Selected Papers from the 9th Conference of the Hellenic Scientific Society MIKROBIOKOSMOS "Beneficial Microbes at the Heart of Mikrobiokosmos"

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 24678

Special Issue Editors


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Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
Interests: aquatic microbial ecology; diversity; food webs; biogeography
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Department of Genetics & Biotechnology, Faculty of Biology, National & Kapodistrian University of Athens, Panepistimiopolis, Ilissia, 15701 Athens, Greece
Interests: gene regulation; horizontal transfer; plasmid biology; bacterial cell-cell signaling; bacterial genomics; microbial biotechnology; strain engineering

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Hellenic Agricultural Organisation-DEMETER, Institute of Technology of Agricultural Products, Sofokli Venizelou 1, Lycovrissi, 14123 Attica, Greece
Interests: food microbiology; food safety; probiotics; microbiology of fermented foods; food microbial ecology
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Guest Editor
School of Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
Interests: water/wastewater microbiology; advanced disinfection processes; bioremediation; ecotoxicology
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Special Issue Information

Dear Colleagues,

Microorganisms have endured and thrived through the beginning of life on our planet and this makes them the most resourceful biology “story-tellers” of all living beings. They play key roles in biogeochemical cycling at different environmental compartments, with reciprocal and cascading effects in agriculture, animal, human and plant health. They are important for a sustainable agriculture, as microbial pesticides, biofertilisers or bioremediating agents, and mediate in environmental cleanup and biodepuration. They support life in lakes and oceans affecting all aquatic organism yields and have an overall impact on the climate; they indeed regulate climate change. They contribute to food production, preservation and safety, and thus in animal and human health and nutrition. They constitute an invaluable source of cellular and molecular materials for exploitation in biotechnology and bioenergy production. Last but not least, they constitute an important and integral part of all other living organisms: the microbiome. Thus, the role of the microbial world—mikrobiokosmos, in Greek—is considered more than ever crucial in the “One Health” and “One Planet” schools of thought, i.e., the emerging concepts advocating the intertwining of healthy global ecosystems with healthy living beings.

This Special Issue will include peer-reviewed articles that will be presented at the 9th Conference of the Hellenic Scientific Society Mikrobiokosmos “Beneficial microbes at the heart of Mikrobiokosmos” to be held on December 16–18, 2021, in Athens, Greece. However, we also welcome contributions relevant to the focus of the conference that may not be presented in the conference.

The conference, as highlighted by its title, will focus on the beneficial role of microorganisms in the following fields/sessions: Agriculture/Fisheries/Aquaculture, Food/Nutrition, Environment, Bioengineering, Biotechnology/Bioenergy. Advances in molecular mechanisms, model organisms, microbiome studies, “omic” approaches and bioinformatics tools, host-microbe associations and interactions are also included.

Prospective authors are kindly encouraged to contribute to and help shape the conference and this Special Issue through submitting their research papers.

Dr. Hera Karayanni
Dr. Katherine Maria Pappas
Dr. Chrysoula Tassou
Dr. Danae Venieri
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.

Keywords

  • beneficial microorganisms
  • host-microbe (and plant-microbe
  • animal-microbe) interactions
  • aquatic and soil microbial habitats
  • bioenergy
  • bioengineering
  • biotechnology
  • microbiomes
  • omics
  • microbial ecology
  • food microbiota
  • viruses

Published Papers (7 papers)

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Research

36 pages, 10116 KiB  
Article
In Silico Genomic and Metabolic Atlas of Limosilactobacillus reuteri DSM 20016: An Insight into Human Health
by Paisleigh Smythe and Georgios Efthimiou
Microorganisms 2022, 10(7), 1341; https://doi.org/10.3390/microorganisms10071341 - 02 Jul 2022
Cited by 3 | Viewed by 3334
Abstract
Probiotics are bacterial strains that are known to provide host health benefits. Limosilactobacillus reuteri is a well-documented lactic acid bacterium that has been cultured from numerous human sites. The strain investigated was L. reuteri DSM 20016, which has been found to produce useful [...] Read more.
Probiotics are bacterial strains that are known to provide host health benefits. Limosilactobacillus reuteri is a well-documented lactic acid bacterium that has been cultured from numerous human sites. The strain investigated was L. reuteri DSM 20016, which has been found to produce useful metabolites. The strain was explored using genomic and proteomic tools, manual searches, and databases, including KEGG, STRING, BLAST Sequence Similarity Search, and UniProt. This study located over 200 key genes that were involved in human health benefit pathways. L. reuteri DSM 20016 has metabolic pathways to produce acetate, propionate, and lactate, and there is evidence of a pathway for butanoate production through a FASII mechanism. The bacterium produces histamine through the hdc operon, which may be able to suppress proinflammatory TNF, and the bacterium also has the ability to synthesize folate and riboflavin, although whether they are secreted is yet to be explored. The strain can bind to human Caco2 cells through srtA, mapA/cnb, msrB, and fbpA and can compete against enteric bacteria using reuterin, which is an antimicrobial that induces oxidative stress. The atlas could be used for designing metabolic engineering approaches to improve beneficial metabolite biosynthesis and better probiotic-based cures. Full article
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25 pages, 4230 KiB  
Article
Biochemical Evaluation of Agaricus and Pleurotus Strains in Batch Cultures for Production Optimization of Valuable Metabolites
by Dimitrios Argyropoulos, Charoula Psallida, Paraskevi Sitareniou, Emmanouil Flemetakis and Panagiota Diamantopoulou
Microorganisms 2022, 10(5), 964; https://doi.org/10.3390/microorganisms10050964 - 03 May 2022
Cited by 14 | Viewed by 2321
Abstract
The production of various biochemical compounds such as proteins, glucans and glucanases, from the mycelium of four strains of Basidiomycetes species, Agaricus bisporus, Agaricus subrufescens, Pleurotus eryngii and Pleurotus ostreatus, during batch culture in shaking flasks, was studied. Fungi were [...] Read more.
The production of various biochemical compounds such as proteins, glucans and glucanases, from the mycelium of four strains of Basidiomycetes species, Agaricus bisporus, Agaricus subrufescens, Pleurotus eryngii and Pleurotus ostreatus, during batch culture in shaking flasks, was studied. Fungi were cultured for 26 days in defined media with glucose as carbon source and were primarily evaluated for their ability to consume glucose and produce mycelial mass and intracellular polysaccharides (IPS). Results showed that on the 26th day of cultivation, P. ostreatus produced the maximum biomass (16.75 g/L), whereas P. eryngii showed the maximum IPS concentration (3.82 g/L). All strains presented a similar pattern in total protein production, with A. bisporus having the highest percentage of total proteins (36%, w/w). The calculated correlation coefficients among ribonucleic acid (RNA) vs. biomass (0.97) and RNA vs. protein (0.97) indicated a very strong relation between RNA and biomass/protein synthesis. The studied strains exhibited an increase in total glucan and glucanase (β-1,6) production during cultivation, with A. bisporus reaching the highest glucan percentage (8%, w/w) and glucanase activity (12.7 units/g biomass). Subsequently, processed analytical data were used in contour-graph analysis for data extrapolation to optimize future continuous culture. Full article
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16 pages, 1643 KiB  
Article
Continuous Culture of Auxenochlorella protothecoides on Biodiesel Derived Glycerol under Mixotrophic and Heterotrophic Conditions: Growth Parameters and Biochemical Composition
by Evagelina Korozi, Vasiliki Tsagou, Io Kefalogianni, Giorgos Markou, Dimitris Antonopoulos, Lambis Chakalis, Yannis Kotzamanis and Iordanis Chatzipavlidis
Microorganisms 2022, 10(3), 541; https://doi.org/10.3390/microorganisms10030541 - 28 Feb 2022
Cited by 5 | Viewed by 2668
Abstract
As crude glycerol comprises a potential substrate for microalga fermentation and value added products’ biosynthesis, Auxenochlorella protothecoides was grown on it under heterotrophic and mixotrophic conditions and its growth kinetics were evaluated in a continuous system under steady state conditions. Increasing initial glycerol [...] Read more.
As crude glycerol comprises a potential substrate for microalga fermentation and value added products’ biosynthesis, Auxenochlorella protothecoides was grown on it under heterotrophic and mixotrophic conditions and its growth kinetics were evaluated in a continuous system under steady state conditions. Increasing initial glycerol concentration (from 30 to 50 g/L) in the heterotrophic culture led to reduced biomass yield (Yx/S) and productivity (Px), but favored lipid accumulation. Under heterotrophic conditions, the microalga was found to grow better (biomass up to 7.888 g/L) and faster (higher growth rates), the system functioned more effectively (higher Px) and crude glycerol was exploited more efficiently. Heterotrophy also favored proteins synthesis (up to 53%), lipids (up to 9.8%), and carbohydrates (up to 44.6%) accumulation. However, different trophic modes had no significant impact on the consistency of proteins and lipids. Oleic acid was the most abundant fatty acid detected (55–61.2% of the total lipids). The algal biomass contained many essential and non-essential amino acids, especially arginine, glutamic acid, lysine, aspartic acid, leucine, and alanine. In all the experimental trials, the protein contents in the microalgal biomass increased with the increasing dilution rate (D), with a concomitant decrease in the lipids and carbohydrates fractions. Full article
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27 pages, 5094 KiB  
Article
Integrated Genomic and Metabolomic Analysis Illuminates Key Secreted Metabolites Produced by the Novel Endophyte Bacillus halotolerans Cal.l.30 Involved in Diverse Biological Control Activities
by Polina C. Tsalgatidou, Eirini-Evangelia Thomloudi, Eirini Baira, Konstantinos Papadimitriou, Aggeliki Skagia, Anastasia Venieraki and Panagiotis Katinakis
Microorganisms 2022, 10(2), 399; https://doi.org/10.3390/microorganisms10020399 - 09 Feb 2022
Cited by 16 | Viewed by 3405
Abstract
The endophytic strain Cal.l.30, isolated from the medicinal plant Calendula officinalis, was selected among seven Bacillus strains with plant growth promoting activity and strong biological potential against the postharvest fungal pathogen Botrytis cinerea. Treatment by inoculating Cal.l.30 bacterial cell culture or [...] Read more.
The endophytic strain Cal.l.30, isolated from the medicinal plant Calendula officinalis, was selected among seven Bacillus strains with plant growth promoting activity and strong biological potential against the postharvest fungal pathogen Botrytis cinerea. Treatment by inoculating Cal.l.30 bacterial cell culture or cell free supernatant on harvested grapes and cherry tomato fruits, significantly reduced gray mold disease severity index and disease incidence. Based on 16S rRNA sequence analysis and whole genome phylogeny, Cal.l.30 was identified as Bacillus halotolerans. Genome mining revealed that B. halotolerans Cal.l.30 is endowed with a diverse arsenal of secondary metabolite biosynthetic gene clusters (SM-BGCs) responsible for metabolite production with antimicrobial properties. A sub-set of the identified SM-BGCs (mojavensin A, ‘bacillunoic acid’) appears to be the result of recent horizontal gene transfer events. Its genome was also mined for CAZymes associated with antifungal activity. Further UHPLC-HRMS analysis indicated that Cal.l.30 synthesizes and secretes secondary metabolites with antimicrobial activity, including the lipopeptides, fengycin, surfactin and mojavensin A, bacillaene isoforms, L-dihydroanticapsin and bacillibactin. Other compounds with known antimicrobial activity were also detected, such as azelaic acid, 15- hydroxypentadecanoid acid and 2-hydroxyphenylacetic acid. The genomic and metabolomic features of the B. halotolerans Cal.l.30 provided new perspectives on the exploitation of novel Bacillus sp. as a biocontrol agent. Full article
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22 pages, 3514 KiB  
Article
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types
by Haris Zafeiropoulos, Savvas Paragkamian, Stelios Ninidakis, Georgios A. Pavlopoulos, Lars Juhl Jensen and Evangelos Pafilis
Microorganisms 2022, 10(2), 293; https://doi.org/10.3390/microorganisms10020293 - 26 Jan 2022
Cited by 12 | Viewed by 3823
Abstract
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to [...] Read more.
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes. Full article
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32 pages, 7460 KiB  
Article
Genomic and Metabolomic Insights into Secondary Metabolites of the Novel Bacillus halotolerans Hil4, an Endophyte with Promising Antagonistic Activity against Gray Mold and Plant Growth Promoting Potential
by Eirini-Evangelia Thomloudi, Polina C. Tsalgatidou, Eirini Baira, Konstantinos Papadimitriou, Anastasia Venieraki and Panagiotis Katinakis
Microorganisms 2021, 9(12), 2508; https://doi.org/10.3390/microorganisms9122508 - 03 Dec 2021
Cited by 15 | Viewed by 4093
Abstract
The endophytic bacterial strain Hil4 was isolated from leaves of the medicinal plant Hypericum hircinum. It exhibited antifungal activity against Botrytis cinerea and a plethora of plant growth promoting traits in vitro. Whole genome sequencing revealed that it belongs to Bacillus halotolerans [...] Read more.
The endophytic bacterial strain Hil4 was isolated from leaves of the medicinal plant Hypericum hircinum. It exhibited antifungal activity against Botrytis cinerea and a plethora of plant growth promoting traits in vitro. Whole genome sequencing revealed that it belongs to Bacillus halotolerans and possesses numerous secondary metabolite biosynthetic gene clusters and genes involved in plant growth promotion, colonization, and plant defense elicitation. The Mojavensin cluster was present in the genome, making this strain novel among plant-associated B. halotolerans strains. Extracts of secreted agar-diffusible compounds from single culture secretome extracts and dual cultures with B. cinerea were bioactive and had the same antifungal pattern on TLC plates after bioautography. UHPLC-HRMS analysis of the single culture secretome extract putatively annotated the consecutively produced antimicrobial substances and ISR elicitors. The isolate also proved efficient in minimizing the severity of gray mold post-harvest disease on table grape berries, as well as cherry tomatoes. Finally, it positively influenced the growth of Arabidopsis thaliana Col-0 and Solanum lycopersicum var. Chondrokatsari Messinias after seed biopriming in vitro. Overall, these results indicate that the B. halotolerans strain Hil4 is a promising novel plant growth promoting and biocontrol agent, and can be used in future research for the development of biostimulants and/or biological control agents. Full article
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12 pages, 1337 KiB  
Article
Metataxonomic Analysis of Bacteria Entrapped in a Stalactite’s Core and Their Possible Environmental Origins
by George Michail, Lefkothea Karapetsi, Panagiotis Madesis, Angeliki Reizopoulou and Ioannis Vagelas
Microorganisms 2021, 9(12), 2411; https://doi.org/10.3390/microorganisms9122411 - 23 Nov 2021
Cited by 4 | Viewed by 2384
Abstract
Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite [...] Read more.
Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria. Full article
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