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Microorganisms
Special Issues
Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications
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Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 23338

Special Issue Editors

Prof. Pedro M. Santos

E-Mail Website
Guest Editor
CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Interests: microbial genomics; environmental microbiology; microbial adaptation and evolution; microbial biotechnology
Dr. Pedro Castro

E-Mail Website
Guest Editor
CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Interests: microbial functional genomics; microbial synthetic biology; pseudomonas biotechnology; microbial valorization of plant-based feedstocks
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms thrive as part of complex microcosms in almost every abiotic and biotic niche. Microbial communities drive fundamental processes in ecosystems and are clearly the first responders to any environmental change.

Advances in high throughput technologies have enabled the evaluation of the community ecology, composition, and function without full dependence on laboratory-based culturing, as well as the characterization of microbial responses to the changing environment in situ, in laboratory enrichments with reduced complexity, in pure cultures or even as single cells.

Significantly, the characterization of the genomic repertoire of microbial communities is paving the way to the development of novel biotechnological applications in different fields, including bioremediation, biocatalysis, biomedicine, and biomonitoring.

The aim of this Special Issue is to provide an adequate multidisciplinary platform for the interchange of valuable information, both basic and applied research, devoted to the sustainability of ecosystems and the biotechnological application of microbial communities. As a Guest Editor of the Special Issue, I invite you to submit research articles, review articles, and short communications related to the following topics:

  • Characterization of microbial communities via high-throughput approaches (metagenomics, metabarcoding, metatranscriptomics, metaproteomics, among others)
  • Ecosystem biomonitoring through microbial diversity and functionality
  • Biotechnological applications of microbial communities and microbial products
  • Engineered microbial consortia and synthetic microbial networks
  • Response of microbial communities to environmental changes

Prof. Pedro M. Santos
Dr. Pedro Castro
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

  • Microbiome
  • DNA metabarcoding
  • Shotgun metagenomics
  • Metatranscriptomics Metaproteomics
  • Community metabolomics
  • Microbial functional genomics
  • Synthetic microbial communities

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Published Papers (6 papers)

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Research

14 pages, 990 KiB  
Article
Cork Oak Forests Soil Bacteria: Potential for Sustainable Agroforest Production
by Francisca Reis, Ana João Pereira, Rui M. Tavares, Paula Baptista and Teresa Lino-Neto
Microorganisms 2021, 9(9), 1973; https://doi.org/10.3390/microorganisms9091973 - 16 Sep 2021
Cited by 6 | Viewed by 2608
Abstract
Plant growth promoting rhizobacteria (PGPR) are in increasing demand due to their role in promoting sustainable practices, not only in agriculture but also in forestry. Keeping in mind the future application of PGPR for increasing cork oak sustainability, the aim of this study [...] Read more.
Plant growth promoting rhizobacteria (PGPR) are in increasing demand due to their role in promoting sustainable practices, not only in agriculture but also in forestry. Keeping in mind the future application of PGPR for increasing cork oak sustainability, the aim of this study was to find cork oak PGPR isolates with increased nutrient solubilisation traits, able to promote root morphological changes and/or antagonize cork oak bark phytopathogens. Soils from three cork oak forests with distinct bioclimates (humid, semi-humid and semi-arid) were used for isolating bacteria. From the 7634 colony-forming units, 323 bacterial isolates were biochemically assayed for PGPR traits (siderophores production, phosphate solubilizing and organic acids production), and 51 were found to display all these traits. These PGPR were able to induce root morphological changes on Arabidopsis thaliana, like suppression of primary root growth, increase of lateral roots or root hairs formation. However, the most proficient PGPR displayed specific ability in changing a single root morphological trait. This ability was related not only to bacterial genotype, but also with the environment where bacteria thrived and isolation temperature. Bacteria from semi-arid environments (mainly Bacillus megaterium isolates) could hold a promising tool to enhance plant development. Other isolates (Serratia quinivorens or B. cereus) could be further explored for biocontrol purposes. Full article
(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)
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12 pages, 2692 KiB  
Article
First Insight into the Diversity and Antibacterial Potential of Psychrophilic and Psychotrophic Microbial Communities of Abandoned Amber Quarry
by Margarita Shevchenko, Stanislav Sukhikh, Olga Babich, Svetlana Noskova, Svetlana Ivanova, Valery Lisun, Viktoriya Skripskaya, Andrey Lomtev and Maria Zimina
Microorganisms 2021, 9(7), 1521; https://doi.org/10.3390/microorganisms9071521 - 16 Jul 2021
Cited by 4 | Viewed by 2451
Abstract
Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial [...] Read more.
Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial communities of the flooded Walter amber quarry (Kaliningrad region, Russia). As a result of 16S rDNA high-throughput profiling, 127 genera of bacteria belonging to 12 phyla of bacteria were found in sediment samples: Acidobacteria sp., Actinobacteria sp., Armatimonadetes sp., Bacteroidetes sp., Chloroflexi sp., Cyanobacteria sp., Firmicutes sp., Gemmatimonadetes sp., Planctomycetes sp., Proteobacteria sp., Tenericutes sp., and Verrucomicrobia sp. The dominant bacteria groups were the families Ruminococcaceae and Lachnospiraceae, belonging to the order Clostridiales phylum Firmicutes. Analysis of enrichment cultures obtained from sediments showed the presence of antibacterial and cellulolytic activity. It seems likely that the bacteria of the studied communities are producers of antimicrobial compounds and have the potential for biotechnological use. Full article
(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)
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15 pages, 1940 KiB  
Article
Multiple Potential Plant Growth Promotion Activities of Endemic Streptomyces spp. from Moroccan Sugar Beet Fields with Their Inhibitory Activities against Fusarium spp.
by Yassine Aallam, Bouchra El Maliki, Driss Dhiba, Sanaa Lemriss, Amal Souiri, Abdelmajid Haddioui, Mika Tarkka and Hanane Hamdali
Microorganisms 2021, 9(7), 1429; https://doi.org/10.3390/microorganisms9071429 - 2 Jul 2021
Cited by 28 | Viewed by 3769
Abstract
The characterized 10 Streptomyces isolates were previously selected by their abilities to solubilize phosphates. To investigate whether these isolates represent multifaceted plant growth-promoting rhizobacteria (PGPR), their potassium-solubilizing, auxin-producing and inhibitory activities were determined. The 10 Streptomyces spp. yielded a variable biomass in the [...] Read more.
The characterized 10 Streptomyces isolates were previously selected by their abilities to solubilize phosphates. To investigate whether these isolates represent multifaceted plant growth-promoting rhizobacteria (PGPR), their potassium-solubilizing, auxin-producing and inhibitory activities were determined. The 10 Streptomyces spp. yielded a variable biomass in the presence of insoluble orthoclase as the sole potassium (K) source, indicating that they were able to extract different amounts of K from this source for their own growth. Three strains (AZ, AYD and DE2) released soluble K from insoluble orthoclase in large amounts into the culture broth. The production levels ranged from 125.4 mg/L to 216.6 mg/L after 5 days of culture. Only two strains, Streptomyces enissocaesilis (BYC) and S. tunisiensis (AI), released a larger amount of soluble K from orthoclase and yielded much more biomass. This indicated that the rate of K released from this insoluble orthoclase exceeded its consumption rate for bacterial growth and that some strains solubilized K more efficiently than others. The results also suggest that the K solubilization process of AZ, AYD and DE2 strains, the most efficient K-solubilizing strains, involves a slight acidification of the medium. Furthermore, these 10 Streptomyces spp. were able to secrete indole acetic acid (IAA) in broth medium and ranged from 7.9 ± 0.1 µg/mL to 122.3 ± 0.1 µg/mL. The results of the antibiosis test proved the potential of the 10 tested strains to limit the growth of fungi and bacteria. In dual culture, S. bellus (AYD) had highest inhibitory effect against the three identified fungal causal agents of root rot of sugar beet: Fusarium equiseti and two F. fujikuroi at 55, 43 and 36%, respectively. Streptomyces enissocaesilis (BYC), S. bellus (AYD) and S. saprophyticus (DE2) exhibited higher multifaceted PGPR with their potassium-solubilizing, auxin-producing and inhibitory activities, which could be expected to lead to effectiveness in field trials of sugar beet. Full article
(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)
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21 pages, 5055 KiB  
Article
Microbial Communities of Cladonia Lichens and Their Biosynthetic Gene Clusters Potentially Encoding Natural Products
by Tânia Keiko Shishido, Matti Wahlsten, Pia Laine, Jouko Rikkinen, Taina Lundell and Petri Auvinen
Microorganisms 2021, 9(7), 1347; https://doi.org/10.3390/microorganisms9071347 - 22 Jun 2021
Cited by 11 | Viewed by 4450
Abstract
Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit [...] Read more.
Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies. Full article
(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)
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15 pages, 2830 KiB  
Article
Isolation and Characterization of Phosphate Solubilizing Streptomyces sp. Endemic from Sugar Beet Fields of the Beni-Mellal Region in Morocco
by Yassine Aallam, Driss Dhiba, Sanaâ Lemriss, Amal Souiri, Fatma Karray, Taoufik El Rasafi, Nezha Saïdi, Abdelmajid Haddioui, Saâd El Kabbaj, Marie Joëlle Virolle and Hanane Hamdali
Microorganisms 2021, 9(5), 914; https://doi.org/10.3390/microorganisms9050914 - 24 Apr 2021
Cited by 21 | Viewed by 3786
Abstract
In the course of our research, aimed at improving sugar beets phosphorus nutrition, we isolated and characterized Streptomyces sp. strains, endemic from sugar beet fields of the Beni-Mellal region, which are able to use natural rock phosphate (RP) and tricalcium phosphate (TCP) as [...] Read more.
In the course of our research, aimed at improving sugar beets phosphorus nutrition, we isolated and characterized Streptomyces sp. strains, endemic from sugar beet fields of the Beni-Mellal region, which are able to use natural rock phosphate (RP) and tricalcium phosphate (TCP) as sole phosphate sources. Ten Streptomyces sp. isolates yielded a comparable biomass in the presence of these two insoluble phosphate sources, indicating that they were able to extract similar amount of phosphorus (P) from the latter for their own growth. Interestingly, five strains released soluble P in large excess from TCP in their culture broth whereas only two strains, BP, related to Streptomyces bellus and BYC, related to Streptomyces enissocaesilis, released a higher or similar amount of soluble P from RP than from TCP, respectively. This indicated that the rate of P released from these insoluble phosphate sources exceeded its consumption rate for bacterial growth and that most strains solubilized TCP more efficiently than RP. Preliminary results suggested that the solubilization process of BYC, the most efficient RP and TCP solubilizing strain, involves both acidification of the medium and excretion of siderophores. Actinomycete strains possessing such interesting RP solubilizing abilities may constitute a novel kind of fertilizers beneficial for plant nutrition and more environmentally friendly than chemical fertilizers in current use. Full article
(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)
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27 pages, 11834 KiB  
Article
Microenvironmental Conditions Drive the Differential Cyanobacterial Community Composition of Biocrusts from the Sahara Desert
by Smail Mehda, Maria Ángeles Muñoz-Martín, Mabrouka Oustani, Baelhadj Hamdi-Aïssa, Elvira Perona and Pilar Mateo
Microorganisms 2021, 9(3), 487; https://doi.org/10.3390/microorganisms9030487 - 25 Feb 2021
Cited by 26 | Viewed by 4705
Abstract
The Sahara Desert is characterized by extreme environmental conditions, which are a unique challenge for life. Cyanobacteria are key players in the colonization of bare soils and form assemblages with other microorganisms in the top millimetres, establishing biological soil crusts (biocrusts) that cover [...] Read more.
The Sahara Desert is characterized by extreme environmental conditions, which are a unique challenge for life. Cyanobacteria are key players in the colonization of bare soils and form assemblages with other microorganisms in the top millimetres, establishing biological soil crusts (biocrusts) that cover most soil surfaces in deserts, which have important roles in the functioning of drylands. However, knowledge of biocrusts from these extreme environments is limited. Therefore, to study cyanobacterial community composition in biocrusts from the Sahara Desert, we utilized a combination of methodologies in which taxonomic assignation, for next-generation sequencing of soil samples, was based on phylogenetic analysis (16S rRNA gene) in parallel with morphological identification of cyanobacteria in natural samples and isolates from certain locations. Two close locations that differed in microenvironmental conditions were analysed. One was a dry salt lake (a “chott”), and the other was an extension of sandy, slightly saline soil. Differences in cyanobacterial composition between the sites were found, with a clear dominance of Microcoleus spp. in the less saline site, while the chott presented a high abundance of heterocystous cyanobacteria as well as the filamentous non-heterocystous Pseudophormidium sp. and the unicellular cf. Acaryochloris. The cyanobacteria found in our study area, such as Microcoleus steenstrupii, Microcoleus vaginatus, Scytonema hyalinum, Tolypothrix distorta, and Calothrix sp., are also widely distributed in other geographic locations around the world, where the conditions are less severe. Our results, therefore, indicated that some cyanobacteria can cope with polyextreme conditions, as confirmed by bioassays, and can be considered extremotolerant, being able to live in a wide range of conditions. Full article
(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)
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