My experience in science communication

Writing

PhD in soil and plant microbiome

With the results of my 4-year research, I wrote a thesis about the olive tree microbiome and its stress response. Here I described the effect of agricultural management on the microbial community inhabiting the soil and roots of olive trees, with several impacts on the diversity and composition of the microbial community and the soil nutrient content. The relationship between the root microbiota and the olive verticilosis was also assessed. Moreover, my thesis included the first description of the olive seed microbiota, setting the path for future research in this area. To achieve this, I used next-generation sequencing and bioinformatic tools for data analysis. I developed and published a bioinformatic workflow that unifies different tools frequently used in this type of analysis, hoping to increase reproducibility for other users. I also used extensive molecular biology and microbiology techniques in the laboratory, in order to extract DNA, biomass quantification, bacterial isolation, identification and storage.

This work involved extensive writing skills (e.g., 30-page introduction about the olive tree), reference analysis, data analysis and graphic design.

Read it here.

Research article published in Environmental Microbiome

During my internship in Graz (Austria) in the laboratory of Prof. Dr. Gabriele Berg, I developed my research on the microbial composition of the olive seed. We explored how the tree genotype influences the community structure and composition and compared it to what was found in other plant compartments, as a first approximation to study the microbial inheritance across generations in the olive tree. This study constitutes the first description of the olive seed microbiota, setting a precedent in its field. The results showed unique characteristics of the olive seed microbiota compared with other plant species, with Malassezia and Streptomyces dominating the fungal and bacterial communities, respectively. This is especially interesting considering the importance of Actinobacteria in other olive tree compartments, such as the rhizosphere.

Read it here.

Research article published in Computational and Structural Biotechnology

There is a considerable knowledge gap regarding the impact of manure application on the root-associated microbiome of woody species. In this study, I analysed the olive tree root microbiota under two agricultural managements: conventional and organic with ovine manure applied to the soil. The diversity and richness of fungi were increased in the organic farm, coupled with higher fungal biomass in the rhizosphere. The soil nutrient content was also affected, with an increase in organic matter, nitrogen, phosphorous, potassium and sulfate. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.

This research was developed using next-generation sequencing techniques (Illumina MiSeq) and required several bioinformatic tools. In my research group, we realised the need for a unified workflow where different tools could be integrated, decreasing the analysis effort and increasing reproducibility. We decided to publish a full workflow to make these analyses more accessible to any researcher and I was proud to be the main developer. Micro4all was published along with this study and the full workflow and tutorial can be found here.

Read it here.

Research article published in PLOS one

One of the most devastating diseases affecting olive trees is caused by the soilborne fungal pathogen Verticillium dahliae Kleb. This pathogen induces a vascular disease, entering the plant vascular tissue and obstructing nutrient flow, severely affecting plant health. The incidence of this pathogen is particularly high in Spain, the world's leading producer of olive oil, making it a top priority to find effective strategies to combat this disease.

One approach employed by farmers is replacing affected trees with olive cultivars that exhibit resistance to the pathogen. However, the mechanisms underlying this differential resistance remain poorly understood. To investigate whether the root microbiome plays a role, we studied olive trees from two cultivars—Picual (susceptible) and Frantoio (resistant)—grown under identical agronomical conditions.

We analyzed the composition and diversity of their microbial communities but found no significant differences between the cultivars. Based on our results, the structure and composition of rhizospheric microbial communities do not appear to play a major role in olive tree resistance to V. dahliae.

To further explore the impact of agricultural management on microbial communities, we also examined a neighbouring holm oak forest. Interestingly, while olive trees showed no distinction between soil and root-associated microbiota, this difference was clear in oak trees.

Read it here.

Research article published in Frontiers Microbiology

In this research article, I had the pleasure of collaborating with Carmen Gómez-Lama Cabanás, the main author. Her research was focused on the Fusarium wilt of banana (FWB), caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. cubense (Foc), which is considered one of the most destructive diseases for this crop worldwide. The use of bacterial strains for the biocontrol of this disease has proved to be a useful alternative in the fight against FWB. This is the case of Pseudomonas simiae PICF7, a bacterial isolate from olive trees. In this study, we wanted to explore the mechanisms underlying its biocontrol properties against FWB and whether its introduction poses any change to the native microbial community of the banana root. This is of special interest considering the importance of not disrupting the local biodiversity when applying biocontrol agents. I was in charge of the metabarcoding analysis of the bacterial and fungal community inhabiting the banana root. We found no significant differences in the structure and composition of the microbial community when the inoculant was applied. Nevertheless, significant changes were observed in the interactions among community members as shown by the network analysis. Moreover, the collaborators of this research also performed a gene expression analysis that showed suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers in the banana plant when PICF7 reached its highest abundance in the root, a finding that sheds light on the mechanisms underlying the biocontrol capacities of PICF7.

Read it here.

Posters and conferences

National Congress of the Spanish Society of Microbiology (SEM)

I designed and presented this poster at the XXIX Congress of the Spanish Society of Microbiology (SEM) celebrated in Burgos (Spain) in 2023. The poster shows the results of my research on the microbial composition of the olive seed, constituting its first description.

For more details about this research, you can find the summary in the section above, check the full-size poster here or read the full article.

International Congress: 4th Ecology of Soil Microorganisms meeting

The 4th Ecology of Soil Microorganisms meeting was held in Prague in 2022, where I had the opportunity to show my latest research on the effects of agricultural management on the olive tree root. We studied both organic and conventional farms and found significant changes in the microbial communities along with the soil nutritional content related with the agronomical practices implemented.

For more details about this research, you can find the summary in the section above, check the full-size poster here or read the full article.

International Congress Microbiotec’19

The international Congress Microbiotec’ 19 took place at the University of Coimbra (Portugal) in 2019 and was organised by the Portuguese Society of Microbiology and the Portuguese Society of Biotechnology. I designed a poster with the results of my recently published paper about the olive tree belowground microbial communities and their relation with agricultural management and the differential susceptibility to the Verticilosis Wilt of Olive (VWO) of various cultivars.

For more details about this research, you can find the summary in the section above, check the full-size poster here or read the full article.

These results were also presented at the National Congress MiP 2021, organized by the Spanish Society of Microbiology. On this occasion, they were shared through an oral presentation.

Teaching

University of Granada

As part of my PhD program, I was a lecturer in various subjects at the University of Granada, including 'Conceptual Development of Biology' and 'Laboratory Practice' for first-year biology students, as well as 'Advanced Microbiology' for more experienced students. Teaching has always been one of my greatest passions, and this opportunity further reinforced my appreciation for science communication. In addition, I developed key professional skills by managing multiple responsibilities, including class preparation, teaching, exam design, and student assessment.

Invited lecturer at “Introduction to the use of bioinformatics technologies as tools for DNA sequence analysis”

I was honoured to be an invited lecturer for the course "Introduction to the Use of Bioinformatics Technologies as Tools for DNA Sequence Analysis," organized by the National University of Barranca in March 2023. My sessions focused on introducing R as a powerful programming language for bioinformatics, demonstrating its versatility in data analysis. I also presented my published workflow for metabarcoding data, providing participants with practical insights into its application in microbial ecology studies. It was a great opportunity to share my expertise and engage with students and professionals interested in bioinformatics.

Other experience

Video presented at the National Contest of CSIC

Part of the committee of 'FPU Investiga,' an organization advocating for PhD students' rights

Here is my video submission for the national contest organized by the Higher Scientific Research Council of Spain (CSIC), where I explained my research project to a general audience. It was a challenging task, as I created all the graphics myself, but it was also an incredibly enriching experience.

Grant proposals

Through grant proposal writing, I secured funding for my entire PhD program and a three-month internship in the laboratory of Prof. Dr. Gabriele Berg, with a total amount of 83,200€. In addition to the project proposal, I also wrote annual reports detailing my research milestones to secure continued funding each year.

During three years, I was a collaborator and member of “FPU Investiga”. As a PhD student, I suffered from unfair working conditions and instability inherent to the Spanish scientific system. For instance, our contracts belonged to a unique category with several legal loopholes. Although being official workers for 4 years, the right to receive an end-of-contract compensation was denied to us with no legal justification. In less than a year, we gained this right back and now thousands of PhD have benefited from it.

My roles in FPU Investiga included content creation (videos, infographics), organization and finance management. Find some of the content I created here: