Publications by authors named "Massimo Pindo"

45 Publications

A pilot study of eDNA metabarcoding to estimate plant biodiversity by an alpine glacier core (Adamello glacier, North Italy).

Sci Rep 2021 Jan 13;11(1):1208. Epub 2021 Jan 13.

Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy.

Current biodiversity loss is a major concern and thus biodiversity assessment of modern ecosystems is compelling and needs to be contextualized on a longer timescale. High Throughput Sequencing (HTS) is progressively becoming a major source of data on biodiversity time series. In this multi proxy study, we tested, for the first time, the potential of HTS to estimate plant biodiversity archived in the surface layers of a temperate alpine glacier, amplifying the trnL barcode for vascular plants from eDNA of firn samples. A 573 cm long core was drilled by the Adamello glacier and cut into sections; produced samples were analyzed for physical properties, stable isotope ratio, and plant biodiversity by eDNA metabarcoding and conventional light microscopy analysis. Results highlighted the presence of pollen and plant remains within the distinct layers of snow, firn and ice. While stable isotope ratio showed a scarcely informative pattern, DNA metabarcoding described distinct plant species composition among the different samples, with a broad taxonomic representation of the biodiversity of the catchment area and a high-ranking resolution. New knowledge on climate and plant biodiversity changes of large catchment areas can be obtained by this novel approach, relevant for future estimates of climate change effects.
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http://dx.doi.org/10.1038/s41598-020-79738-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807053PMC
January 2021

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota.

Sci Rep 2021 Jan 13;11(1):889. Epub 2021 Jan 13.

Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.
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http://dx.doi.org/10.1038/s41598-020-79474-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7806629PMC
January 2021

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet.

PLoS One 2020 6;15(8):e0237262. Epub 2020 Aug 6.

Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.

The factors that influence the diversity and composition of raw milk and fecal microbiota in healthy commercial dairy herds are not fully understood, partially because the majority of metataxonomic studies involve experimental farms and/or single factors. We analyzed the raw milk and fecal microbiota of 100 healthy cows from 10 commercial alpine farms from the Province of Trento, Italy, using metataxonomics and applied statistical modelling to investigate which extrinsic and intrinsic parameters (e.g. herd, diet and milk characteristics) correlated with microbiota richness and composition in these relatively small traditional farms. We confirmed that Firmicutes, Ruminococcaceae and Lachnospiraceae families dominated the fecal and milk samples of these dairy cows, but in addition, we found an association between the number of observed OTUs and Shannon entropy on each farm that indicates higher microbiota richness is associated with increased microbiota stability. Modelling showed that herd was the most significant factor affecting the variation in both milk and fecal microbiota composition. Furthermore, the most important predictors explaining the variation of microbiota richness were milk characteristics (i.e. percentage fat) and diet for milk and fecal samples, respectively. We discuss how high intra-herd variation could affect the development of treatments based on microbiota manipulation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237262PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410245PMC
October 2020

Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine.

Sci Rep 2020 07 22;10(1):12193. Epub 2020 Jul 22.

Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige, Italy.

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12-mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins.
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http://dx.doi.org/10.1038/s41598-020-69051-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376207PMC
July 2020

Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach.

Front Microbiol 2020 7;11:789. Epub 2020 May 7.

Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

The structure of microbial communities, microalgae, heterotrophic protozoa and fungi contributes to characterize food webs and productivity and, from an anthropogenic point of view, the qualitative characteristics of water bodies. Traditionally, in freshwater environments many investigations have been directed to the study of pelagic microalgae ("phytoplankton") and periphyton (i.e., photosynthetic and mixotrophic protists) through the use of light microscopy (LM). While the number of studies on bacterioplankton communities have shown a substantial increase after the advent of high-throughput sequencing (HTS) approaches, the study of the composition, structure, and spatio-temporal patterns of microbial eukaryotes in freshwater environments was much less widespread. Moreover, the understanding of the correspondence between the relative phytoplankton abundances estimated by HTS and LM is still incomplete. Taking into account these limitations, this study examined the biodiversity and seasonality of the community of eukaryotic microplankton in the epilimnetic layer of a large and deep perialpine lake (Lake Garda) using HTS. The analyses were carried out at monthly frequency during 2014 and 2015. The results highlighted the existence of a rich and well diversified community and the presence of numerous phytoplankton taxa that were never identified by LM in previous investigations. Furthermore, the relative abundances of phytoplankton estimated by HTS and LM showed a significant relationship at different taxonomic ranks. In the 2 years of investigation, the temporal development of the whole micro-eukaryotic community showed a clear non-random and comparable distribution pattern, with the main taxonomic groups coherently distributed in the individual seasons. In perspective, the results obtained in this study highlight the importance of HTS approaches in assessing biodiversity and the relative importance of the main protist groups along environmental gradients, including those caused by anthropogenic impacts (e.g., eutrophication and climate change).
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http://dx.doi.org/10.3389/fmicb.2020.00789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7221148PMC
May 2020

Unraveling the genetic origin of 'Glera', 'Ribolla Gialla' and other autochthonous grapevine varieties from Friuli Venezia Giulia (northeastern Italy).

Sci Rep 2020 04 29;10(1):7206. Epub 2020 Apr 29.

JKI - Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany.

'Glera' and 'Ribolla Gialla' are the most economically relevant local grapevine cultivars of Friuli Venezia Giulia region (north-eastern Italy). 'Glera' is used to produce the world-renowned Prosecco wine. 'Ribolla Gialla' cultivation is constantly increasing due to the strong demand for sparkling wine and is the most important variety in Brda (Slovenia). Knowledge of local varieties history in terms of migration and pedigree relationships has scientific and marketing appeal. Following prospections, genotyping and ampelographic characterization of minor germplasm in Friuli Venezia Giulia, a further research was developed to understand the parentage relationships among the grapevine varieties grown in this region. An integrated strategy was followed combining the analysis of nuclear and chloroplast microsatellites with the Vitis 18k SNP chip. Two main recurrent parents were found, which can be regarded as "founders": 'Vulpea', an Austrian variety parent-offspring related with at least ten Friuli Venezia Giulia cultivars, among them 'Glera', and 'Refosco Nostrano', first degree related with other six Friuli Venezia Giulia varieties. 'Ribolla Gialla' was shown to be another member of the impressively long list of offspring derived from the prolific 'Heunisch Weiss'. Combining molecular markers and historical references was a high-performance strategy for retracing and adjusting the history of cultivars.
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http://dx.doi.org/10.1038/s41598-020-64061-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190720PMC
April 2020

Novel Aspects on The Interaction Between Grapevine and : Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection.

Genes (Basel) 2020 02 28;11(3). Epub 2020 Feb 28.

Dipartimento di Scienze Agrarie e Ambientali (DISAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.

Mgaloblishvili, a cultivar, exhibits unique resistance traits against , the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen were used to identify effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in . Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in of a putative susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to .
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http://dx.doi.org/10.3390/genes11030261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140796PMC
February 2020

Alpine headwaters emerging from glaciers and rock glaciers host different bacterial communities: Ecological implications for the future.

Sci Total Environ 2020 May 4;717:137101. Epub 2020 Feb 4.

Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, Italy.

Mountain glacier shrinkage represents a major effect of the current global warming and 80-100% of the Alpine glaciers are predicted to vanish within the next few decades. As the thawing rate of mountain permafrost ice is much lower than for glacier ice, a shift from glacial to periglacial dynamics is predicted for Alpine landscapes during the 21st century. Despite the growing literature on the impacts of deglaciation on Alpine hydrology and ecosystems, chemical and biological features of waters emerging from Alpine rock glaciers (i.e. permafrost landforms composed by a mixture of ice and debris) have been poorly investigated so far, and knowledge on microbial biodiversity of headwaters is still sparse. A set of glacier-, rock glacier- and groundwater/precipitation-fed streams was investigated in the Italian Central Alps in late summer 2016, aiming at exploring bacterial community composition and diversity in epilithic and surface sediment biofilm and at verifying the hypothesis that rock glacier-fed headwaters represent peculiar ecosystems from both a chemical and biological point of view. Rock glacier-fed waters showed high values of electrical conductivity and trace elements related to their bedrock lithology, and their highly diverse bacterial assemblages significantly differed from those detected in glacier-fed streams. Bacterial taxonomic composition appeared to be mainly related to water and substrate type, as well as to water chemistry, the latter including concentrations of nutrients and trace metals. The results of this study confirm the chemical and biological peculiarity of rock glacier-fed waters compared to glacial waters, and suggest a potential driving role of thawing permafrost in modulating future ecological traits of Alpine headwaters within the context of progressing deglaciation.
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http://dx.doi.org/10.1016/j.scitotenv.2020.137101DOI Listing
May 2020

Changes in Microbiota Across Developmental Stages of , an Invasive Mosquito Vector in Europe: Indications for Microbiota-Based Control Strategies.

Front Microbiol 2019 10;10:2832. Epub 2019 Dec 10.

Fondazione Edmund Mach, Research and Innovation Centre, Trento, Italy.

Since it has been understood that gut microbiota of vector mosquitoes can influence their vector competence, efforts have been undertaken to develop new control strategies based on host microbiota manipulation, and aimed at suppressing the vector population or replacing it with a less competent one. For the proper design of such control strategies it is necessary to know the microbiota composition of the target vector species, how it is acquired, and how it changes throughout the host's life cycle. In this study, 16S rRNA amplicon high-throughput sequencing was used to characterize the changes in microbiota from the aquatic environment (larval breeding sites) to the different developmental stages of field-collected in Italy, an emerging invasive mosquito species in Europe and a potential vector of several pathogens. The bacterial communities of the aquatic breeding sites, larvae, pupae and adults showed distinctive structures to one another. Indeed, 84% of community members were unique to a given sample type. Nevertheless, almost 40% of the sequences generated were assigned to bacteria detected in all sample types, suggesting the importance of bacteria transstadially transmitted from water to the adult stage in constituting mosquito microbiota. Among these, genus largely constituted water microbiota, family was the most abundant in larvae and pupae, and genus dominated adult communities. In addition, constituted a core microbiota across all sample types. Our results suggest that the microbiota of mosquitoes is composed by a community which derives from the aquatic bacteria of the larval breeding sites, is then filtered by the larval gut, where only certain members are able to persist, rearranged by metamorphosis and finally modified by the change in diet at the adult stage. Understanding how the microbiota of changes through the mosquito life cycle represents a first step in selecting bacterial candidates for use in microbiota-based intervention measures for this species. The properties which exhibits in this species, such as dominance, high prevalence and transstadial transmission, prevent the use of but make an ideal candidate for paratransgenesis.
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http://dx.doi.org/10.3389/fmicb.2019.02832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6914824PMC
December 2019

Microbiome of vineyard soils is shaped by geography and management.

Microbiome 2019 11 8;7(1):140. Epub 2019 Nov 8.

Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, Italy.

Background: Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management.

Results: Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil.

Conclusions: Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.
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http://dx.doi.org/10.1186/s40168-019-0758-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839268PMC
November 2019

Reduced fire blight susceptibility in apple cultivars using a high-efficiency CRISPR/Cas9-FLP/FRT-based gene editing system.

Plant Biotechnol J 2020 03 3;18(3):845-858. Epub 2019 Oct 3.

Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

The bacterium Erwinia amylovora, the causal agent of fire blight disease in apple, triggers its infection through the DspA/E effector which interacts with the apple susceptibility protein MdDIPM4. In this work, MdDIPM4 knockout has been produced in two Malus × domestica susceptible cultivars using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens. Fifty-seven transgenic lines were screened to identify CRISPR/Cas9-induced mutations. An editing efficiency of 75% was obtained. Seven edited lines with a loss-of-function mutation were inoculated with the pathogen. Highly significant reduction in susceptibility was observed compared to control plants. Sequencing of five potential off-target sites revealed no mutation event. Moreover, our construct contained a heat-shock inducible FLP/FRT recombination system designed specifically to remove the T-DNA harbouring the expression cassettes for CRISPR/Cas9, the marker gene and the FLP itself. Six plant lines with reduced susceptibility to the pathogen were heat-treated and screened by real-time PCR to quantify the exogenous DNA elimination. The T-DNA removal was further validated by sequencing in one plant line. To our knowledge, this work demonstrates for the first time the development and application of a CRISPR/Cas9-FLP/FRT gene editing system for the production of edited apple plants carrying a minimal trace of exogenous DNA.
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http://dx.doi.org/10.1111/pbi.13253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004915PMC
March 2020

Multifaceted aspects of synchrony between freshwater prokaryotes and protists.

Mol Ecol 2019 10 17;28(19):4500-4512. Epub 2019 Sep 17.

Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

Community composition of freshwater prokaryotes and protists varies through time. Few studies contemporarily investigate temporal variation of these freshwater communities for more than 1 year. We compared the temporal patterns of prokaryotes and protists in three distinct habitats for 4 years (2014-2017) in Lake Tovel, a cold-water lake. This lake showed a marked temperature increase in 2017 linked to altered precipitation patterns. We investigated whether microbial communities reflected this change across habitats and whether changes occurred at the same time and to the same extent. Furthermore, we tested the concept of hydrological year emphasizing the ecological effect of water renewal on communities for its explanatory power of community changes. Microbe diversity was assessed by Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and 18S rRNA gene, and we applied co-inertia analysis and asymmetric eigenvector maps modelling to infer synchrony and temporal patterns of prokaryotes and protists. When considering community composition, microbes were invariable in synchrony across habitats and indicated a temporal gradient linked to decreasing precipitation; however, when looking at temporal patterns, the extent of synchrony was reduced. Small-scale patterns were similar across habitats and microbes and linked to seasonally varying environmental variables, while large-scale patterns were different and partially linked to an ecosystem change as indicated by increasing water transparency and temperature and decreasing dissolved oxygen. Our advanced statistical approach outlined the multifaceted aspect of synchrony when linked to community composition and temporal patterns.
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http://dx.doi.org/10.1111/mec.15228DOI Listing
October 2019

Global change-driven use of onshore habitat impacts polar bear faecal microbiota.

ISME J 2019 12 5;13(12):2916-2926. Epub 2019 Aug 5.

School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK.

The gut microbiota plays a critical role in host health, yet remains poorly studied in wild species. Polar bears (Ursus maritimus), key indicators of Arctic ecosystem health and environmental change, are currently affected by rapid shifts in habitat that may alter gut homeostasis. Declining sea ice has led to a divide in the southern Beaufort Sea polar bear subpopulation such that an increasing proportion of individuals now inhabit onshore coastal regions during the open-water period ('onshore bears') while others continue to exhibit their typical behaviour of remaining on the ice ('offshore bears'). We propose that bears that have altered their habitat selection in response to climate change will exhibit a distinct gut microbiota diversity and composition, which may ultimately have important consequences for their health. Here, we perform the first assessment of abundance and diversity in the faecal microbiota of wild polar bears using 16S rRNA Illumina technology. We find that bacterial diversity is significantly higher in onshore bears compared to offshore bears. The most enriched OTU abundance in onshore bears belonged to the phylum Proteobacteria, while the most depleted OTU abundance within onshore bears was seen in the phylum Firmicutes. We conclude that climate-driven changes in polar bear land use are associated with distinct microbial communities. In doing so, we present the first case of global change mediated alterations in the gut microbiota of a free-roaming wild animal.
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http://dx.doi.org/10.1038/s41396-019-0480-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864082PMC
December 2019

Reduced diversity of gut microbiota in two Aedes mosquitoes species in areas of recent invasion.

Sci Rep 2018 10 31;8(1):16091. Epub 2018 Oct 31.

Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Trento, Italy.

Aedes mosquitoes are considered highly successful global invasive species and vectors of several pathogens of relevance for public health. Their midgut's microbiota can play an important role in affecting not only their vectorial competence but also their fitness, physiology, food digestion, metabolism, immunity and adaptation to new environmental conditions. Using high-throughput sequencing we compared the microbiota of Aedes albopictus collected in Italy with those reported in populations from France and Vietnam. We also analysed Aedes koreicus gut microbiota for the first time. We found remarkable individual difference along with common bacterial taxa in both species. Ae. albopictus collected in Italy had a lower richness and a different composition of microbiota in respect to specimens collected in France and Vietnam. It also showed a core microbiota formed mainly of bacteria of the genus Pseudomonas. Overall, the two Aedes species (Ae. albopictus and Ae. koreicus) collected in Italy, showed a large core microbiota with 75.98% of the identified Operational Taxonomic Units. Furthermore, Ae. albopictus had 2.5% prevalence of Wolbachia and 0.07% of Asaia spp, while Ae. koreicus had 14.42% of Asaia spp. and no Wolbachia. This study provides new informations on the spatial variation of the midgut bacterial communities in mosquitoes of medical relevance within areas of recent invasion and provide the basis for further studies aimed at assessing the effects of such variation on vectorial capacity for a range of pathogens.
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http://dx.doi.org/10.1038/s41598-018-34640-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208342PMC
October 2018

Temporal variability of bacterioplankton is habitat driven.

Mol Ecol 2018 11 26;27(21):4322-4335. Epub 2018 Sep 26.

Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

Temporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, nonmetric multidimensional scaling and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to meltwater inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats.
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http://dx.doi.org/10.1111/mec.14855DOI Listing
November 2018

Unique resistance traits against downy mildew from the center of origin of grapevine (Vitis vinifera).

Sci Rep 2018 08 21;8(1):12523. Epub 2018 Aug 21.

Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), via Celoria 2, 20133, Milano, Italy.

The Eurasian grapevine (Vitis vinifera), an Old World species now cultivated worldwide for high-quality wine production, is extremely susceptible to the agent of downy mildew, Plasmopara viticola. The cultivation of resistant V. vinifera varieties would be a sustainable way to reduce the damage caused by the pathogen and the impact of disease management, which involves the economic, health and environmental costs of frequent fungicide application. We report the finding of unique downy mildew resistance traits in a winemaking cultivar from the domestication center of V. vinifera, and characterize the expression of a range of genes associated with the resistance mechanism. Based on comparative experimental inoculations, confocal microscopy and transcriptomics analyses, our study shows that V. vinifera cv. Mgaloblishvili, native to Georgia (South Caucasus), exhibits unique resistance traits against P. viticola. Its defense response, leading to a limitation of P. viticola growth and sporulation, is determined by the overexpression of genes related to pathogen recognition, the ethylene signaling pathway, synthesis of antimicrobial compounds and enzymes, and the development of structural barriers. The unique resistant traits found in Mgaloblishvili highlight the presence of a rare defense system in V. vinifera against P. viticola which promises fresh opportunities for grapevine genetic improvement.
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http://dx.doi.org/10.1038/s41598-018-30413-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104083PMC
August 2018

Tissue age and plant genotype affect the microbiota of apple and pear bark.

Microbiol Res 2018 Jun 10;211:57-68. Epub 2018 Apr 10.

Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy. Electronic address:

Plant tissues host complex fungal and bacterial communities, and their composition is determined by host traits such as tissue age, plant genotype and environmental conditions. Despite the importance of bark as a possible reservoir of plant pathogenic microorganisms, little is known about the associated microbial communities. In this work, we evaluated the composition of fungal and bacterial communities in the pear (Abate and Williams cultivars) and apple (Golden Delicious and Gala cultivars) bark of three/four-year-old shoots (old bark) or one-year-old shoots (young bark), using a meta-barcoding approach. The results showed that both fungal and bacterial communities are dominated by genera with ubiquitous attitudes, such as Aureobasidium, Cryptococcus, Deinococcus and Hymenobacter, indicating intense microbial migration to surrounding environments. The shoot age, plant species and plant cultivar influenced the composition of bark fungal and bacterial communities. In particular, bark communities included potential biocontrol agents that could maintain an equilibrium with potential plant pathogens. The abundance of fungal (e.g. Alternaria, Penicillium, Rosellinia, Stemphylium and Taphrina) and bacterial (e.g. Curtobacterium and Pseudomonas) plant pathogens was affected by bark age and host genotype, as well as those of fungal genera (e.g. Arthrinium, Aureobasidium, Rhodotorula, Sporobolomyces) and bacterial genera (e.g. Bacillus, Brevibacillus, Methylobacterium, Sphingomonas and Stenotrophomonas) with possible biocontrol and plant growth promotion properties.
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http://dx.doi.org/10.1016/j.micres.2018.04.002DOI Listing
June 2018

Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake.

Microb Ecol 2018 Jul 1;76(1):125-143. Epub 2017 Dec 1.

Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy.

High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.
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http://dx.doi.org/10.1007/s00248-017-1120-xDOI Listing
July 2018

Measuring the impact of olive pomace enriched biscuits on the gut microbiota and its metabolic activity in mildly hypercholesterolaemic subjects.

Eur J Nutr 2019 Feb 9;58(1):63-81. Epub 2017 Nov 9.

Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy.

Purpose: Olive pomace is a major waste product of olive oil production but remains rich in polyphenols and fibres. We measured the potential of an olive pomace-enriched biscuit formulation delivering 17.1 ± 4.01 mg/100 g of hydroxytyrosol and its derivatives, to modulate the composition and metabolic activity of the human gut microbiota.

Methods: In a double-blind, controlled parallel dietary intervention 62 otherwise healthy hypercholesterolemic (total plasma cholesterol 180-240 mg/dl) subjects were randomly assigned to eat 90 g of olive pomace-enriched biscuit (olive-enriched product, OEP) or an isoenergetic control (CTRL) for 8 weeks. Fasted blood samples, 24-h urine and faecal samples were collected before and after dietary intervention for measurement of microbiota, metabolites and clinical parameters.

Results: Consumption of OEP biscuits did not impact on the diversity of the faecal microbiota and there was no statistically significant effect on CVD markers. A trend towards reduced oxidized LDL cholesterol following OEP ingestion was observed. At the genus level lactobacilli and Ruminococcus were reduced in OEP compared to CTRL biscuits. A trend towards increased bifidobacteria abundance was observed after OEP ingestion in 16S rRNA profiles, by fluorescent in situ hybridization and by qPCR. Targeted LC-MS revealed significant increases phenolic acid concentrations in 24-h urine following OEP ingestion and 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid, derivatives of hydroxytyrosol, were elevated in blood. A sex effect was apparent in urine small phenolic acid concentrations, and this sex effect was mirrored by statistically significant differences in relative abundances of faecal bacteria between men and women.

Conclusion: Ingestion of OEP biscuits led to a significant increase in the metabolic output of the gut microbiota with an apparent sex effect possibly linked to differences in microbiota makeup. Increased levels of homovanillic acid and DOPAC, thought to be involved in reducing oxidative LDL cholesterol, were observed upon OEP ingestion. However, OEP did not induce statistically significant changes in either ox-LDL or urinary isoprostane in this study.
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http://dx.doi.org/10.1007/s00394-017-1572-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424929PMC
February 2019

Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout (Oncorhynchus mykiss).

Int J Food Sci Nutr 2018 May 31;69(3):318-333. Epub 2017 Aug 31.

f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy.

Developing fish farming to meet the demands of food security and sustainability in the 21st century will require new farming systems and improved feeds. Diet and microbe interactions in the gut is an important variable with the potential to make a significant impact on future fish farming diets and production systems. It was monitored the gut microbiota of farmed rainbow trout using 16S rRNA profiling over 51 weeks during standard rearing conditions and feeding diet with supplementation of an essential oils (MixOil) mixture from plants (at a concentration in diet of 200 mg/kg). Gut microbiota 16S rRNA profiling indicated that the fish gut was dominated by Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes. Although the dietary supplementation with MixOil had no impact on either the composition or architecture of gut microbiota, significant changes in alpha and beta diversity and relative abundance of groups of gut bacteria were evident during growth stages on test feeds, especially upon prolonged growth on finishing feed. Fish fillet quality to guarantee palatability and safety for human consumption was also evaluated. Significant differences within the gut microbiota of juvenile and adult trout under the same rearing conditions were observed, The addition of essential oil blend affected some physicochemical characteristics of trout fillets, including their resistance to oxidative damage and their weight loss (as liquid loss and water holding capacity) during the first period of storage, that are two important parameters related to product shelf life and susceptibility to spoilage. The results highlighted the need for further studies concern dietary microbiome modulation at different life stages and its influence on animal health, growth performance and final product quality.
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http://dx.doi.org/10.1080/09637486.2017.1370699DOI Listing
May 2018

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms.

Microbiome 2017 03 10;5(1):32. Epub 2017 Mar 10.

Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145, Florence, Italy.

Background: A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over continental scales and can deposit them in sensitive sink habitats. In winter 2014, the largest ever recorded Saharan dust event in Italy was efficiently deposited on the Dolomite Alps and was sealed between dust-free snow. This provided us the unique opportunity to overcome difficulties in separating dust associated from "domestic" microbes and thus, to determine with high precision microorganisms transported exclusively by desert dust.

Results: Our metagenomic analysis revealed that sandstorms can move not only fractions but rather large parts of entire microbial communities far away from their area of origin and that this microbiota contains several of the most stress-resistant organisms on Earth, including highly destructive fungal and bacterial pathogens. In particular, we provide first evidence that winter-occurring dust depositions can favor a rapid microbial contamination of sensitive sink habitats after snowmelt.

Conclusions: Airborne microbial depositions accompanying extreme meteorological events represent a realistic threat for ecosystem and public health. Therefore, monitoring the spread and persistence of storm-travelling alien microbes is a priority while considering future trajectories of climatic anomalies as well as anthropogenically driven changes in land use in the source regions.
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http://dx.doi.org/10.1186/s40168-017-0249-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345179PMC
March 2017

Fine-tuning of the flavonoid and monolignol pathways during apple early fruit development.

Planta 2017 May 11;245(5):1021-1035. Epub 2017 Feb 11.

Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all' Adige, Italy.

Main Conclusion: A coordinated regulation of different branches of the flavonoid pathway was highlighted that may contribute to elucidate the role of this important class of compounds during the early stages of apple fruit development. Apple (Malus × domestica Borkh.) is an economically important fruit appreciated for its organoleptic characteristics and its benefits for human health. The first stages after fruit set represent a very important and still poorly characterized developmental process. To enable the profiling of genes involved in apple early fruit development, we combined the suppression subtractive hybridization (SSH) protocol to next-generation sequencing. We identified and characterized genes induced and repressed during fruit development in the apple cultivar 'Golden Delicious'. Our results showed an opposite regulation of genes coding for enzymes belonging to flavonoid and monolignol pathways, with a strong induction of the former and a simultaneous repression of the latter. Two isoforms of phenylalanine ammonia-lyase and 4-coumarate:CoA ligase, key enzymes located at the branching point between flavonoid and monolignol pathways, showed opposite expression patterns during the period in analysis, suggesting a possible regulation mechanism. A targeted metabolomic analysis supported the SSH results and revealed an accumulation of the monomers catechin and epicatechin as well as several forms of procyanidin oligomers in apple fruitlets starting early after anthesis, together with a decreased production of other classes of flavonoids such as some flavonols and the dihydrochalcone phlorizin. Moreover, gene expression and metabolites accumulation of 'Golden Delicious' were compared to a wild apple genotype of Manchurian crabapple (Malus mandshurica (Maxim.) Kom.). Significant differences in both gene expression and metabolites accumulation were found between the two genotypes.
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http://dx.doi.org/10.1007/s00425-017-2660-5DOI Listing
May 2017

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status.

Front Microbiol 2016 26;7:1703. Epub 2016 Oct 26.

Department of Neuroscience, Psychology, Drug Research and Child Health, Meyer Children's Hospital, University of FlorenceFlorence, Italy; Rheumatology Unit, Anna Meyer Children's Hospital, University of FlorenceFlorence, Italy.

Alteration of gut microbiota is involved in several chronic inflammatory and autoimmune diseases, including rheumatoid arthritis, and gut microbial "pro-arthritogenic" profiles have been hypothesized. Intestinal inflammation may be involved in spondyloarthropathies and in a subset of patients affected by Juvenile Idiopathic Arthritis (JIA), the most common chronic rheumatic disease of childhood. We compared the fecal microbiota composition of JIA patients with healthy subjects (HS), evaluating differences in microbial profiles between sub-categories of JIA, such as enthesitis-related arthritis (JIA-ERA), in which inflammation of entheses occurs, and polyarticular JIA, non-enthesitis related arthritis (JIA-nERA). Through taxon-level analysis, we discovered alteration of fecal microbiota components that could be involved in subclinical gut inflammation, and promotion of joint inflammation. We observed abundance in in both JIA categories, reduction in and in JIA-ERA, and increase in in JIA-nERA, respectively, compared with HS. Among the more relevant genera, we found an increase in , involved in colitis and arthritis, in JIA-ERA patients compared with HS, and a trend of decrease in , known for anti-inflammatory properties, in JIA-nERA compared with JIA-ERA and HS. Differential abundant taxa identified JIA patients for the HLA-B27 allele, including , and . Prediction analysis of metabolic functions showed that JIA-ERA metagenome was differentially enriched in bacterial functions related to cell motility and chemotaxis, suggesting selection of potential virulence traits. We also discovered differential microbial profiles and intra-group variability among active disease and remission, suggesting instability of microbial ecosystem in autoimmune diseases with respect to healthy status. Similarly to other chronic autoimmune and inflammatory diseases, different microbial profiles, as observed among different JIA subgroups compared to HS, and potential functional acquisition related to migration, could promote inflammation and contribute to the disease pathogenesis.
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http://dx.doi.org/10.3389/fmicb.2016.01703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080347PMC
October 2016

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine.

Front Plant Sci 2016 19;7:1053. Epub 2016 Jul 19.

Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy.

Protein derivatives and carbohydrates can stimulate plant growth, increase stress tolerance, and activate plant defense mechanisms. However, these molecules can also act as a nutritional substrate for microbial communities living on the plant phyllosphere and possibly affect their biocontrol activity against pathogens. We investigated the mechanisms of action of a protein derivative (nutrient broth, NB) against grapevine downy mildew, specifically focusing on the effects of foliar treatments on plant defense stimulation and on the composition and biocontrol features of the phyllosphere microbial populations. NB reduced downy mildew symptoms and induced the expression of defense-related genes in greenhouse- and in vitro-grown plants, indicating the activation of grapevine resistance mechanisms. Furthermore, NB increased the number of culturable phyllosphere bacteria and altered the composition of bacterial and fungal populations on leaves of greenhouse-grown plants. Although, NB-induced changes on microbial populations were affected by the structure of indigenous communities originally residing on grapevine leaves, degrees of disease reduction and defense gene modulation were consistent among the experiments. Thus, modifications in the structure of phyllosphere populations caused by NB application could partially contribute to downy mildew control by competition for space or other biocontrol strategies. Particularly, changes in the abundance of phyllosphere microorganisms may provide a contribution to resistance induction, partially affecting the hormone-mediated signaling pathways involved. Modifying phyllosphere populations by increasing natural biocontrol agents with the application of selected nutritional factors can open new opportunities in terms of sustainable plant protection strategies.
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http://dx.doi.org/10.3389/fpls.2016.01053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4949236PMC
August 2016

Altered gut microbiota in Rett syndrome.

Microbiome 2016 07 30;4(1):41. Epub 2016 Jul 30.

Institute of Biometeorology (IBIMET), National Research Council (CNR), Via Giovanni Caproni 8, I-50145, Florence, Italy.

Background: The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by mutations in MeCP2 gene, is commonly associated with gastrointestinal dysfunctions and constipation, suggesting a link between RTT's gastrointestinal abnormalities and the gut microbiota. The aim of this study was to evaluate the bacterial and fungal gut microbiota in a cohort of RTT subjects integrating clinical, metabolomics and metagenomics data to understand if changes in the gut microbiota of RTT subjects could be associated with gastrointestinal abnormalities and inflammatory status.

Results: Our findings revealed the occurrence of an intestinal sub-inflammatory status in RTT subjects as measured by the elevated values of faecal calprotectin and erythrocyte sedimentation rate. We showed that, overall, RTT subjects harbour bacterial and fungal microbiota altered in terms of relative abundances from those of healthy controls, with a reduced microbial richness and dominated by microbial taxa belonging to Bifidobacterium, several Clostridia (among which Anaerostipes, Clostridium XIVa, Clostridium XIVb) as well as Erysipelotrichaceae, Actinomyces, Lactobacillus, Enterococcus, Eggerthella, Escherichia/Shigella and the fungal genus Candida. We further observed that alterations of the gut microbiota do not depend on the constipation status of RTT subjects and that this dysbiotic microbiota produced altered short chain fatty acids profiles.

Conclusions: We demonstrated for the first time that RTT is associated with a dysbiosis of both the bacterial and fungal component of the gut microbiota, suggesting that impairments of MeCP2 functioning favour the establishment of a microbial community adapted to the costive gastrointestinal niche of RTT subjects. The altered production of short chain fatty acids associated with this microbiota might reinforce the constipation status of RTT subjects and contribute to RTT gastrointestinal physiopathology.
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http://dx.doi.org/10.1186/s40168-016-0185-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967335PMC
July 2016

Development and validation of the Axiom(®) Apple480K SNP genotyping array.

Plant J 2016 Apr;86(1):62-74

Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.

Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
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http://dx.doi.org/10.1111/tpj.13145DOI Listing
April 2016

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation.

Sci Rep 2015 Oct 7;5:14862. Epub 2015 Oct 7.

Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy.

The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations.
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http://dx.doi.org/10.1038/srep14862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595646PMC
October 2015

Kinase domain-targeted isolation of defense-related receptor-like kinases (RLK/Pelle) in Platanus×acerifolia: phylogenetic and structural analysis.

BMC Res Notes 2014 Dec 8;7:884. Epub 2014 Dec 8.

Plant Pathology Research Center, CRA-PAV Agricultural Research Council, V, C,G, Bertero 22, 00156 Rome, Italy.

Background: Plant receptor-like kinase (RLK/Pelle) family regulates growth and developmental processes and interaction with pathogens and symbionts.Platanaceae is one of the earliest branches of Eudicots temporally located before the split which gave rise to Rosids and Asterids. Thus investigations into the RLK family in Platanus can provide information on the evolution of this gene family in the land plants.Moreover RLKs are good candidates for finding genes that are able to confer resistance to Platanus pathogens.

Results: Degenerate oligonucleotide primers targeting the kinase domain of stress-related RLKs were used to isolate for the first time 111 RLK gene fragments in Platanus×acerifolia. Sequences were classified as candidates of the following subfamilies: CrRLK1L, LRR XII, WAK-like, and LRR X-BRI1 group. All the structural features typical of the RLK kinase domain were identified, including the non-RD motif which marks potential pathogen recognition receptors (PRRs). The LRR XII candidates, whose counterpart in Arabidopsis and rice comprises non-RD PRRs, were mostly non-RD kinases, suggesting a group of PRRs. Region-specific signatures of a relaxed purifying selection in the LRR XII candidates were also found, which is novel for plant RLK kinase domain and further supports the role of LRR XII candidates as PRRs. As we obtained CrRLK1L candidates using primers designed on Pto of tomato, we analysed the phylogenetic relationship between CrRLK1L and Pto-like of plant species. We thus classified all non-solanaceous Pto-like genes as CrRLK1L and highlighted for the first time the close phylogenetic vicinity between CrRLK1L and Pto group. The origins of Pto from CrRLK1L is proposed as an evolutionary mechanism.

Conclusions: The signatures of relaxed purifying selection highlight that a group of RLKs might have been involved in the expression of phenotypic plasticity and is thus a good candidate for investigations into pathogen resistance.Search of Pto-like genes in Platanus highlighted the close relationship between CrRLK1L and Pto group. It will be exciting to verify if sensu strictu Pto are present in taxonomic groups other than Solanaceae, in order to further clarify the evolutionary link with CrRLK1L.We obtained a first valuable resource useful for an in-depth study on stress perception systems.
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http://dx.doi.org/10.1186/1756-0500-7-884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295470PMC
December 2014

Bacterial endophytic communities in the grapevine depend on pest management.

PLoS One 2014 11;9(11):e112763. Epub 2014 Nov 11.

Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy.

Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112763PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227848PMC
March 2016