Biology subjects

Palma, D. E.

Publications and source records attributed to Palma, D. E..

3 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

Mobile-CRISPRi as a tool for genetic manipulation in the intracellular pathogen Piscirickettsia salmonis

Piscirickettsia salmonis is the causative agent of Salmonid Rickettsial Septicemia (SRS), the main bacterial disease affecting the salmon industry in Chile. In this work, we implemented a Mobile-CRISPRi system to generate gene silencing using a catalytically inactive dCas9 protein and an IPTG-inducible single-guide RNA (sgRNA). We demonstrate the efficacy of the CRISPRi system in P. salmonis by silencing an exogenous gene encoding green fluorescent protein (sfGFP), and the endogenous homolog of the fur gene, whose gene product regulates intracellular iron homeostasis in bacteria. The inducible expression of dcas9 and the sfGFP-directed sgRNA caused a 98.7% decrease in fluorescence in the knockdown strain. This silencing system was effective in seven P. salmonis strains from both genogroups. Furthermore, the same system was used to construct fur knockdown strains. A 50-fold decrease in fur expression level was determined in these strains, when the expression of the fur gRNA was induced with IPTG. By RNA-seq we detected a significant increase in the expression of genes encoding the Fe+2 and Fe+3 acquisition systems and iron mobilization in the fur1 knockdown, after IPTG induction. All the genes with over two-fold increased expression in the RNA-seq presented the Fur box consensus sequence in their regulatory region. The successful implementation of the Mobile-CRISPRi system in P. salmonis paves the way for systematic analysis of gene function in this pathogen We anticipate that these analyses will be very valuable in identifying genes involved in the mechanisms of pathogenesis of P. salmonis. ImportanceSalmon Rickettsial Septicemia (SRS) is an infectious disease caused by the marine bacterium Piscirickettsia salmonis. This Gamma-proteobacteria is a fastidious and facultative intracellular pathogen that has a nearly worldwide distribution, particularly impacting Chilean salmonid aquaculture. Its fastidious nature has made it hard to grow in labs, hindering research into its virulence and treatment, especially because of the lack of molecular techniques to study gene function. We show here the successful implementation of the Mobile-CRISPRi system for gene silencing. Significantly, we have adapted this technique for use with the marine pathogen P. salmonis, inserting exogenous genes into the bacteriums chromosome to ensure their constitutive and inducible expression, and silencing both exogenous and endogenous gene expression. The Mobile-CRISPRi system was also used to study the iron regulator Fur, confirming Furs relevance to the iron metabolism in the pathogen.

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↗