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. (2) Results: The microbiome composition revealed that Sphingomonadaceae was the most abundant family in all samples, accounting for 9.4-45.8%. In contrast, other families seem to be linked to a specific tissue or niche. Families Microbacteriaceae and Hymenobacteraceae increased their presence in stem and leaf samples, while Burkholderiaceae abundance was important in riverside samples. Alpha and beta diversity analyses showed that root samples were the most diverse, and they gathered together in the same cluster, apart from the rest of the samples. (3) Conclusions: The analysis of the microbiome of R. ulmifolius plants revealed that the composition was essentially the same in different niches; the differences were primarily influenced by plant tissue factors with a core genome dominated by Sphingomonadaceae. Additionally, it was observed that R. ulmifolius can select its own microbiome, and this remains constant in all tissues evaluated regardless the niche of sampling.

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. While a standard temperature of 4 °C is the common choice, due to its general growth control effect, it does have a potential drawback. This is due to the fact that some cold-tolerant genera present a proteolytic activity with uncompleted proliferation, which could negatively affect curd clotting and regular cheese maturation. Moreover, accidental thermal variations of milk before cheese-making, in a plus or minus direction, can occur both at farm collection sites and during transfer to dairy plant. This present research, directly commissioned by a major fresh cheese-producing company, includes an in-factory trial. In this trial, a gradient of temperatures from 4 °C to 13 °C, which were subsequently reversed, was purposely adopted to: (a) verify sensory alterations in the resulting product at different maturation stages, and, (b) analyze, in parallel, using DNA extraction and 16S-metabarcoding sequencing from the same samples, the presence, abundance and corresponding taxonomical identity of all the bacteria featured in communities found in milk and cheese samples. Overall, 1,714 different variants were detected and sorted into 394 identified taxa. Significant bacterial community shifts in cheese were observed in response to milk refrigeration temperature and subsequently associated with samples having altered scores in sensory panel tests. In particular, proteolytic psychrotrophes were outcompeted by Enterobacteriales and by other taxa at the peak temperature of 13 °C, but aggressively increased in the descent phases, upon the cooling down of milk to values of 7 °C. Relevant clues have been collected for better anticipation of thermal abuse effects or parameter variations allowing for improved handling of technical processing conditions by the cheese manufacturing industry.