujeron las comunidades bacterianas, la IgA+ y el TGF-beta, se aumentó el CD19+, y además, se incrementaron la IL-12 y la IL-17 en las placas de Peyer; en la lámina propia, aumentaron todos estos valores. En cambio, con la estevia mejoraron la diversidad bacteriana y el porcentaje de linfocitos CD19+, y hubo poco incremento de IgA+, TGF-ß e IL-17, pero con disminución de la IL-17. Conclusión. La sacarosa y la sucralosa alteraron negativamente la diversidad bacteriana y los parámetros inmunitarios después de 12 semanas, en contraste con la estevia que resultó benéfica para la mucosa intestinal.

Abstract Introduction: Sweeteners are additives used in different foods. They can be natural (sucrose and stevia) or artificial (sucralose). Currently, they are routinely consumed in multiple products and their effects on the mucosa of the small intestine and its microbiota are still controversial. Objective: To relate the consumption of sweeteners and their effect on the immune system and the microbiota of the small intestine in CD1 mice. Materials and methods: We used 54 three-week-old CD1 mice divided into three groups in the experiments: 1) A group of three weeks without treatment, 2) a group treated for six weeks, and 3) a group treated for 12 weeks using sucrose, sucralose, and stevia. We obtained CD19+ B lymphocytes, IgA+ antibodies, transforming growth factor-beta (TGF-b), and interleukins 12 and 17 (IL-12 and -17) from Peyer's patches and lamina propria cells while DNA was obtained from intestinal solids to identify bacterial species. Results: After 12 weeks, sucrose and sucralose consumption caused a reduction in bacterial communities with an increase in CD19+, a decrease in IgA+ and TGF-b, and an increase in IL-12 and -17 in the Peyer's patches while in the lamina propria there was an increase in all parameters. In contrast, stevia led to an improvement in bacterial diversity and percentage of CD19+ lymphocytes with minimal increase in IgA+, TGF-b, and IL-12, and a decrease in IL-17. Conclusion: Sucrose and sucralose caused negative alterations in bacterial diversity and immune parameters after 12 weeks; in contrast, stevia was beneficial for the intestinal mucosa.

Composition, Structure, and PGPR Traits of the Rhizospheric Bacterial Communities Associated With Wild and Cultivated Echinocactus platyacanthus and Neobuxbaumia polylopha.

The Queretaro semi-desert in central Mexico is the most southern extension of the Chihuahua desert. This semi-arid zone shelters a vast cactus diversity with many endemic species. Currently, two cacti species from this semi-desert namely, Echinocactus platyacanthus and Neobuxbaumia polylopha are under a threat to their survival. So far, there are no reports on the bacterial communities associated with these plants. In this study, we assessed the structure and diversity of the rhizospheric bacterial communities associated with Echinocactus platyacanthus and Neobuxbaumia polylopha growing in wild and cultivated conditions. Samples of E. platyacanthus were also approached with culture-based methods in search of isolates with plant growth promoting abilities. Metagenomic DNA was extracted from rhizospheric samples and used for Illumina sequencing of the 16S rRNA gene. α-diversity and amplicon sequence variant (ASV) richness were higher in both groups of E. platyacanthus samples. All samples accounted for 14 phyla, and the major 6 were common to all treatments. The dominant phyla in all four sample groups were Actinobacteria and Proteobacteria. Analysis at family and genus levels showed association patterns with the cultivated samples from both species grouping together, while the wild samples of each cactus species were grouping apart. High abundance values of Rubrobacteraceae (15.9-18.4%) were a characteristic feature of wild E. platyacanthus samples. In total, 2,227 ASVs were scored in all 12 rhizospheric samples where E. platyacanthus samples showed higher richness with 1,536 ASVs. Regarding the growing conditions, both groups of cultivated samples were also richer accounting for 743 and 615 ASVs for E. platyacanthus and N. polylopha, respectively. The isolates from E. platyacanthus rhizosphere were mainly assigned to Bacilli and Gammaproteobacteria. In total 35 strains were assayed for PGPR traits (IAA and siderophore production, phosphate solubilization, and fungal growth inhibition). Strains obtained from plants growing in the wild displayed better PGPR characteristics, stressing that naturally occurring wild plants are a source of bacteria with diverse metabolic activities, which can be very important players in the adaptation of cacti to their natural environments.

Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.

Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.

Polymorphism in the regulatory regions of genes CgYPS1 and CgYPS7 encoding yapsins in Candida glabrata is associated with changes in expression levels.

Candida glabrata is an opportunistic fungus infecting mainly immunocompromised people. Its adherence capacity and exoenzymes contribute to damaging host cells. In particular, the yapsins are a family of aspartyl proteases involved in maturation of proteins and cell wall function, and yapsins 1 and 7, respectively encoded by genes CgYPS1 and CgYPS7, are potential virulence factors. In this study, the polymorphism of regulatory regions and the expression profiles of both genes were compared in C. glabrata clinical strains. The sequence analysis of regulatory regions revealed that the distribution of transcription factor binding sites (TFBSs) was similar, although some TFBSs were not universally distributed. The quantita-tive expression of CgYPS1 and CgYPS7 genes of different C. glabrata strains in rich and poor media was estimated by RT-qPCR. The primary sequences of genes CgYPS1 and CgYPS7 of C. glabrata strains were highly conserved among different strains, but the regulatory regions were polymorphic, harboring different TFBS arrays, and showing differential expression profiles.

Evaluation of the simultaneous removal of recalcitrant drugs (bezafibrate, gemfibrozil, indomethacin and sulfamethoxazole) and biodegradable organic matter from synthetic wastewater by electro-oxidation coupled with a biological system.

Pharmaceutical degradation in conventional wastewater treatment plants (WWTP) represents a challenge since municipal wastewater and hospital effluents contain pharmaceuticals in low concentrations (recalcitrant and persistent in WWTP) and biodegradable organic matter (BOM) is the main pollutant. This work shows the feasibility of coupling electro-oxidation with a biological system for the simultaneous removal of recalcitrant drugs (bezafibrate, gemfibrozil, indomethacin and sulfamethoxazole (BGIS)) and BOM from wastewater. High removal efficiencies were attained without affecting the performance of activated sludge. BGIS degradation was performed by advanced electrochemical oxidation and the activated sludge process for BOM degradation in a continuous reactor. The selected electrochemical parameters from microelectrolysis tests (1.2 L s(-1) and 1.56 mA cm(-2)) were maintained to operate a filter press laboratory reactor FM01-LC using boron-doped diamond as the anode. The low current density was chosen in order to remove drugs without decreasing BOM and chlorine concentration control, so as to avoid bulking formation in the biological process. The wastewater previously treated by FM01-LC was fed directly (without chemical modification) to the activated sludge reactor to remove 100% of BGIS and 83% of BOM; conversely, the BGIS contained in wastewater without electrochemical pre-treatment were persistent in the biological process and promoted bulking formation.

Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island, Mexico.

Isabel Lake is a moderate saline soda crater lake located in Isabel Island in the eastern tropical Pacific coast of Mexico. Lake is mainly formed by rainfall and is strongly affected by evaporation and high input of nutrients derived from excretions of a large bird community inhabiting the island. So far, only the island macrobiota has been studied. The knowledge of the prokaryotic biota inhabiting the upper layers of this meromictic lake can give clues for the maintenance of this ecosystem. We assessed the diversity and composition of prokaryotic community in sediments and water of the lake by DGGE profiling, 16S rRNA gene amplicon pyrosequencing, and cultivation techniques. The bacterial community is largely dominated by halophilic and halotolerant microorganisms. Alpha diversity estimations reveal higher value in sediments than in water (P > 0.005). The lake water is dominated by γ-Proteobacteria belonging to four main families where Halomonadaceae presents the highest abundance. Aerobic, phototrophic, and halotolerant prokaryotes such as Cyanobacteria GPIIa, Halomonas, Alcanivorax, Idiomarina, and Cyclobacterium genera are commonly found. However, in sediment samples, Formosa, Muricauda, and Salegentibacter genera corresponding to Flavobacteriaceae family accounted for 15-20 % of the diversity. Heterotrophs like those involved in sulfur cycle, Desulfotignum, Desulfuromonas, Desulfofustis, and Desulfopila, appear to play an important role in sediments. Finally, a collection of aerobic halophilic bacterial isolates was created from these samples; members of the genus Halomonas were predominantly isolated from lake water. This study contributes to state the bacterial diversity present in this particular soda saline crater lake.

Degradation of benzene, toluene, and xylene isomers by a bacterial consortium obtained from rhizosphere soil of Cyperus sp. grown in a petroleum-contaminated area.

Increasing contamination of soil and groundwater with benzene, toluene, and xylene (BTX) due to activities of the chemical and oil refinery industry has caused serious environmental damage. Efficient methods are required to isolate and degrade them. Microorganisms associated with rhizosphere soil are considered efficient agents to remediate hydrocarbon contamination. In this study, we obtained a stabilized bacterial consortium from the rhizosphere soil of Cyperus sp. grown in a petroleum-contaminated field in Southern Mexico. This consortium was able to completely degrade BTX in 14 days. Bacteria isolated from the consortium were identified by 16S rRNA gene sequence analysis as Ralstonia insidiosa, Cellulomonas hominis, Burkholderia kururiensis, and Serratia marcescens. The BTX-degradation capacity of the bacterial consortium was confirmed by the detection of genes pheA, todC1, and xylM, which encoded phenol hydroxylase, toluene 1,2-dioxygenase, and xylene monooxygenase, respectively. Our results demonstrate feasibility of BTX biodegradation by indigenous bacteria that might be used for soil remediation in Southern Mexico.