Biology subjects

Gaete, A.

Publications and source records attributed to Gaete, A..

4 recordsLinked to original sources

bioRxiv2025

The rhizosphere of Pappostipa frigida as a hotspot of active bacterial communities in the Andean steppe of the Atacama Desert

BackgroundThe rhizosphere is a resource-rich microenvironment where plants, soil nutrients, and microorganisms interact. In arid and semi-arid regions, this tripartite relationship must withstand long periods of drought followed by brief periods of rainfall. In the present study, we employed a combination of RNA/DNA metabarcoding and shotgun metagenomic sequencing to provide insights into the functional capabilities and activity levels of the bacterial communities present in the bulk soil and rhizosphere samples of Pappostipa frigida, a grass species endemic to the Andean steppe of the Atacama Desert. ResultsThe active bacterial community in the rhizosphere of P. frigida exhibited greater diversity and a higher Shannon index than the total bacterial community. In terms of beta diversity, the structures of the total and active communities differed markedly between the BS and the RZ. Furthermore, active bacteria in the RZ showed a stronger correlation with total bacterial populations than those in the BS. This finding is consistent with the low proportion of ASVs derived from RNA extractions detected in the BS. Notably, 64% of these putative inactive bacterial populations were identified as active RZ members and 73% grew in culture media, suggesting they were likely dormant. The bacterial communities of the BS exhibited higher abundances of sporulation genes. In contrast, active bacterial communities in the RZ consistently contained higher abundances of genes associated with halotolerance, siderophore synthesis, and resuscitation-promoting factors. ConclusionsThe results emphasize the importance of the conditions created by plants in recruiting bacterial populations from the soil and provide insights into how the rhizosphere of arid native plants influences the activity and functional traits of soil microorganisms in their natural habitat. Additionally, this study advances our understanding of the mechanisms employed by soil microorganisms to cope with desiccation in natural environments, establishing P. frigida as a model in plant science for studying grass traits and responses to extreme environments.

microbiology↗

bioRxiv2025

Development of a Plant Growth Promoting Bacterial EcoBiome Derived from Desert Soil Isolates

The application of plant growth-promoting (PGP) bacteria is increasingly studied for its potential to improve plant tolerance to biotic and abiotic stress. Developing synthetic microbial consortia represents a promising strategy, as it can enhance colonization success and functional synergy within the rhizosphere. In this study, we designed a stable EcoBiome derived from a synthetic community (SynCom) of 17 bacterial isolates obtained from three desert environments. We evaluated their PGP traits, including siderophore production, indoleacetic acid (IAA) synthesis, phosphate solubilization, and nitrogen fixation. Using Oxford Nanopore Technologies (ONT) sequencing of 16S rRNA genes, we tracked changes in relative abundance across successive subcultures under four temperature conditions. From this analysis, Erwinia rhapontici 1SR, Pseudomonas yamanorum RZ5, and Plantibacter sp. RU18 were identified as the dominant isolates and subsequently selected to construct the EcoBiome. Functional characterization showed that these isolates exhibited complementary PGP traits, biofilm formation capacity, and tolerance to water stress, both individually and in combinations. These findings highlight the potential of desert- derived bacterial consortia as microbial resources for developing biostimulants to enhance plant resilience under environmental stress conditions. ImportanceSeveral studies have focused on obtaining bacterial isolates with plant growth promoting traits, however, their success as microbial inoculants with plant stimulant activity is diminished (or null) because they do not have the ability to compete efficiently with the natural soil microbiome. Thus, in this study we designed a synthetic community of 17 bacteria from desert environments and individually characterized their plant growth-promoting attributes, and in parallel we subjected this synthetic community to co-culture, subsequently evaluating its temporal prevalence (24 and 48 hours of culture) and at four different temperatures. With this, we developed and presented a stable EcoBiome of three isolates (one from each desert), stable over time, with attributes that promote plant growth and proliferation in hostile conditions, such as drought, with the purpose of being used as microbial inoculants as a whole, capable of competing, proliferating and forming part of the rhizosphere microbiome.

microbiology↗

bioRxiv2024

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert

The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Despite the highly restrictive conditions, microbial life has been found in these environments, although with limited information on their genetic properties and functional capabilities. Moreover, the accelerated melting of the Antarctic permafrost, the increasing exposure of soils, and the growing human transit pose the question of whether these environments could be a source of microbes or genes that could emerge and cause global health problems. In this line, although a high bacterial diversity and autochthonous multidrug-resistant bacteria have been found in soils of the Antarctic Peninsula, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a high-latitude cold desert in West Antarctica. Despite the low organic matter content, diverse bacterial lineages were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. We recovered more than 80 species-level representative genomes (SRGs) of predominant bacterial taxa and the archaeon Nitrosocosmicus sp. Diverse putative resistance and virulence genes were predicted among the SRGs, metagenomic reads, and contigs. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarcticas soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in the white continent. HIGHLIGHTS-Union Glacier soils host a microbial community dominated by bacteria, mainly from the phylum Actinomycetota. -Archaea from the Nitrosocosmicus genus (family Nitrosphaeraceae) were ubiquitously detected. -Although extreme and remote, these soils host multidrug-resistant and potentially pathogenic bacteria. Some were cultured and tested in vitro. -Metagenomes and species-level representative genomes revealed diverse putative resistance and virulence genes. -Part of the putative antimicrobial resistance genes and virulence factors could be associated with mobile elements in bacterial genomes.

microbiology↗

bioRxiv2021

Mapping the microbial diversity and natural resistome of north Antarctica soils

The rising of multiresistant bacterial pathogens is currently one of the most critical threats to global health, demanding a better understanding of the origin and spread of antibiotic resistance. In this regard, the resistome hosted by the microbiota from natural and remote environments remains poorly explored. Moreover, little is known about the availability of antimicrobial resistance genes (ARGs) from these environments to be disseminated through horizontal transfer, potentially mediating the rise of novel resistance factors among clinically relevant pathogens. In this context, the North Antarctica soils are attractive ecosystems to study due to the presence of a microbiota naturally adapted to thrive in harsh conditions, including potential factors to resist natural toxic substances. In this work, we evaluated the antibiotic resistance of bacteria isolated from soils collected in humanized and non-intervened areas of North Antarctica. We identified resistance to a wide array of antibiotics, with isolates harboring up to 10 simultaneous resistances, mainly native Pseudomonas. Genomic analysis revealed the presence of a wide array of genes encoding efflux pumps but the lack of genes explaining some of the resistance phenotypes, suggesting novel uncharacterized mechanisms. Also, using 16S rRNA amplicon and shotgun metagenome sequencing, we explored the microbial diversity in the sampled soils and evaluated the presence of ARGs and their host microbiota. High microbial diversity was found in all the sites, with Proteobacteria, Bacteroidota, Acidobacteriota, and Verrucomicrobiota being the most abundant Phyla, while Candidatus Udaeobacter, RB41, Polaromonas, and Ferruginibacter the most abundant genera. We identified hundreds of genes potentially conferring resistance to more than 15 drug classes, both by short reads analyses and ARG detection among assembled contigs and MAGs obtained combining short and long-read sequence data. Polaromonas, Pseudomonas, Streptomyces, Variovorax, Bhurkolderia, and Gemmatimonas were the main host taxa of the identified ARGs. Part of these ARGs was found inside predicted plasmids, including a putative OXA-like beta-lactamase from Polaromonas harboring the key conserved residues of this kind of enzyme and a conserved predicted protein structure. All this evidence indicates that microbial communities from North Antarctica soil have a highly diverse natural resistome, part of it located inside mobile genetic elements, which would act as a source of novel ARGs.

microbiology↗