Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences.

The microbiota of Protected Designation of Origin (PDO) cheeses plays an essential role in defining their quality and typicity and could be applied to protect these products from counterfeiting. To study the possible role of cheese microbiota in distinguishing Grana Padano (GP) cheese from generical hard cheeses (HC), the microbial structure of 119 GP cheese samples was studied by DNA metabarcoding and DNA metafingerprinting and compared with 49 samples of generical hard cheeses taken from retail. DNA metabarcoding highlighted the presence, as dominant taxa, of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, Streptococcus thermophilus, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus spp., and Lactococcus spp. in both GP cheese and HC. Differential multivariate statistical analysis of metataxonomic and metafingerprinting data highlighted significant differences in the Shannon index, bacterial composition, and species abundance within both dominant and subdominant taxa between the two cheese groups. A supervised Neural Network (NN) classification tool, trained by metagenotypic data, was implemented, allowing to correctly classify GP cheese and HC samples. Further implementation and validation to increase the robustness and improve the predictive capacity of the NN classifier will be needed. Nonetheless, the proposed tool opens interesting perspectives in helping protection and valorization of GP and other PDO cheeses.

Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis.

The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.

Debt, Incarceration, and Re-entry: a Scoping Review.

People involved with the criminal justice system in the United States are disproportionately low-income and indebted. The experience of incarceration intensifies financial hardship, including through worsening debt. Little is known about how people who are incarcerated and their families are impacted by debt and how it affects their reentry experience. We conducted a scoping review to identify what is known about the debt burden on those who have been incarcerated and their families and how this impacts their lives. We searched 14 data bases from 1990 to 2019 for all original research addressing financial debt held by those incarcerated in the United States, and screened articles for relevance and extracted data from pertinent studies. These 31 studies selected for inclusion showed that this population is heavily burdened by debt that was accumulated in three general categories: debt directly from criminal justice involvement such as LFOs, preexisting debt that compounded during incarceration, and debts accrued during reentry for everyday survival. Debt was generally shown to have a negative effect on financial well-being, reentry, family structure, and mental health. Debts from LFOs and child support is very common among the justice-involved population and are largely unpayable. Other forms of debt likely to burden this population remain largely understudied. Extensive reform is necessary to lessen the burden of debt on the criminal justice population in order to improve reentry outcomes and quality of life.

Extracellular and intracellular DNA for bacterial profiling of long-ripened cheeses.

A novel approach was developed to extract the extracellular DNA (eDNA), i.e. the free DNA outside the microbial cell, compared to the intracellular DNA (iDNA). The two DNA fractions were investigated in seven long-ripened cheeses. Among different buffer solutions tested, EDTA 0.5 M at pH 8 enabled a mild homogenization of cheese samples and the highest eDNA recovery. The extraction protocol was tested on single strains of lactic acid bacteria characterizing many Italian long-ripened cheeses, such as Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus rhamnosus. The method resulted suitable for eDNA extraction because it minimized cell-lysis, avoiding the leakage of iDNA from the cells. The yields of eDNA, ranging from 0.01 to 0.36 µg g-1 cheese, were generally higher than the iDNA, indicating that autolytic phenomena prevailed over intact cells after 8-12 months of ripening. In four of the seven cheeses, the same LAB species were detected in the eDNA and iDNA fractions by length-heterogeneity PCR, while in the remaining three samples, a higher number of species was highlighted in the eDNA compared to the corresponding iDNA. The sequential extraction of eDNA and iDNA can be applied to obtain additional information on the composition of the bacterial community in long-aged cheeses.

Publisher Correction: Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood.

Deadwood decomposition is relevant in nature and wood inhabiting fungi (WIF) are its main decomposers. However, climate influence on WIF community and their interactions with bacteria are poorly understood. Therefore, we set up an in-field mesocosm experiment in the Italian Alps and monitored the effect of slope exposure (north- vs. south-facing slope) on the decomposition of Picea abies wood blocks and their microbiome over two years. Unlike fungal richness and diversity, we observed compositional and functional differences in the WIF communities as a function of exposure. Wood-degrading operational taxonomic units (OTUs) such as Mycena, and mycorrhizal and endophytic OTUs were characteristic of the south-facing slope. On the north-facing one, Mucoromycota, primarily Mucor, were abundant and mixotrophic basidiomycetes with limited lignin-degrading capacities had a higher prevalence compared to the southern slope. The colder, more humid conditions and prolonged snow-coverage at north exposure likely influenced the development of the wood-degrading microbial communities. Networks between WIF and N2-fixing bacteria were composed of higher numbers of interacting microbial units and showed denser connections at the south-facing slope. The association of WIF to N2-fixing Burkholderiales and Rhizobiales could have provided additional competitive advantages, especially for early wood colonization.

Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment.

Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition.

Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories.

Deadwood decay employs a complex metabolism and provides carbon and nutrients for soils. Although being highly diverse, the contribution of the bacterial deadwood colonizing community is underexplored compared with the fungal one. Therefore, we performed an in-field mesocosm study and monitored the bacterial communities in decaying experimental Picea abies wood blocks and their underlying soil on north- and south- exposed slopes in the Italian Alps over a 2-year period. The faster deadwood decay at the south-facing slope was associated with a higher bacterial richness and a higher number of specialist operational taxonomic units (OTUs) which were more strongly correlated to environmental parameters than other bacterial community members. With progressing decay, the wood and soil bacterial communities became more similar in terms of richness, diversity and evenness and especially at the south-facing slope, they also became more similar in terms of community composition. Exposure-specific OTUs suggest wood-soil interaction. However, despite the strong influence of exposure on the soil bacterial communities, the P. abies wood blocks shared a comparably high number of OTUs with the soil irrespective of the slope. At finer taxonomic scale, we identified Pseudomonas, Microbacteria, Sphingomonas, Xanthomonas, Methylovirgula and Burkholderia as decay associated, although their functional role needs further studies.

Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps.

Due to their sensitivity to changing environmental conditions sub- and alpine soils are often monitored in the context of climate change, usually, however, neglecting slope exposure. Therefore, we set up a climosequence-approach to study the effect of exposure and, in general, climate, on the microbial biomass and microbial diversity and activity, comprising five pairs of north (N)- and south (S)-facing sites along an altitudinal gradient ranging from 1200 to 2400m a.s.l. in the Italian Alps (Trentino Alto Adige, Italy). Soil physico-chemical properties were related to microbiological properties (microbial biomass: double strand DNA yield vs. substrate-induced respiration; diversity of bacterial, fungal and archaeal communities: genetic fingerprinting DGGE vs. real-time PCR; microbial activity: basal respiration vs. multiple hydrolytic enzyme assays) to monitor shifts in the diversity and activity of microbial communities as a function of slope exposure and to evaluate the most determinant chemical parameters shaping the soil microbiota. The exposure-effect on several hydrolytic key-enzymes was enzyme-specific: e.g. acid phosphomonoesterase potential activity was more pronounced at the N-facing slope while the activities of alkaline phosphomonoesterase, pyrophosphate-phosphodiesterase and arylsulfatase were higher at the S-facing slope. Furthermore, this exposure-effect was domain-specific: bacteria (S>N, altitude-independent); fungi (N~S); and archaea (N>S; altitude-dependent). Additionally, the abiotic parameters shaping the community composition were in general depending on soil depth. Our multidisciplinary approach allowed us to survey the exposure and altitudinal effects on soil physico-chemical and microbiological properties and thus unravel the complex multiple edaphic factor-effects on soil microbiota in mountain ecosystems.

Soil attributes and microclimate are important drivers of initial deadwood decay in sub-alpine Norway spruce forests.

Deadwood is known to significantly contribute to global terrestrial carbon stocks and carbon cycling, but its decay dynamics are still not thoroughly understood. Although the chemistry of deadwood has been studied as a function of decay stage in temperate to subalpine environments, it has generally not been related to time. We therefore studied the decay (mass of deadwood, cellulose and lignin) of equal-sized blocks of Picea abies wood in soil-mesocosms over two years in the Italian Alps. The 8 sites selected were along an altitudinal sequence, reflecting different climate zones. In addition, the effect of exposure (north- and south-facing slopes) was taken into account. The decay dynamics of the mass of deadwood, cellulose and lignin were related to soil parameters (pH, soil texture, moisture, temperature) and climatic data. The decay rate constants of Picea abies deadwood were low (on average between 0.039 and 0.040y(-1)) and of lignin close to zero (or not detectable), while cellulose reacted much faster with average decay rate constants between 0.110 and 0.117y(-1). Our field experiments showed that local scale factors, such as soil parameters and topographic properties, influenced the decay process: higher soil moisture and clay content along with a lower pH seemed to accelerate wood decay. Interestingly, air temperature negatively correlated with decay rates or positively with the amount of wood components on south-facing sites. It exerted its influence rather on moisture availability, i.e. the lower the temperature the higher the moisture availability. Topographic features were also relevant with generally slower decay processes on south-facing sites than on north-facing sites owing to the drier conditions, the higher pH and the lower weathering state of the soils (less clay minerals). This study highlights the importance of a multifactorial consideration of edaphic parameters to unravel the complex dynamics of initial wood decay.

Effects of a three-year exposure to ambient ozone on biomass allocation in poplar using ethylenediurea.

We examined the effect of ambient ozone on visible foliar injury, growth and biomass in field-grown poplar cuttings of an Oxford clone sensitive to ozone (Populus maximoviczii Henry × berolinensis Dippel) irrigated with ethylenediurea (EDU) or water for three years. EDU is used as an ozone protectant for plants. Protective effects of EDU on ozone visible injury were found. As a result, poplar trees grown under EDU treatment increased leaves, lateral branches and root density in the third year, although no significant enhancement of stem height and diameter was found. Ambient ozone (AOT40, 24.6 ppm h; diurnal hourly average, 40.3 ppb) may finally reduce carbon gain by reducing the number of branches, and thus sites for leaf formation, in ozone-sensitive poplar trees under not-limiting conditions.