microorganisms Article Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity? Daniela Sangiorgio 1,† , Antonio Cellini 1,† , Francesco Spinelli 1, * , Brian Farneti 2 , Iuliia Khomenko 2 , Enrico Muzzi 1 , Stefano Savioli 1 , Chiara Pastore 1 , María Teresa Rodriguez-Estrada 1 and Irene Donati 1,3   Citation: Sangiorgio, D.; Cellini, A.; Spinelli, F.; Farneti, B.; Khomenko, I.; Muzzi, E.; Savioli, S.; Pastore, C.; Rodriguez-Estrada, M.T.; Donati, I. Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity? Microorganisms 2021, 9, 1617. https://doi.org/10.3390/ microorganisms9081617 Academic Editor: Denis Faure Received: 9 June 2021 Accepted: 2 July 2021 Published: 29 July 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; daniela.sangiorgio2@unibo.it (D.S.); antonio.cellini2@unibo.it (A.C.); enrico.muzzi@unibo.it (E.M.); stefano_savioli@fastwebnet.it (S.S.); chiara.pastore@unibo.it (C.P.); maria.rodriguez@unibo.it (M.T.R.-E.); irene.donati@zespri.com (I.D.) 2 Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; brian.farneti@fmach.it (B.F.); iuliia.khomenko@fmach.it (I.K.) 3 Zespri Fresh Produce, 40132 Bologna, Italy * Correspondence: francesco.spinelli3@unibo.it; Tel.: +39-051-2096443 † These authors contributed equally. Abstract: Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences observed in the nutritional quality of differently grown fruits might be due to variations in the microbiome taxonomic and functional composition. Here, the influence of organic and integrated pest management (IPM) cultivation on quality, aroma and microbiome of raspberry (Rubus idaeus L.) fruits was evaluated. Differences in the fruit microbiome of organic and IPM raspberry were examined by next-generation sequencing and bacterial isolates characterization to highlight the potential contribution of the resident-microflora to fruit characteristics and aroma. The cultivation method strongly influenced fruit nutraceutical traits, aroma and epiphytic bacterial biocoenosis. Organic cultivation resulted in smaller fruits with a higher anthocyanidins content and lower titratable acidity content in comparison to IPM berries. Management practices also influenced the amounts of acids, ketones, aldehydes and monoterpenes, emitted by fruits. Our results suggest that the effects on fruit quality could be related to differences in the population of Gluconobacter, Sphingomonas, Rosenbergiella, Brevibacillus and Methylobacterium on fruit. Finally, changes in fruit aroma can be partly explained by volatile organic compounds (VOCs) emitted by key bacterial genera characterizing organic and IPM raspberry fruits. Keywords: Rubus idaeus L.; VOCs; microbiome; volatilome; Gluconobacter; anthocyanins 1. Introduction Raspberry (Rubus idaeus L.) is a highly valuable crop with a large agricultural potential, both in Europe and worldwide. Raspberry consumer demand, as well as its cultivation, have been steadily increasing in the past 20 years, with a further acceleration since 2010 [1]. Russia is the top producing country, with a production volume of 165,800 tonnes accounting approx. for 20% of the world production [1]. Raspberry is also widely cultivated in other European (Serbia, Poland) and north-American (Mexico, USA) countries [1,2]. Hedonic characteristics and nutraceutical properties of raspberry are the main drivers of consumer appreciation. In fact, raspberry is rich in health-beneficial compounds, such as flavonols, catechins, ascorbic acid and ellagic acid derivatives [3,4]. Additionally, more than 300 volatile organic compounds (VOCs) have been reported as constituents of raspberry aroma [5], including alcohols, aldehydes, ketones, esters and terpenoids [6,7]. Among the main aroma-active compounds (i.e., those with low perception threshold compared to emission rates), C6 aldehydes (hexanal, hexenal isomers) and norisoprenoids (e.g., ionones) are responsible for grassy and floral notes of raspberry fruit aroma [8]. Microorganisms 2021, 9, 1617. https://doi.org/10.3390/microorganisms9081617 https://www.mdpi.com/journal/microorganisms