Plant species dominance over PFAAs in structuring bacterial communities and their functional profiles in treatment wetlands.

This study investigates the impact of different plant species (Iris pseudacorus L., Phragmites australis (Cav.) Trin.

ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies.

In microbial community sequencing, involving bacterial ribosomal 16S rDNA or fungal ITS, the targeted genes are the basis for taxonomical assignment. The traditional bioinformatical procedure has for decades made use of a clustering protocol by which sequences are pooled into packages of shared percent identity, typically at 97%, to yield Operational Technical Units (OTUs). Progress in the data processing methods has however led to the possibility of minimizing technical sequencers errors, which were the main reason for the OTU choice, and to analyze instead the exact Amplicon Sequence Variants (ASV) which is a choice yielding much less agglomerated reads.

Surprising concentrations of hydrogen and non-geological methane and carbon dioxide in the soil.

Due to its potential use as a carbon-free energy resource with minimal environmental and climate impacts, natural hydrogen (H) produced by subsurface geochemical processes is today the target of intensive research. In H exploration practices, bacteria are thought to swiftly consume H and, therefore, small near-surface concentrations of H, even orders of 10 ppmv in soils, are considered a signal of active migration of geological gas, potentially revealing underground resources. Here, we document an extraordinary case of a widespread occurrence of H (up to 1 vol%), together with elevated concentrations of CH and CO (up to 51 and 27 vol%, respectively), in aerated meadow soils along Italian Alps valleys.

Metataxonomic analysis of endophytic bacteria of blackberry (Rubus ulmifolius Schott) across tissues and environmental conditions.

(1) Background: Endophytic bacteria represent an important component of plant wellness. They have been widely studied for their involvement in plant development and enhancement of stress tolerance. In this work, the endophytic communities of roots, stems, and leaves of blackberry (Rubus ulmifolius Schott) were studied in three different niches: natural, riverside, and human-impacted niches.

Characterization of dry-cured ham microbiota at 12 months of seasoning obtained from different rearing strategies using 16S rRNA profiling.

In this study, we investigated the microbiota of 72 Italian ham samples collected after 12 months of seasoning. The hams were elaborated from pigs fed different rearing methods, including the traditional restricted medium protein diet chosen as control (C group); restrictive low protein diet (LP group); two ad libitum high-protein diet groups (HP9M group: slaughter at 9 months of age; HP170 group: slaughter at 170 kg). A multi-amplicon 16S metabarcoding approach was used, and a total of 2845 Amplicon Sequence Variants were obtained from the 72 ham samples.

Determining the hierarchical order by which intestinal tract, administered diet, and individual relay can shape the gut microbiome of fattening quails.

A bacterial metabarcoding approach was used to compare the microbiome composition of caecal and faecal samples from fattening Japanese quails (Coturnix coturnix japonica) fed three different diet regimes. The tested feedstuffs included (1) a commercial diet for fattening quails, (2) a commercial diet containing 12% full-fat silkworm (Bombyx mori) pupae meal, and (3) a commercial diet containing 12% defatted silkworm pupae meal. The aim of the experiment was to verify the relative effect of three variables (diet type, gut tract comparing caecum to rectum, and individual animal) in determining the level of bacterial community dissimilarity to rank the relevance of each of the three factors in affecting and shaping community composition.

Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity.

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites.

Smart selection of soil microbes for resilient and sustainable viticulture.

The grapevine industry is of high economic importance in several countries worldwide. Its growing market demand led to an acceleration of the entire production processes, implying increasing use of water resources at the expense of environmental water balance and the hydrological cycle. Furthermore, in recent decades climate change and the consequent expansion of drought have further compromised water availability, making current agricultural systems even more fragile from ecological and economical perspectives.

Method to evaluate the microbial degradation activity in silage, cow rumen with test, and in manure and slurry.

Microorganisms are present everywhere and can influence a variety of processes. In agriculture and husbandry, the level of microbial activity can be crucial information, yet the methods for determining microbial activity are usually very long, complex, and costly. In this work, a novel and easy-to-use method, already in use for determining soil microbial activity, named Fertimetro was tested as a fast and cheap solution for measuring microbial activity in silages, in vitro rumen fluids, and manure and slurry.

Subclinical Mastitis from and spp. Induces Changes in Milk Peptidome in Holstein Cattle.

Early detection of bovine subclinical mastitis may improve treatment strategies and reduce the use of antibiotics. Herein, individual milk samples from Holstein cows affected by subclinical mastitis induced by and spp. were analyzed by untargeted and targeted mass spectrometry approaches to assess changes in their peptidome profiles and identify new potential biomarkers of the pathological condition.

The impact of milk storage temperatures on cheese quality and microbial communities at dairy processing plant scale.

Cheese production is an applied biotechnology whose proper outcome relies strictly on the complex interactive dynamics which unfold within defined microbial groups. These may start being active from the collection of milk and continue up to its final stages of maturation. One of the critical parameters playing a major role is the milk refrigeration temperature before pasteurization as it can affect the proportion of psychrotrophic taxa abundance in the total milk bacterial population.

Nutritional additives dominance in driving the bacterial communities succession and bioremediation of hydrocarbon and heavy metal contaminated soil microcosms.

Soil quality and microbial diversity are essential to the health of ecosystems. However, it is unclear how the use of eco-friendly natural additives can improve the quality and microbial diversity of contaminated soils. Herein, we used high-throughput 16 S rDNA amplicon Illumina sequencing to evaluate the stimulation and development of microbial diversity and concomitant bioremediation in hydrocarbon (HC) and heavy metal (HM)-rich waste disposal site soil when treated with meat and bone meal (MBM), cyclodextrin (Cdx), and MBM and cyclodextrin mixture (Cdx MBM) over a period of 3 months.

Brown Seaweed Extract (BSE) Application Influences Auxin- and ABA-Related Gene Expression, Root Development, and Sugar Yield in L.

The molecular and phenotypic effects of a brown seaweed extract (BSE) were assessed in sugar beet ( L.). Transcript levels of BSE-treated and untreated plants were studied by RNA-seq and validated by quantitative real-time PCR analysis (RT-qPCR).

Dataset on bio-stimulation experiments for the removal of hydrocarbons and the monitoring of certain elements in a contaminated soil.

Meat and Bone Meal (MBM) and β-cyclodextrin were added to a soil sample co-contaminated by hydrocarbons (diesel fraction C-C and lubricant oil fraction C-C) and heavy metals to promote soil remediation. The pilot study was conducted in the laboratory, maintaining optimal conditions (i.e.

Bacterial endophytes as indicators of susceptibility to Cercospora Leaf Spot (CLS) disease in Beta vulgaris L.

The fungus Cercospora beticola causes Cercospora Leaf Spot (CLS) of sugar beet (Beta vulgaris L.). Despite the global importance of this disease, durable resistance to CLS has still not been obtained.

Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination.

A meta-analysis was carried out on published literature covering the topic of interactive plant microbiology for botanical species of legumes occurring within the boundary of the Italian island Sardinia, lying between the Tyrrhenian and the western Mediterranean seas. Reports were screened for the description of three types of bacterial occurrences; namely, (a) the nitrogen-fixing symbionts dwelling in root nodules; (b) other bacteria co-hosted in nodules but having the ancillary nature of endophytes; (c) other endophytes isolated from different non-nodular portions of the legume plants. For 105 plant species or subspecies, over a total of 290 valid taxonomical descriptions of bacteria belonging to either one or more of these three categories were found, yielding 85 taxa of symbionts, 142 taxa of endophytes in nodules, and 33 in other plant parts.

Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne AG-2-2-IIIB Resistance in Sugar Beet.

, causing crown and root rot, is a major risk to sugar beet ( L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs.

Pedosedimentary and microbial investigation of a karst sequence record.

A 3-m thick sediment sequence, found in a limestone mine located in the south of Italy at a depth of ca. 25-30 m from the current ground level, was investigated. Samples from 5 layers were analysed by X-ray diffraction, elemental analysis, Inductively Coupled Plasma Mass Spectrometry and micromorphology.

Characterization of bacterial communities isolated from municipal waste compost and screening of their plant-interactive phenotypes.

Four batches of commercial compost obtained from the organic fraction of municipal solid waste were analyzed from chemical and microbiological standpoints. The working hypothesis was that, being this type of compost derived partly from plant waste, it could contain plant-growth promoting bacterial endophytes, prone to be active again upon its usual delivery as fertilizer. Culturable bacteria were isolated at different temperatures, quantified by colony morphology, identified taxonomically by 16S sequencing and screened for plant-growth promoting phenotypes including auxin and siderophore production, phosphate solubilization and peptide mineralization to ammonia.

SNP Alleles Associated With Low Bolting Tendency in Sugar Beet.

The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet ( L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study.

Endophytic Microbiome Responses to Sulfur Availability in (L.).

Sulfur is an essential plant macronutrient, and its adequate supply allows an efficient root storage and sugar extractability in sugar beets (  L.). In this study, we investigated the effect of changes in sulfur availability on the endophytic community structure of sugar beets.

Novel Effects of Leonardite-Based Applications on Sugar Beet.

The present study aimed to explore the effects of foliar application of a leonardite-based product on sugar beet ( L.) plants grown in the field. The approach concerned the evaluation of the community compositional structure of plant endophytic bacteria through a metabarcoding approach, the expression level of a gene panel related to hormonal metabolism and signaling, and the main sugar beet productivity traits.