First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna

Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O2 pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.Fil: Perez, Maria Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Kurth, Daniel German. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Soria, Mariana Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Castillo Villamizar, Genis Andrés. Universität Göttingen; AlemaniaFil: Poehlein, Anja. Universität Göttingen; AlemaniaFil: Daniel, Rolf. Universität Göttingen; AlemaniaFil: Dib, Julian Rafael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentin

Unveiling soil bacterial ecosystems in andean citrus orchards of Santander, Colombia

Citrus cultivation is vital to global agriculture, necessitating a comprehensive understanding of the soil microbiome’s diversity for sustainable practices. This study provides initial insights into the bacteriome in citrus crops in Santander, Colombia, employing a holistic approach combining culture-based techniques, sequencing methods, and bioinformatics analyses. The study explores organic and non-organic cultivation systems, revealing statistically significant differences in bacterial community composition between both practices. In general, the communities are dominated by members of the Actinobacteria and Proteobacteria, along with bacterial orders Gaiellales and Burkholderiales, all contributing to intricate ecological processes. Culture-based methods aided in the isolation of potential biotechnologically relevant strains. Among them, strain CP102 showed a pronounced carboxymethylcellulose (CMC) degradation capacity. Genetic analysis of the isolate resulted in the generation of the first closed genome of a member of the species Enterobacter soli and identified an unreported 109 kb plasmid. Further genomic examination revealed genes potentially associated with cellulose degradation in this species, which provides the isolate with biotechnological potential. This research significantly advances the global understanding of citrus-associated bacteriomes, shaping future agricultural practices and promoting the development of sustainable bioproducts

Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases

Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth’s phosphatase pools.Phosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments

Characteristics of the first protein tyrosine phosphatase with phytase activity from a soil metagenome

Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP6) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP6 as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity

Multiple origins of Lima Bean landraces in the Americas: evidence from chloroplast and nuclear DNA polymorphisms

Crop wild relatives that have experienced multiple and independent domestication events provide an excellent model for understanding adaptation processes in crop populations and a first and relevant aspect to investigate is the geographic origin of landraces. The aim of this research was to establish the origin of Mesoamerican and Andean Lima bean (Phaseolus lunatus L.) landraces by analyzing chloroplast DNA and ITS polymorphisms in a sample of 59 wild and 50 landrace accessions. According to seed size, genetic distance analyses, and haplotype networks, at least two independent domestication events are proposed. The first one would have taken place in the Andes of southern Ecuador northwestern Peru and would have given rise to the large-seeded landraces collectively known as the Big Lima cultivars. The second one would have taken place in central western Mexico, more likely in the area to the north and northwest of the Isthmus of Tehuantepec. This event, along with post-domestication migrations of landraces in South America, would have given rise to the great variety of small-seeded Mesoamerican landraces that exist today. We did not find any evidence supporting the existence of two discrete groups within Mesoamerican landraces that might correspond to the previously proposed Sieva and Potato cultigroups. A severe reduction in genetic diversity because of domestication, known as the founder effect , was detected, which may have implications for the conservation of genetic resources in this species

DataSheet1_Microbiologically influenced corrosion: The gap in the field.PDF

Microorganisms have evolved to inhabit virtually all environments on the planet, from oceanic hot-seeps to pipelines transporting crude and refined hydrocarbons. Often microbial colonization of man-made structures results in the reduction of their service life requiring preemptive or corrective human intervention. Microbiologically Influenced Corrosion (MIC) is caused by a set of intricate bioelectrochemical interactions between a diverse group of microorganisms and metallic surfaces. The complexity of MIC microbiomes and their mechanisms as well as the logistics constraints of industrial facilities are factors to consider when choosing suitable analytical methods for MIC monitoring. These generally reflect only a partial view of the phenomenon and in consequence, might lead to ineffective mitigation measures. This paper acknowledges the discrepancies between the fieldwork for MIC monitoring and the currently available technological advancements. It also highlights the most pressing issues that operators have in the field in light of the diversity of the microbial key players present in corrosive microbiomes. Finally, it compiles and outlines a strategy for the integration of novel molecular approaches aiming for a practical and accurate assessment of the microbial threat.</p