Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots

We investigated the potential plant growth-promoting traits of 377 culturable endophytic bacteria, isolated from Vitis vinifera cv. Glera, as good biofertilizer candidates in vineyard management. Endophyte ability in promoting plant growth was assessed in vitro by testing ammonia production, phosphate solubilization, indole-3-acetic acid (IAA) and IAA-like molecule biosynthesis, siderophore and lytic enzyme secretion. Many of the isolates were able to mobilize phosphate (33%), release ammonium (39%), secrete siderophores (38%) and a limited part of them synthetized IAA and IAA-like molecules (5%). Effects of each of the 377 grapevine beneficial bacteria on Arabidopsis thaliana root development were also analyzed to discern plant growth-promoting abilities (PGP) of the different strains, that often exhibit more than one PGP trait. A supervised model-based clustering analysis highlighted six different classes of PGP effects on root architecture. A. thaliana DR5::GUS plantlets, inoculated with IAA-producing endophytes, resulted in altered root growth and enhanced auxin response. Overall, the results indicate that the Glera PGP endospheric culturable microbiome could contribute, by structural root changes, to obtain water and nutrients increasing plant adaptation and survival. From the complete cultivable collection, twelve promising endophytes mainly belonging to the Bacillus but also to Micrococcus and Pantoea genera, were selected for further investigations in the grapevine host plants towards future application in sustainable management of vineyards

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

La WISH in zebrafish applicata all'analisi di colocalizzazioni e xenotrapianti

Danio rerio (zebrafish) è un piccolo teleosteo utilizzato con successo per studi di genetica e biologia dello sviluppo. Tra le numerose tecniche messe a punto per questo modello vertebrato, la WISH (whole mount in situ hybridization) è una delle più versatili e utilizzate di routine, in quanto consente di visualizzare l’espressione genica nello spazio e nel tempo mediante una colorazione istochimica su embrioni interi. Durante il tirocinio, la WISH è stata applicata per determinare i profili di espressione genica in neuroni dei gangli della radice dorsale in via di differenziamento, relativamente a quattro geni coinvolti nel differenziamento cellulare tramite la segnalazione cellulare giuxtacrina Notch. Per la prima volta inoltre, la medesima tecnica WISH è stata utilizzata con successo per re-individuare, a distanza di giorni, cellule di glioblastoma umano xenotrapiantate nell’encefalo di embrioni di zebrafish

Bringing soil fungi into action : Options for forward-looking agriculture

Intensively managed agricultural production of food and fiber does often coincide with negative side-effects such as environmental pollution and soil degradation. The integration of ecology-based agricultural practices has a promising perspective to bring agriculture to a more sustainable level. Many studies point at the importance of re-integrating traditional agricultural practices, such as the use of organic amendments and crop diversification (intercropping, wider crop rotations, cover crops). Other lines of research explore the possibilities of soil inoculation with microbial strains as biofertilizers and biopesticides. Arable soils harbor a diverse community of saprotrophic fungi, however their biomass and activity is mostly limited. This is due to intensive management practices, such as the use of synthetic rather than organic fertilizers, use of chemical pesticides and mechanical disturbances of soils. Having an active community of saprotrophic fungi is essential for soil functioning, as can be seen in natural and semi-natural ecosystems. In this Ph.D. thesis study, I explore options for boosting the biomass of saprotrophic fungi in arable soils. I also test the impact of stimulation of saprotrophic fungi on plants and other soil microbial inhabitants, including bacteria, pathogenic- and mycorrhizal fungi.Saprotrophic soil fungi can respond to organic inputs both in the form of dead plant parts (litter) and rhizodeposits derived from living roots. Therefore, two possible approaches were examined for the stimulation of saprotrophic fungi in arable soil, namely the addition of exogenous organic substrates and the modification of root exudate composition.In a series of pot experiments, organic materials of varying quality and origin were amended into arable soil, to test the response of fungi in terms of biomass and community composition (Chapter 2). Based on a first screening, paper pulp and beech wood sawdust amendment resulted in a rapid increase in ascomycete saprotrophic fungi (mainly Sordariomycetes), which persisted for a period of at least two months. Using the same setup, I further tested the effect of wood sawdusts from distinct tree species, alone or in combination with mineral nitrogen. The fungus-stimulating effect of wood sawdust amendment was also tested in four arable soils with different soil characteristics. The results revealed that saprotrophic fungal communities of arable soils retain a good ability to respond to wood sawdust of deciduous trees, but not to sawdust of coniferous tree species. Combination of sawdust with mineral nitrogen resulted in extra stimulation of saprotrophic fungi.The aim of Chapter 3 was to test the effect of phenolic root exudates on the biomass and community composition of rhizosphere fungi. To this end, an artificial rhizosphere model system was established. It allowed to introduce artificial exudate mixtures via diffusion into the soil, thereby simulating root exudation. In this way, phenolic acids were added both alone and in combination with a mixture of primary root exudate metabolites. Phenolic acids were applied at a rate consistent with the levels found for phenolic acids deposited in soils (0.02 - 0.2 mg g-1 soil). Phenolic acids had little effect on the total fungal biomass in the simulated rhizosphere. The same result was obtained in a follow-up experiment, where rhizosphere fungal biomass was measured for Arabidopsis thaliana mutants with an altered composition of phenolic root exudates. This indicates that selecting crop varieties for a higher exudation of phenolic acids is not a promising strategy for promoting saprotrophic fungi in the rhizosphere of crop plants. This study also showed that phenolic acids promote specific root-infecting fungi (Fusarium, Fusicolla and Trichoderma) in the simulated rhizosphere. Consequently, this indicates phenolic root exudates as potential modulators of rhizosphere and root fungal communities.The composition and activity of microbes in bulk soil has a strong influence on the assembly of microbial communities in the rhizosphere and roots. Having established that wood sawdust amendment causes an effective stimulation of saprotrophic fungi in arable soil, Chapter 4 showed how this affects the biomass, activity and composition of microbial communities associated with crop seedlings. 13CO2-pulse labelling of carrot seedlings grown in sawdust-amended and control soil revealed that sawdust-stimulated fungi in soil can extend into the rhizosphere and actively consume plant-derived carbon. The total bacterial abundance and active uptake of root exudates was not affected by sawdust addition, while AMF abundance and activity were promoted. The analysis of rhizosphere and root-associated communities using DNA(-SIP) illustrated that Sordariomycetes, Glomeromycetes, Bacteroidia and Rhizobiales increased in relative abundance. Based on sequencing data, the sub-community of potential pathogenic fungi did not increase relative to the total fungal community. Hence, the conditioning of arable soil with sawdust promotes a higher activity of saprotrophic fungi in the rhizosphere, thereby steering root-associated microbial communities.After individuating fungus-stimulating organic amendments (Chapter 2), assessing their ability to stimulate rhizosphere-competent fungi and describing their effects on bacteria (Chapter 4), I studied if the stimulation of saprotrophic fungi by woody materials and paper pulp can be used to control Rhizoctonia solani, one of the most widespread causal agents of soil-borne plant diseases (Chapter 5). To this end, a R. solani isolate was exposed to woody materials and paper pulp in a Petri dish assay. This showed that paper pulp is a highly suitable substrate for the growth of R. solani, while its performance was lower on sawdusts, but varied according to tree species identity. This was followed by two bioassays performed with an arable soil naturally infected by R. solani, where I planted seeds of a red beet variety which is  susceptible to this pathogen. The bioassays showed that oak and elder wood resulted in a consistent improved control of disease. In addition, paper pulp caused a short-term, transient stimulation of R. solani, which coincided with a poor performance of beets sown immediately after amendment. An interval of two weeks or longer between paper pulp addition and sowing resulted in disease suppression. These results point at the importance of timing of organic amendments relative to sowing, as a factor affecting the efficacy of disease-suppressing soil treatments.Overall, this thesis provides information on how cellulose-rich organic amendments and phenolic root exudates affect the abundance and composition of saprotrophic fungi, bacteria and soil-borne pathogenic fungi in arable soils and in the rhizosphere of crops. Based on these results, I depict a promising perspective for the use of cellulose-rich materials as a tool to promote sustainable biocontrol via managing microbial communities and microbial interactions in arable soils. In addition, a possible role of phenolic root exudates in modulating the recruitment of root-infecting fungi is indicated

Saprotrofe schimmels bieden perspectief voor verduurzaming landbouw

Op 10 Februari, verdedigde Anna Clocchiatti haarproefschrift “Bringing Soil Fungi into Action –Options for forward-looking agriculture” in dedigitale aula van de Wageningen Universiteit.Met dit proefschrift laat ze zien dat stimulatie vansaprotrofe bodemschimmels een belangrijke rolkan spelen bij de verduurzaming van gewasteelten, en met name bij het verhogen van natuurlijkeonderdrukking van wortelinfecterende, pathogeneschimmels

Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2-pulse-labeling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.,See the published article

Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose‐rich materials. Here, we examined if sawdust‐stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust‐amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2‐pulse‐labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA‐SIP) and nucleic acids (DNA‐SIP). Sawdust‐stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α‐Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate‐consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root‐associated microbiomes

Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose‐rich materials. Here, we examined if sawdust‐stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust‐amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2‐pulse‐labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA‐SIP) and nucleic acids (DNA‐SIP). Sawdust‐stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α‐Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate‐consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root‐associated microbiomes

The hidden potential of saprotrophic fungi in arable soil: Patterns of short-term stimulation by organic amendments

Saprotrophic fungi are abundant in soils of (semi-)natural ecosystems, where they play a major role in ecosystem functioning. On the contrary, saprotrophic fungal biomass is remarkably low in intensively managed soils and this can have a negative impact on soil functioning. Nevertheless, arable soils harbour a diverse pool of fungi, which can be stimulated by organic amendments. Management targeted towards increasing soil organic matter often coincides with an increase of fungal biomass, but it can take years before effects are seen. However, a rapid stimulation of fungal biomass at the start of the growing season could immediately benefit crop production, by improving nutrient availability, soil structure and suppression of soil-borne diseases. The objective of this study is to realize a rapid increase of saprotrophic fungal biomass with organic amendments. In controlled pot experiments, dried and milled organic materials of different quality were added to an arable sandy soil. Ergosterol-based fungal biomass and ITS2-based fungal community structure were measured over a period of two months. Wood sawdust of deciduous tree species and paper pulp resulted in a high and lasting increase of fungal biomass, as opposed to transient effects given by cover crops and other non-woody plant materials. Little or no stimulation of fungi was seen for coniferous wood sawdust and agro-industrial by-products. Nitrogen immobilization induced by sawdust and paper pulp was compensated by supplementing mineral nitrogen, which enhanced the stimulation of saprotrophic fungi. The composition of the stimulated fungi was influenced by the quality of organic amendments. In particular, deciduous wood sawdust and paper pulp favoured saprotrophic ascomycete fungi (mainly Sordariomycetes), with no increment in potential plant-pathogenic fungi. Overall, our results point at a good perspective to use woody materials as sustainable soil improver via stimulation of saprotrophic fungi

The hidden potential of saprotrophic fungi in arable soil: Patterns of short-term stimulation by organic amendments

Saprotrophic fungi are abundant in soils of (semi-)natural ecosystems, where they play a major role in ecosystem functioning. On the contrary, saprotrophic fungal biomass is remarkably low in intensively managed soils and this can have a negative impact on soil functioning. Nevertheless, arable soils harbour a diverse pool of fungi, which can be stimulated by organic amendments. Management targeted towards increasing soil organic matter often coincides with an increase of fungal biomass, but it can take years before effects are seen. However, a rapid stimulation of fungal biomass at the start of the growing season could immediately benefit crop production, by improving nutrient availability, soil structure and suppression of soil-borne diseases. The objective of this study is to realize a rapid increase of saprotrophic fungal biomass with organic amendments. In controlled pot experiments, dried and milled organic materials of different quality were added to an arable sandy soil. Ergosterol-based fungal biomass and ITS2-based fungal community structure were measured over a period of two months. Wood sawdust of deciduous tree species and paper pulp resulted in a high and lasting increase of fungal biomass, as opposed to transient effects given by cover crops and other non-woody plant materials. Little or no stimulation of fungi was seen for coniferous wood sawdust and agro-industrial by-products. Nitrogen immobilization induced by sawdust and paper pulp was compensated by supplementing mineral nitrogen, which enhanced the stimulation of saprotrophic fungi. The composition of the stimulated fungi was influenced by the quality of organic amendments. In particular, deciduous wood sawdust and paper pulp favoured saprotrophic ascomycete fungi (mainly Sordariomycetes), with no increment in potential plant-pathogenic fungi. Overall, our results point at a good perspective to use woody materials as sustainable soil improver via stimulation of saprotrophic fungi