Plant growth-promoting microbes impact on plant performance, resilience, and rhizosphere microbiome assembly

Tese de mestrado, Biologia Evolutiva e do Desenvolvimento, Universidade de Lisboa, Faculdade de Ciências, 2020Interactions between microorganisms and plants have occurred for millions of years. Combining the capacity of light and CO2 usage by the plants with the capacity of efficient substrate usage by their microbiota, the water-to-land-transition was possible. Since then, plants and plant microbiota have coevolved, and today, the microbiome is considered as an extension of the plant’s genetic assembly. However, the agricultural revolution led to progressive alterations in habitat, crop managing practices, and breeding to promote crop production changing their evolutionary trajectory. Moreover, the trajectory of the co-evolution between crops and their microbiome is also changed. The soil, the plant, and the microorganisms are connected and impact each other. The rhizosphere is considered to be the most dynamic interface on Earth, and the microorganisms that exist there might promote plant growth and resilience. These microorganisms are referred to as Plant Growth-Promoting Microbes (PGPM), including Plant Growth-Promoting Rhizobacteria (PGPR) and Arbuscular Mycorrhizal Fungi (AMF). The experimental work is divided into three chapters according to the plant-model. In the first one, microorganisms (AMF and bacteria) were collected from a wild relative of chrysanthemum (Dendranthema grandiflora). Plant Growth Promoting Rhizobacteria (PGPR) was submitted for molecular analysis. Three of them (previously selected by plant growth-promoting traits) were inoculated on five chrysanthemum commercial cultivars to test their impact on plant performance and root microbiome assembly. AMF was also inoculated with the same propose. PGPR impacted the number of nodes and root biomass of commercial chrysanthemum cultivars. AMF affected the root biomass of cultivars of chrysanthemum cultivated in autoclaved and non-autoclaved soil. AMF root colonization was not found. All the treatments impacted the microbiome assembly in the tested commercial cultivars. Concluding, PGPR and AMF obtained from wild chrysanthemum impacted growth performance and microbiome assembly in five commercial cultivars. In the second one, AMF collected from wild chrysanthemum were proliferated using millet (Panicum miliaceum) as a host in order to have an inoculum of two morphotypes. The two morphotypes of AMF spores were successfully multiplied in millet roots and sorrowing soil. Millet appeared as a good host for the propagation of AMF spores. Lastly, in the third chapter, the same AMF were inoculated in sorghum (Sorghum bicolor) to test their impact on plant performance and resilience against Striga hermonthica, a parasitic weed. Sorghum growth performance and resilience were impacted by the presence of S. hermonthica and/or AMF in the soil. AMF root colonization on sorghum was observed and AMF treatments reduced S. hermonthica germination by 59%. However, the reduction of the germination of S. hermonthica seeds did not increase the sorghum growth performance, so more studies are needed to understand these mechanisms. Promising results were found, but additional work is needed to understand how these inocula are best applied in the field and the mechanisms behind it. It is also necessary to comprehend how the entire microbiome is affected by the inocula and how these changes impact growth performance and resilience in both, chrysanthemum, and sorghum species

TNF-α Regulates the Effects of Irradiation in the Mouse Bone Marrow Microenvironment

BACKGROUND Secondary bone marrow (BM) myelodysplastic syndromes (MDS) are increasingly common, as a result of radio or chemotherapy administered to a majority of cancer patients. Patients with secondary MDS have increased BM cell apoptosis, which results in BM dysfunction (cytopenias), and an increased risk of developing fatal acute leukemias. In the present study we asked whether TNF-alpha, known to regulate cell apoptosis, could modulate the onset of secondary MDS. PRINCIPAL FINDINGS We show that TNF-alpha is induced by irradiation and regulates BM cells apoptosis in vitro and in vivo. In contrast to irradiated wild type (WT) mice, TNF-alpha deficient (TNF-alpha KO) mice or WT mice treated with a TNF-alpha-neutralizing antibody were partially protected from the apoptotic effects of irradiation. Next we established a 3-cycle irradiation protocol, in which mice were sub-lethally irradiated once monthly over a 3 month period. In this model, irradiated WT mice presented loss of microsatellite markers on BM cells, low white blood cell (WBC) counts, reduced megakaryocyte (MK) and platelet levels (thrombocytopenia) and macrocytic anemia, phenoypes that suggest the irradiation protocol resulted in BM dysfunction with clinical features of MDS. In contrast, TNF-alpha KO mice were protected from the irradiation effects: BM cell apoptosis following irradiation was significantly reduced, concomitant with sustained BM MK numbers and absence of other cytopenias. Moreover, irradiated WT mice with long term (> or = 5 months) BM dysfunction had increased BM angiogenesis, MMPs and VEGF and NFkB p65, suggestive of disease progression. CONCLUSION Taken together, our data shows that TNF-alpha induction following irradiation modulates BM cell apoptosis and is a crucial event in BM dysfunction, secondary MDS onset and progression.publishersversionpublishe

HERA - Environmental Risk Assessment of a contaminated estuarine environment: a case study

Sado River estuary is located in the west coast of Portugal. Previous environmental studies identified industrial contamination, non-point anthropogenic sources and contamination coming from the river, all promoting accumulation of polluted sediments with known impacts on the ecological system. Surrounding human populations have intense economic fishery activities. Together with agriculture, estuary fishing products are available to local residents. Food usage previously characterized through ethnographic studies suggests exposure to estuarine products, farming products, and water in daily activities, as potential routes of contamination. It is well established that long term exposure to heavy metals are associated with renal and neurological diseases, most heavy metals are classified as carcinogenic and teratogenic.Instituição Financiadora: FCT; Instituições participantes: IMAR -Instituto do Mar (coord.)e PRÓ-INSA, Associação para a Promoção da Investigação em Saúde, Instituto Nacional de Saúde Doutor Ricardo Jorg

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

Transient elastography: should XL probe be used in all overweight patients?

Background: Obesity is one of the main factors of transient elastography (TE) failure, considering body mass index (BMI) ≥28 kg/m2 as a limiting factor. The XL probe was designed to overcome this limitation. Aim: To compare the feasibility of the M and XL probes in patients with BMI ≥ 28 kg/m2, to evaluate differences in mean values of controlled attenuation parameter (CAP) and liver stiffness measurement (LSM) between the two probes and find predictive factors of TE failure. Material and methods: Prospective study, including all patients with BMI ≥ 28 kg/m2 consecutively admitted for TE. Results: Included 161 patients. Measurements with M probe were reliable in 69.6% of the patients, with 68.2% of valid measurements in obese population and 58.9% in patients with skin-capsule distance (SCD) >25 mm. In 40 patients (81.6%) with an invalid M probe measurement, a reliable result was obtained with XL probe. We found that SCD >25 mm was the only predictor of M probe failure (OR: 4.9, CI: 1.64-14.63, p = .004). In those patients in which TE was possible with both probes (n = 112), mean CAP was 304 ± 49 dB/m2 with M probe and 301 ± 50 dB/m2 with XL probe (p = .59). Regarding liver stiffness, a mean value of 7.58 ± 3.47 kpas was obtained with the M probe and 6.21 ± 3.44 kpas with the XL probe (p 25 mm was the only predictive factor of M probe failure. Mean values of LSM with XL probe were lower than those obtained with M probe

Revisão sistematizada da literatura e opinião de peritos

Objective: The 3E (Evidence, Expertise, Exchange) Initiative is a multinational effort of rheumatologists aimed at developing evidence-based recommendations addressing specific questions relevant to clinical practice. The objective of the Portuguese contribution for the 3E Initiative was to develop evidence-based recommendations on how to investigate, follow-up and treat undifferentiated peripheral inflammatory arthritis (UPIA) adapted to local reality and develop additional recommendations considered relevant in the national context. Methods: An international scientific committee from 17 countries selected a set of questions concerning the diagnosis and monitoring of UPIA using a Delphi procedure. Evidence-based answers to each question were sought by a systematic literature search, performed in Medline, Embase, the Cochrane Library and ACR/EULAR 2007-2009 meeting abstracts. Relevant articles were reviewed for quality assessment, data extraction and synthesis. In a national meeting, a panel of 63 Portuguese rheumatologists used the evidence which was gathered to develop recommendations, and filled the gaps in the evidence with their expert opinion. Finally, national recommendations were formulated and agreement among the participants was assessed. Results: A total of 54754 references were identified, of which 267 were systematically reviewed. Thirteen national key recommendations about the investigation, follow-up and treatment of UPIA were formulated. One recommendation addressed differential diagnosis and investigations prior to the established operational diagnosis of UPIA, eight recommendations were related to the diagnostic and prognostic value of clinical and laboratory assessments in established UPIA (history and physical examination, acute phase reactants, serologies, autoantibodies, radiographs, magnetic resonance imaging and ultrasound, genetic markers and synovial biopsy), one recommendation highlighted predictors of persistence (chronicity), one addressed monitoring of clinical disease activity in UPIA, one aimed to find an useful method/score to predict a definitive diagnosis and the last one was related to treatment. Conclusion: Portuguese evidence-based recommendations for the management of UPIA in everyday practice were developed. Their dissemination and implementation in daily clinical practice should help to improve practice uniformity and optimize the management of UPIA patients.publishersversionpublishe

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved