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Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest

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A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (30 September 2019) | Viewed by 56758

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Dr. Ilaria Mannazzu

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Department of Agricultural Sciences, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
Interests: fermented beverages; yeast physiology; yeast biotechnology; microbial interactions; natural antimicrobials non-conventional yeasts, carotenoids
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Prof. Dr. Marilena Budroni

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Department of Agriculture Sciences, University of Sassari, 07100 Sassari, Italy
Interests: microbiology; biotechnology; food microbiology; yeasts; microbial collections; biofilm; beer; wine; sustainability
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Dr. Giacomo Zara

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Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
Interests: microbiology of food and beverages; valorization of food wastes; microbiota dynamics in food and soil; Saccharomyces cerevisiae; wine yeast
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Severino Zara

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General and Applied Microbiology, Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy
Interests: wine and food microbiology; antimicrobial activity of natual molecules; microbial biofilms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The impact of microorganisms on human activities is largely recognized. Microorganisms are the most abundant and important living organisms with respect to environmental nutrient cycling. They have a pivotal role in the preservation of natural habitats and in the production of almost all benefits that humans gather from properly functioning ecosystems. They establish symbiotic relationships with animals and plants and influence their health and illness. Moreover, microorganisms are the main protagonists in the biotech industry and in food and beverage fermentation.

Recent predictions of global species richness underline that our knowledge of microbial diversity is still much limited and suggest the existence of an enormous reservoir of species, genes, enzymes, and metabolic functions that have to be disclosed. In fact, the characterization and preservation of microbial biodiversity is indispensable not only for the maintenance of natural ecosystems but also for research purposes and for the development of applications in the biotech and food industries.

In this context, this Special Issue aims at collecting original research or review articles regarding: i) new strategies and tools for the characterization, preservation, and valorization of microbial biodiversity; ii) the exploitation of microbial biodiversity for food quality and safety; iii) the importance of microbial biodiversity for environmental and agricultural sustainability; iv) the impact of microbial biodiversity on the biotech industry.

Dr. Ilaria Mannazzu
Prof. Dr. Marilena Budroni
Dr. Giacomo Zara
Prof. Dr. Severino Zara
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

3 pages, 156 KiB

Open AccessEditorial

Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest

by Ilaria Mannazzu, Marilena Budroni, Giacomo Zara and Severino Zara

Microorganisms 2020, 8(12), 1938; https://doi.org/10.3390/microorganisms8121938 - 7 Dec 2020

Cited by 2 | Viewed by 1506

Abstract

This Special Issue collects original contributions in the form of review or research articles, dealing with different aspects of the preservation, characterization and exploitation of the biodiversity of bacteria, yeast, algae and filamentous fungi of different origins [...] Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

Research

Jump to: Editorial, Review

18 pages, 2642 KiB

Open AccessArticle

Changes of Quality of Minimally-Processed Pineapple (Ananas comosus, var. ‘Queen Victoria’) during Cold Storage: Fungi in the Leading Role

by Charlène Leneveu-Jenvrin, Baptiste Quentin, Sophie Assemat, Mathilde Hoarau, Jean-Christophe Meile and Fabienne Remize

Microorganisms 2020, 8(2), 185; https://doi.org/10.3390/microorganisms8020185 - 28 Jan 2020

Cited by 28 | Viewed by 6272

Abstract

Minimally-processed pineapple stored under refrigerated conditions is highly perishable. We aimed to characterize the evolution of physicochemical, sensory and microbiological quality during cold storage. Pineapple batches were sampled from several locations in Reunion Island and then minimally processed. In the processing step, the variability of firmness and counts of yeasts and molds were observed. Moreover, correlations between the sampling season and pH and b* color component, as well as between fungal population and b* parameter were observed. During storage, the visual aspect of pineapple cuts changed to brown and shiny, whereas olfactive descriptors shifted from fruity descriptors and fresh to fermented, alcoholic and milky. The values for pH, TA and TSS did not significantly vary according to storage time. A decrease in firmness and C* color parameter was observed. Yeast and mold counts were significantly higher after 7 days of storage. The diversity in yeasts and molds was mainly dependent on the considered batches observed from PCR-DGGE profiles. Fungal species were isolated from spoiled pineapple cuts. The implication of Penicilllium citrtrinum, Talaromyces amestolkiae, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, and Meyerozyma caribbica in the spoilage of minimally-processed pineapple cuts was further demonstrated. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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19 pages, 274 KiB

Open AccessArticle

Bacterial Biodiversity of Extra Virgin Olive Oils and Their Potential Biotechnological Exploitation

by Francesco Fancello, Chiara Multineddu, Mario Santona, Pierfrancesco Deiana, Giacomo Zara, Ilaria Mannazzu, Marilena Budroni, Sandro Dettori and Severino Zara

Microorganisms 2020, 8(1), 97; https://doi.org/10.3390/microorganisms8010097 - 10 Jan 2020

Cited by 19 | Viewed by 4709

Abstract

Bacterial diversity of 15 extra virgin olive oils, obtained from different Italian varieties, including Frantoio, Coratina, Bosana, and Semidana, was analyzed in this study. All bacterial isolates were genotyped using RAPD and REP-PCR method and grouped by means of cluster analyses. Sequencing of 16S rDNA of 51 isolates, representative of 36 clusters, led to the identification of Bacillus spp., Brevibacillus spp., Micrococcus spp., Staphylococcus spp., Pantoea spp., Kocuria spp., Lysinbacillus spp., and Lactobacillus spp., most of which reported for first time in olive oils. Phenotypic characterization of the 51 isolates, some of which ascribed to potentially probiotic species, indicate that two of them have beta-glucosidase activity while 37% present lipolytic activity. Preliminary evaluation of probiotic potential indicates that 31% of the isolates show biofilm formation ability, 29% acidic pH resistance, and 25% bile salt resistance. Finally, 29% of the isolates were sensitive to antibiotics while the remaining 71%, that include bacterial species well-recognized for their ability to disseminate resistance genes in the environment, showed a variable pattern of antibiotic resistance. The results obtained underline that microbial diversity of extra virgin olive oils represents an unexpected sink of microbial diversity and poses safety issues on the possible biotechnological exploitation of this microbial biodiversity. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

26 pages, 3556 KiB

Open AccessArticle

Evolutionary Engineering of an Iron-Resistant Saccharomyces cerevisiae Mutant and Its Physiological and Molecular Characterization

by Berrak Gülçin Balaban, Ülkü Yılmaz, Ceren Alkım, Alican Topaloğlu, Halil İbrahim Kısakesen, Can Holyavkin and Zeynep Petek Çakar

Microorganisms 2020, 8(1), 43; https://doi.org/10.3390/microorganisms8010043 - 24 Dec 2019

Cited by 23 | Viewed by 3803

Abstract

Iron plays an essential role in all organisms and is involved in the structure of many biomolecules. It also regulates the Fenton reaction where highly reactive hydroxyl radicals occur. Iron is also important for microbial biodiversity, health and nutrition. Excessive iron levels can cause oxidative damage in cells. Saccharomyces cerevisiae evolved mechanisms to regulate its iron levels. To study the iron stress resistance in S. cerevisiae, evolutionary engineering was employed. The evolved iron stress-resistant mutant “M8FE” was analysed physiologically, transcriptomically and by whole genome re-sequencing. M8FE showed cross-resistance to other transition metals: cobalt, chromium and nickel and seemed to cope with the iron stress by both avoidance and sequestration strategies. PHO84, encoding the high-affinity phosphate transporter, was the most down-regulated gene in the mutant, and may be crucial in iron-resistance. M8FE had upregulated many oxidative stress response, reserve carbohydrate metabolism and mitophagy genes, while ribosome biogenesis genes were downregulated. As a possible result of the induced oxidative stress response genes, lower intracellular oxidation levels were observed. M8FE also had high trehalose and glycerol production levels. Genome re-sequencing analyses revealed several mutations associated with diverse cellular and metabolic processes, like cell division, phosphate-mediated signalling, cell wall integrity and multidrug transporters. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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28 pages, 3130 KiB

Open AccessArticle

Study of Metabolic Adaptation of Red Yeasts to Waste Animal Fat Substrate

by Martin Szotkowski, Dana Byrtusova, Andrea Haronikova, Marie Vysoka, Marek Rapta, Volha Shapaval and Ivana Marova

Microorganisms 2019, 7(11), 578; https://doi.org/10.3390/microorganisms7110578 - 19 Nov 2019

Cited by 36 | Viewed by 4929

Abstract

Carotenogenic yeasts are non-conventional oleaginous microorganisms capable of utilizing various waste substrates. In this work, four red yeast strains (Rhodotorula, Cystofilobasidium, and Sporobolomyces sp.) were cultivated in media containing crude, emulsified, and enzymatically hydrolyzed animal waste fat, compared with glucose and glycerol, as single C-sources. Cell morphology (cryo-SEM (cryo-scanning electron microscopy), TEM (transmission electron microscopy)), production of biomass, lipase, biosurfactants, lipids (gas chromatography/flame ionization detection, GC/FID) carotenoids, ubiquinone, and ergosterol (high performance liquid chromatography, HPLC/PDA) in yeast cells was studied depending on the medium composition, the C source, and the carbon/nitrogen (C/N) ratio. All studied strains are able to utilize solid and processed fat. Biomass production at C/N = 13 was higher on emulsified/hydrolyzed fat than on glucose/glycerol. The production of lipids and lipidic metabolites was enhanced for several times on fat; the highest yields of carotenoids (24.8 mg/L) and lipids (54.5%/CDW (cell dry weight)) were found in S. pararoseus. Simultaneous induction of lipase and biosurfactants was observed on crude fat substrate. An increased C/N ratio (13–100) led to higher biomass production in fat media. The production of total lipids increased in all strains to C/N = 50. Oppositely, the production of carotenoids, ubiquinone, and ergosterol dramatically decreased with increased C/N in all strains. Compounds accumulated in stressed red yeasts have a great application potential and can be produced efficiently during the valorization of animal waste fat under the biorefinery concept. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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17 pages, 1993 KiB

Open AccessArticle

Genetic and Phenotypic Characterisation of a Saccharomyces cerevisiae Population of ‘Merwah’ White Wine

by Nadine Feghali, Warren Albertin, Edouard Tabet, Ziad Rizk, Angela Bianco, Giacomo Zara, Isabelle Masneuf-Pomarede and Marilena Budroni

Microorganisms 2019, 7(11), 492; https://doi.org/10.3390/microorganisms7110492 - 26 Oct 2019

Cited by 10 | Viewed by 3756

Abstract

The study of yeast biodiversity represents an important step in the preservation of the local heritage, and this work in particular has an innovative character since no further studies have investigated ‘Merwah’, one of the main grape varieties used in winemaking in Lebanon. To gain deeper knowledge of the genetic diversity and population structure of native Saccharomyces cerevisiae wine strains, 202 isolates were collected during spontaneous alcoholic fermentation of eight must/wine samples of cultivar ‘Merwah’, over two consecutive years (2016, 2017) in a traditional winery in Mount Lebanon (1400 m a.s.l.). The isolates were identified as S. cerevisiae on the basis of their morphology and preliminary sequence analysis of their internal transcribed spacer (ITS) PCR. They were then characterised at the strain level by interdelta PCR and genotyped using multiplex PCR reactions of 12 microsatellite markers. High genetic diversity was observed for the studied population. To select potential yeast starter strains from this population, micro-fermentations were carried out for 22 S. cerevisiae strains that were selected as representative of the ‘Merwah’ wine yeast population in order to determine their technological and oenological properties. Three indigenous yeast strains might represent candidates for pilot-scale fermentation in the winery, based on relevant features such as high fermentation vigour, low production of volatile acidity and H₂S and low residual sugar content at the end of alcoholic fermentation. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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14 pages, 4306 KiB

Open AccessArticle

Low Temperature (15 °C) Reduces Bacterial Diversity and Prolongs the Preservation Time of Volvariella volvacea

by Xiuling Wang, Shunjie Liu, Mingjie Chen, Changxia Yu, Yan Zhao, Huanling Yang, Lei Zha and Zhengpeng Li

Microorganisms 2019, 7(10), 475; https://doi.org/10.3390/microorganisms7100475 - 20 Oct 2019

Cited by 7 | Viewed by 4133

Abstract

Straw mushroom (Volvariella volvacea) is the most commonly cultivated edible fungus in the world, but the challenges associated with the preservation have limited its marketability. Microbiology, especially bacteria, play a key role in the deterioration of food, this study aimed to reveal the succession of the bacterial community on the surfaces of V. volvacea fruit bodies under different temperature conditions. We amplified 16S rRNA genes of V4 regions, obtained the bacterial species information by using high-throughput sequencing technology, and analyzed the effects of environmental temperature and preservation time on bacterial communities. The relative abundances of Firmicutes, Bacilli, and Bacillales increased significantly when straw mushrooms began to rot. Furthermore, the relative abundances of Paenibacillus, Lysinibacillus and Solibacillus, which belong to Bacillales, increased with the decay of straw mushroom. The Shannon and Simpson indices of V. volvacea stored at 30 °C were significantly higher than those of V. volvacea stored at 15 °C, which indicates that a high temperature contributes to the improvement in the species diversity. According to the linear discriminant analysis (LDA) effect size (LEfSe) results, the number of biomarkers in the 30 °C group (32, 42.11%) was significantly higher than that in the 15 °C group (17, 22.37%), indicating that a high temperature has a clustering effect on some bacterial communities. A Spearman correlation analysis showed that Pseudomonas, Stenotrophomonas and Solibacillus promoted the decay of straw mushroom. In conclusion, a high temperature increases the bacterial diversity on the straw mushroom surfaces and has a clustering effect on the bacterial communities. The bacterial community consisting of Firmicutes, Bacilli, Bacillales, Paenibacillus, Lysinibacillus, Pseudomonas, Stenotrophomonas and Solibacillus could promote the decay of straw mushroom, so new preservation materials research can focus on inhibiting anaerobic and decay-causing bacteria to prolong preservation time. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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8 pages, 212 KiB

Open AccessArticle

Effect of Milk Type on the Microbiological, Physicochemical and Sensory Characteristics of Probiotic Fermented Milk

by Dimitra Dimitrellou, Chrysoula Salamoura, Artemis Kontogianni, Despoina Katsipi, Panagiotis Kandylis, George Zakynthinos and Theodoros Varzakas

Microorganisms 2019, 7(9), 274; https://doi.org/10.3390/microorganisms7090274 - 21 Aug 2019

Cited by 31 | Viewed by 4377

Abstract

The production of fermented milk using cow milk, goat milk and a mixture of them (1:1) was evaluated. The traditional yogurt starter culture was used—Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus, along with Lactobacillus casei ATCC 393. The objective was to monitor the viability of these cultures during the storage of fermented milk at 4 °C for up to 28 days. Storage significantly affected the viability of all microorganisms and especially L. bulgaricus. All microorganisms retained viable numbers higher than 7.5 log CFU g⁻¹, even after 4 weeks of storage, which is important to confirm the probiotic character of the product. The use of goat milk significantly affected the pH and acidity of fermented milk. More specifically, the use of goat milk led to fermented milk with lower pH values and higher acidities than fermented milk with cow milk. The sensory evaluation ascertained the overall quality of fermented milk with a mixture of cow and goat milk, which scored similar values to the commercial sample. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

15 pages, 5683 KiB

Open AccessArticle

The Influence of Fungicide Treatments on Mycobiota of Grapes and Its Evolution During Fermentation Evaluated by Metagenomic and Culture-Dependent Methods

by Alice Agarbati, Laura Canonico, Leonardo Mancabelli, Christian Milani, Marco Ventura, Maurizio Ciani and Francesca Comitini

Microorganisms 2019, 7(5), 114; https://doi.org/10.3390/microorganisms7050114 - 26 Apr 2019

Cited by 18 | Viewed by 4311

Abstract

The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidium pullulans. Starmerella bacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopa uvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast species during the spontaneous fermentation but a different relative abundance. Differently, the NGS method was able to detect a greater biodiversity (lower abundant species) in comparison with the culture-dependent method. In this regard, the methodologies used gave a different picture of yeast dynamics during the fermentation process. The results indicated that the fungal treatments can influence the yeast community of grapes leading must fermentation and the final composition of wine. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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Review

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18 pages, 1767 KiB

Open AccessReview

Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections

by Luciana De Vero, Maria Beatrice Boniotti, Marilena Budroni, Pietro Buzzini, Stefano Cassanelli, Roberta Comunian, Maria Gullo, Antonio F. Logrieco, Ilaria Mannazzu, Rosario Musumeci, Iolanda Perugini, Giancarlo Perrone, Andrea Pulvirenti, Paolo Romano, Benedetta Turchetti and Giovanna Cristina Varese

Microorganisms 2019, 7(12), 685; https://doi.org/10.3390/microorganisms7120685 - 12 Dec 2019

Cited by 41 | Viewed by 12168

Abstract

Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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21 pages, 1883 KiB

Open AccessReview

The Dark Side of Microalgae Biotechnology: A Heterotrophic Biorefinery Platform Directed to ω-3 Rich Lipid Production

by Teresa Lopes da Silva, Patrícia Moniz, Carla Silva and Alberto Reis

Microorganisms 2019, 7(12), 670; https://doi.org/10.3390/microorganisms7120670 - 10 Dec 2019

Cited by 65 | Viewed by 5383

Abstract

Microbial oils have been considered a renewable feedstock for bioenergy not competing with food crops for arable land, freshwater and biodiverse natural landscapes. Microalgal oils may also have other purposes (niche markets) besides biofuels production such as pharmaceutical, nutraceutical, cosmetic and food industries. The polyunsaturated fatty acids (PUFAs) obtained from oleaginous microalgae show benefits over other PUFAs sources such as fish oils, being odorless, and non-dependent on fish stocks. Heterotrophic microalgae can use low-cost substrates such as organic wastes/residues containing carbon, simultaneously producing PUFAs together with other lipids that can be further converted into bioenergy, for combined heat and power (CHP), or liquid biofuels, to be integrated in the transportation system. This review analyses the different strategies that have been recently used to cultivate and further process heterotrophic microalgae for lipids, with emphasis on omega-3 rich compounds. It also highlights the importance of studying an integrated process approach based on the use of low-cost substrates associated to the microalgal biomass biorefinery, identifying the best sustainability methodology to be applied to the whole integrated system. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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