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Research Project
Biosystems and Integrative Sciences Institute
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Publications
Cork oak forests soil bacteria: Potential for sustainable agroforest production
Publication . Reis, Francisca; Pereira, Ana João; Tavares, Rui Manuel; Baptista, Paula; Lino-Neto, Teresa
Plant growth promoting rhizobacteria (PGPR) are in increasing demand due to their role in promoting sustainable practices, not only in agriculture but also in forestry. Keeping in mind the future application of PGPR for increasing cork oak sustainability, the aim of this study was to find cork oak PGPR isolates with increased nutrient solubilisation traits, able to promote root morphological changes and/or antagonize cork oak bark phytopathogens. Soils from three cork oak forests with distinct bioclimates (humid, semi†humid and semi†arid) were used for isolating bacteria. From the 7634 colony†forming units, 323 bacterial isolates were biochemically assayed for PGPR traits (siderophores production, phosphate solubilizing and organic acids production), and 51 were found to display all these traits. These PGPR were able to induce root morphological changes on Arabidopsis thaliana, like suppression of primary root growth, increase of lateral roots or root hairs formation. However, the most proficient PGPR displayed specific ability in changing a single root morphological trait. This ability was related not only to bacterial genotype, but also with the environment where bacteria thrived and isolation temperature. Bacteria from semi†arid environments (mainly Bacillus megaterium isolates) could hold a promising tool to enhance plant development. Other isolates (Serratia quinivorens or B. cereus) could be further explored for biocontrol purposes.
Differences in the endophytic microbiome of olive cultivars infected by xylella fastidiosa across seasons
Publication . Giampetruzzi, Annalisa; Baptista, Paula; Morelli, Massimiliano; Cameirão, Cristina; Neto, Teresa Lino; Costa, Daniela; D’Attoma, Giusy; Kubaa, Raied Abou; Altamura, Giuseppe; Saponari, Maria; Pereira, J.A.; Saldarelli, Pasquale
The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on the same trees at two different stages of the infections: In Spring 2017 when plants were almost symptomless and in Autumn 2018 when the trees of the susceptible cultivar clearly showed desiccations. The progression of the infections detected in both cultivars clearly unraveled that Xylella tends to occupy the whole ecological niche and suppresses the diversity of the endophytic microbiome. However, this trend was mitigated in the resistant cultivar FS17, harboring lower population sizes and therefore lower Xylella average abundance ratio over total bacteria, and a higher α-diversity. Host cultivar had a negligible effect on the community composition and no clear associations of a single taxon or microbial consortia with the resistance cultivar were found with both sequencing approaches, suggesting that the mechanisms of resistance likely reside on factors that are independent of the microbiome structure. Overall, Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes dominated the bacterial microbiome while Ascomycota and Basidiomycota those of Fungi.
Machine Learning Techniques Disclose the Combined Effect of Fermentation Conditions on Yeast Mixed-Culture Dynamics and Wine Quality
Publication . Barbosa, Catarina; Ramalhosa, Elsa; Vasconcelos, Isabel; Reis, Marco; Mendes-Ferreira, Ana
The use of yeast starter cultures consisting of a blend of Saccharomyces cerevisiae and
non-Saccharomyces yeasts has increased in recent years as a mean to address consumers’ demands
for diversified wines. However, this strategy is currently limited by the lack of a comprehensive
knowledge regarding the factors that determine the balance between the yeast-yeast interactions
and their responses triggered in complex environments. Our previous studies demonstrated that
the strain Hanseniaspora guilliermondii UTAD222 has potential to be used as an adjunct of S. cerevisiae
in the wine industry due to its positive impact on the fruity and floral character of wines. To
rationalize the use of this yeast consortium, this study aims to understand the influence of production
factors such as sugar and nitrogen levels, fermentation temperature, and the level of co-inoculation of
H. guilliermondii UTAD222 in shaping fermentation and wine composition. For that purpose, a Central
Composite experimental Design was applied to investigate the combined effects of the four factors
on fermentation parameters and metabolites produced. The patterns of variation of the response
variables were analyzed using machine learning methods, to describe their clustered behavior and
model the evolution of each cluster depending on the experimental conditions. The innovative
data analysis methodology adopted goes beyond the traditional univariate approach, being able to
incorporate the modularity, heterogeneity, and hierarchy inherent to metabolic systems. In this line,
this study provides preliminary data and insights, enabling the development of innovative strategies
to increase the aromatic and fermentative potential of H. guilliermondii UTAD222 by modulating
temperature and the availability of nitrogen and/or sugars in the medium. Furthermore, the strategy
followed gathered knowledge to guide the rational development of mixed blends that can be used to
obtain a particular wine style, as a function of fermentation conditions.
Olive fungal epiphytic communities are affected by their maturation stage
Publication . Castro, Joana; Costa, Daniela; Tavares, Rui Manuel; Baptista, Paula; Lino-Neto, Teresa
The phyllosphere comprises the aerial parts of plants and is colonized by a great diversity of
microorganisms, either growing inside (as endophytes) or on the surface (as epiphytes) of plant tissues.
The factors that structure the diversity of epiphytes and the importance of these microorganisms for
host plant protection have been less studied when compared to the case of endophytes. In this work,
the epiphytic fungal communities from fruits of the olive tree (olives) in different maturation stages
(green and semi-ripened), obtained from different olive orchard managements (integrated and organic
production) and from distinct cultivars displaying different susceptibilities to olive anthracnose
(Cobrançosa and Madural), are compared by using a metabarcoding approach. We discuss whether
such differences in host resistance against anthracnose depend on both the fungal taxa or fungal
community composition. A total of 1565 amplicon sequence variants (ASVs) were obtained, mainly
belonging to the Ascomycota phylum and Saccharomycetes class. Although significant differences
on epiphytic fungal richness were observed among olives obtained in different production systems
and maturation stages, these factors in addition to host cultivar did not influence the composition
of the epiphytes. Despite these results, a co-inertia analysis showed that Aureobasidium spp. and
Sporocadaceae spp. were positively associated with the green olives of the cv. Madural produced
under integrated production, while Saccharomycetales spp. (Kluyveromyces, Candida, Kazachstania
and Saccharomyces) were positively associated with the semi-ripened olives of the cv. Cobrançosa
obtained from organic production. The discriminant power of these fungi, some of them recognized
as biocontrol agents, suggest that they might be important in conferring differences on host plant
susceptibility to anthracnose.
Phylogenetic analysis and genetic diversity of the xylariaceous ascomycete Biscogniauxia mediterranea from cork oak forests in different bioclimates
Publication . Costa, Daniela; Ramos, Vitor; Tavares, Rui Manuel; Baptista, Paula; Lino-Neto, Teresa
Cork oak is a tree species with ecological importance that contributes to economic and social
development in the Mediterranean region. Cork oak decline is a major concern for forest sustainability
and has negative impacts on cork oak growth and production. This event has been increasingly
reported in the last decades and seems to be related with climate changes. Biscogniauxia
mediterranea is an endophytic fungus of healthy cork oak trees that turns into a pathogen in trees
weaken by environmental stress. Understanding the drivers of B. mediterranea populations diversity
and differentiation is expected to allow a better control of cork oak decline and preserve forest
sustainability. Endophyte isolates from different cork oak forests were identified as B. mediterranea
and their genetic diversity was evaluated using phylogenetic and microsatellite-primed PCR analyses.
Genetic diversity and variability of this fungus was correlated with environmental/phytosanitary
conditions present in forests/trees from which isolates were collected. High genetic diversity and
variability was found in B. mediterranea populations obtained from different forests, suggesting
some degree of isolation by distance. Bioclimate was the most significant effect that explained the
genetic variability of B. mediterranea, rather than precipitation or temperature intensities alone or
disease symptoms. These findings bring new implications for the changing climate to cork oak forests
sustainability, cork production and quality.
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Funding agency
Fundação para a Ciência e a Tecnologia
Funding programme
6817 - DCRRNI ID
Funding Award Number
UIDB/04046/2020