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Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia...
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Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia and Clamydia (PVC) Superphylum

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

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 17055

Special Issue Editors

Prof. Dr. Lise Øvreås

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Guest Editor
Department of Biological Sciences, University of Bergen, Bergen, Norway
Interests: microbial diversity; evolution; ecology. phylogeny; marine microbiology
Dr. Olga Maria Lage

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Guest Editor
1. Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
2. CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de 3 Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
Interests: bacteria; Planctomycetota; antibiotic resistance; novel small molecules; new taxa; One Health
Special Issues, Collections and Topics in MDPI journals
Dr. Damien P. Devos

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Guest Editor
Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de OlavideUniversity, Seville, Spain
Interests: bioinformatics; evolution; eukaryogenesis; microbiology

Special Issue Information

Dear Colleagues,

The PVC superphylum is one of the most unknown and enigmatic clusters of microorganisms and consists of the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, which are comprised of unusual characteristics and traits. There has recently been increasing and exciting interest in the cell biology, physiology, and ecology of members of this superphylum, including evolutionary implications of the complex cell organization of some species. The PVC cluster of microorganisms contains several biotechnologically and medically important members, but are still highly underrepresented in culture collections and in databases. Members within this superphylum play an important role in global carbon and nitrogen cycles; they are of biotechnological relevance for waste water treatment and suspected to produce important bioactive small molecules. These bacteria remain an infinite source of exciting discoveries. Cultivation-independent studies have revealed the existence of diverse groups of PVC bacteria that have not yet been cultured and represent a challenge for further cultivation studies as well as for cultivation-independent omics approaches. We welcome all kinds of studies covering various aspects of ecology, diversity, and functions of planctomycetes, verrucomicrobia, and chlamydia bacteria. Potential topics include but are not limited to the following: novel PVC bacteria; genome-based systematics of and metabolic traits of members of the PVC superphylum.

Prof. Dr. Lise Øvreås
Prof. Dr. Olga Maria Lage
Dr. Damien P. Devos
Guest Editors

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Published Papers (4 papers)

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Research

18 pages, 3390 KiB  
Article
Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments
by Inês Rosado Vitorino, Dominika Klimek, Magdalena Calusinska, Alexandre Lobo-da-Cunha, Vítor Vasconcelos and Olga Maria Lage
Microorganisms 2022, 10(11), 2151; https://doi.org/10.3390/microorganisms10112151 - 30 Oct 2022
Cited by 6 | Viewed by 2458
Abstract
The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleria isolate designated as strain ICT_E10.1T, obtained from [...] Read more.
The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleria isolate designated as strain ICT_E10.1T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 x 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1T into the genus Stieleria with Stieleria neptunia Enr13T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1T as the type of strain (=CECT 30514T= DSM 113784T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia and Clamydia (PVC) Superphylum)
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23 pages, 1479 KiB  
Article
iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments
by José Diogo Neves dos Santos, Susana Afonso João, Jesús Martín, Francisca Vicente, Fernando Reyes and Olga Maria Lage
Microorganisms 2022, 10(7), 1471; https://doi.org/10.3390/microorganisms10071471 - 20 Jul 2022
Cited by 10 | Viewed by 4018
Abstract
Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from [...] Read more.
Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an “one strain many compounds” approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia and Clamydia (PVC) Superphylum)
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16 pages, 1016 KiB  
Article
Novel and Conventional Isolation Techniques to Obtain Planctomycetes from Marine Environments
by Inês Vitorino, José Diogo Neves Santos, Ofélia Godinho, Francisca Vicente, Vítor Vasconcelos and Olga Maria Lage
Microorganisms 2021, 9(10), 2078; https://doi.org/10.3390/microorganisms9102078 - 1 Oct 2021
Cited by 15 | Viewed by 3765
Abstract
Bacteria from the distinctive Planctomycetes phylum are well spread around the globe; they are capable of colonizing many habitats, including marine, freshwater, terrestrial, and even extreme habitats such as hydrothermal vents and hot springs. They can also be found living in association with [...] Read more.
Bacteria from the distinctive Planctomycetes phylum are well spread around the globe; they are capable of colonizing many habitats, including marine, freshwater, terrestrial, and even extreme habitats such as hydrothermal vents and hot springs. They can also be found living in association with other organisms, such as macroalgae, plants, and invertebrates. While ubiquitous, only a small fraction of the known diversity includes axenic cultures. In this study, we aimed to apply conventional techniques to isolate, in diverse culture media, planctomycetes from two beaches of the Portuguese north-coast by using sediments, red, green, and brown macroalgae, the shell of the mussel Mytilus edulis, an anemone belonging to the species Actinia equina, and seawater as sources. With this approach, thirty-seven isolates closely related to seven species from the families Planctomycetaceae and Pirellulaceae (class Planctomycetia) were brought into pure culture. Moreover, we applied an iChip inspired in-situ culturing technique to successfully retrieve planctomycetes from marine sediments, which resulted in the isolation of three additional strains, two affiliated to the species Novipirellula caenicola and one to a putative novel Rubinisphaera. This work enlarges the number of isolated planctomycetal strains and shows the adequacy of a novel methodology for planctomycetes isolation. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia and Clamydia (PVC) Superphylum)
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33 pages, 4948 KiB  
Article
Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov.
by Sandra Wiegand, Patrick Rast, Nicolai Kallscheuer, Mareike Jogler, Anja Heuer, Christian Boedeker, Olga Jeske, Timo Kohn, John Vollmers, Anne-Kristin Kaster, Christian Quast, Frank Oliver Glöckner, Manfred Rohde and Christian Jogler
Microorganisms 2021, 9(7), 1494; https://doi.org/10.3390/microorganisms9071494 - 13 Jul 2021
Cited by 17 | Viewed by 5289
Abstract
Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., [...] Read more.
Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Members of the Planctomycetes, Verrucomicrobia and Clamydia (PVC) Superphylum)
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