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Diversity
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Microbial Diversity and Culture Collections Hotspots in 2024
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Microbial Diversity and Culture Collections Hotspots in 2024

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4160

Special Issue Editor

Dr. Ipek Kurtboke

E-Mail Website
Guest Editor
School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
Interests: microbial ecology and diversity; microbial systematics; biodiscovery; microbial biotechnology applied; environmental and industrial microbiology; marine microbiology; biological control; actinomycetology; bacteriophages
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

First published in 2009, we are now proud to celebrate the 15th anniversary of Diversity. To mark this occasion, a Special Issue dedicated to the field of “Microbial Diversity and Culture Collections Hotspots in 2024” is being prepared.

Environmental threats such as chemical pollution, overexploitation of forests, and urban growth still continue. In addition, with the defrosting of the permafrost, microbial diversity and ecosystems are also changing. Rising sea levels in the Pacific and Oceania are also altering the microbial existence and microorganisms’ functions. In view of the pressures of climate change, questions on how microbial diversity might be affected are timely and persistent. Predictions regarding the loss of microbial diversity are difficult to make, as the evidence and data on the true existence of microorganisms at different niches are patchy. If microorganisms cannot adapt to new environmental conditions, they will be replaced with ones that can. Microorganisms that cannot alter their metabolisms are susceptible to habitat disturbances. The impact of geographical, environmental, geological and climate changes on microflora can only be understood with continuous surveys using modern molecular tools, as well as by culturing the key representatives of microbial diversity and preserving them in culture collections, which play a key role in the preservation of new representatives from these changing ecosystems.

Here, we invite researchers to contribute papers containing microbial diversity including metagenome analysis of different microbial niches, leading to the selective culturing of rare taxa as well as defining their key genes and their long-term preservation in culture collections to fill the gaps in knowledge regarding the true compositions and functional diversity of microorganisms in natural environments.  Experts in the field are invited to submit high-quality papers to this Special Issue. 

Dr. Ipek Kurtboke
Guest Editor

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. Diversity 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 2100 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

  • microbial diversity
  • functional diversity
  • selective isolation
  • culturable and unculturable diversity
  • microbial genetic resources
  • conservation
  • preservation
  • culture collections
  • biological resource centres
  • unexplored microbial diversity
  • metagenomics
  • bioinformatics

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Published Papers (4 papers)

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Research

12 pages, 1670 KiB  
Article
Fishing for Estuarine Oomycetes
by Petya Koeva Christova
Diversity 2024, 16(9), 530; https://doi.org/10.3390/d16090530 - 1 Sep 2024
Viewed by 625
Abstract
Oomycetes are water molds that are frequently isolated during a survey of waterways. Biodiversity of oomycetes in the estuary region of the Veleka River in Bulgaria was investigated in 2021. A total number of 32 isolates were derived using the baiting method. Species [...] Read more.
Oomycetes are water molds that are frequently isolated during a survey of waterways. Biodiversity of oomycetes in the estuary region of the Veleka River in Bulgaria was investigated in 2021. A total number of 32 isolates were derived using the baiting method. Species identification based on sequencing of the ITS region divided them into four different genera: Phytophthora (P.), Phytopythium (Pp.), Pythium (Py.) and Elongisporangium (E.). The most abundant species in the studied region was P. lacustris (sixteen isolates), followed by P. honggalleglyana (nine isolates). P. bilorbang and P. inundata were represented by only one isolate each and were recognized for the first time in Bulgaria. The genus Phytopythium was presented by two isolates that belong to different species, Pp. litorale and Pp. citrinum. In the obtained collection, the genera Pythium and Elongisporangium were represented by only one species each, Py. angustatum (one isolate) and E. anandrum (two isolates), respectively. Colony morphology of the eight collected oomycete species was characterized by cultivation of selected isolates on three different media. Potential host species of the isolated estuarine oomycetes were estimated by pathogenicity tests conducted with sixteen plants from ten diverse families. P. lacustris and P. honggalleglyana demonstrated a higher aggressiveness among Phytophthora isolates, whereas P. bilorbang and P. inundata showed less ability to infect the tested plant species. Similar pathogenicity and a potential host range for both Phytopythium species were observed. Less aggressive against analyzed plants in this study were Py. angustatum and E. anandrum. Full article
(This article belongs to the Special Issue Microbial Diversity and Culture Collections Hotspots in 2024)
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15 pages, 5311 KiB  
Article
Diversity of Endophytic Fungi and Bacteria Inhabiting the Roots of the Woodland Grass, Festuca gigantea (Poaceae)
by Izolda Pašakinskienė, Violeta Stakelienė, Saulė Matijošiūtė and Justas Martūnas
Diversity 2024, 16(8), 453; https://doi.org/10.3390/d16080453 - 1 Aug 2024
Viewed by 798
Abstract
We studied the occurrence of endophytic fungi and bacteria in the roots of F. gigantea, a woodland perennial grass common throughout Europe and temperate Asia. The taxonomic assignment was carried out according to the isolate’s colony and cytological species morphotype characteristics and [...] Read more.
We studied the occurrence of endophytic fungi and bacteria in the roots of F. gigantea, a woodland perennial grass common throughout Europe and temperate Asia. The taxonomic assignment was carried out according to the isolate’s colony and cytological species morphotype characteristics and confirmed by the assessment of the standard DNA sequences, ITS, RPB2, SSU, and TEF1-a for fungi and 16S rDNA for bacteria. Our study has shown that F. gigantea roots are the habitat to a wide range of fungi and bacteria. The occurrence of fungal structures was determined in ~40% of the roots examined by Trypan Blue staining. In a surface-sterile root-cutting culture on PDA medium, we obtained isolates of six endophytic fungi species: four members of Ascomycota—Alternaria alternata, Cadophora fastigiata, Chaetomium funicola, and Microdochium bolleyi—and two of Basidiomycota—Coprinellus sp. and Sistotrema brinkmannii. In addition, we report bacteria co-occurring endophytically in the roots of this grass. The Firmicutes group was the most prevalent, consisting of four Gram-positive, endospore-forming bacteria taxa. The isolates were identified as Bacillus pumilus, Bacillus sp., Lysinibacillus sp., and Priestia aryabhattai. Moreover, two Gram-negative bacteria were detected—Kosakonia sp. (Proteobacteria) and Pedobacter sp. (Bacteroidetes). Thus, applying the isolate-culture approach, we identified a set of microorganisms in the roots of a typical grass native to the deciduous forest floor. The functional roles of these endophytes are diverse, and many of them, saprotrophs and decomposers of wood and plant debris, are linked to the decomposition of organic matter. This is the first detailed report on fungal and bacterial endophytes inhabiting the roots of F. gigantea. This study fills in a research gap on endophytes associated with the below-ground parts of Festuca spp., hitherto extensively studied for Epichloë/Neotyphodium associations in their foliar parts. Full article
(This article belongs to the Special Issue Microbial Diversity and Culture Collections Hotspots in 2024)
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11 pages, 719 KiB  
Article
Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil
by Nhan Le Thi Tuyet and Jaisoo Kim
Diversity 2024, 16(5), 292; https://doi.org/10.3390/d16050292 - 11 May 2024
Viewed by 996
Abstract
Two rod-shaped, non-spore-forming, Gram-negative bacteria, strain KR3-3T isolated from fresh soil in Korea and strain VNH31T obtained from soil samples from motorbike repair workshop floors in Vietnam, were identified. Phylogenetic analysis utilizing 16S rRNA gene sequences revealed their affiliation with the [...] Read more.
Two rod-shaped, non-spore-forming, Gram-negative bacteria, strain KR3-3T isolated from fresh soil in Korea and strain VNH31T obtained from soil samples from motorbike repair workshop floors in Vietnam, were identified. Phylogenetic analysis utilizing 16S rRNA gene sequences revealed their affiliation with the family Sphingobacteriaceae and their relation to the genus Pedobacter, exhibiting 16S rRNA gene sequence similarities lower than 98.00% with all known species within the genus Pedobacter. Growth of VNH31T and KR3-3T was impeded by NaCl concentrations exceeding >0.5% and 1.5%, respectively, while they both thrived optimally at temperatures ranging between 25 and 30 °C. Notably, neither strain reduced nitrate to nitrite nor produced indole. Negative results were observed for the acidification of D-glucose and hydrolysis of urea, gelatin, casein, and starch. VNH31T exhibited growth on β-galactosidase, sodium acetate, L-serine, and L-proline, whereas KR 3-3T demonstrated growth on D-glucose, D-mannose, D-maltose, N-acetyl-glucosamine, sucrose, sodium acetate, L-serine, 4-Hydroxybenzoic acid, and L-proline. Core genome-based phylogenetic analysis revealed that the two isolates formed distinct clusters within the genus Pedobacter. The DNA G+C contents of KR3-3T and VNH31T were determined to be 44.12 mol% and 32.96 mol%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values (67.19–74.19% and 17.6–23.6%, respectively) between the Pedobacter isolates and the closely related type strains fell below the threshold values utilized for species delineation. Following comprehensive genomic, chemotaxonomic, phenotypic, and phylogenetic analyses, the isolated strains are proposed as two novel species within the genus Pedobacter, named Pedobacter albus sp. nov. (type strain KR3-3T = KACC 23486T = NBRC 116682T) and Pedobacter flavus sp. nov. (type strain VNH31T = KACC 23297T = CCTCC AB 2023109T). Full article
(This article belongs to the Special Issue Microbial Diversity and Culture Collections Hotspots in 2024)
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12 pages, 1237 KiB  
Article
Roseateles agri sp. nov., a New Species Isolated from Fresh Soil in Uiwang, South Korea
by Yelim You and Jaisoo Kim
Diversity 2024, 16(5), 279; https://doi.org/10.3390/d16050279 - 7 May 2024
Viewed by 1173
Abstract
Two isolates of Roseateles were discovered in soil samples collected from Uiwang-si, Gyeonggi-do, Republic of Korea. These isolates exhibited rod-shaped morphology and were facultatively anaerobic, non-motile, and tested positive for oxidase and catalase. Designated as strains R3-3T and R3-11, their growth was [...] Read more.
Two isolates of Roseateles were discovered in soil samples collected from Uiwang-si, Gyeonggi-do, Republic of Korea. These isolates exhibited rod-shaped morphology and were facultatively anaerobic, non-motile, and tested positive for oxidase and catalase. Designated as strains R3-3T and R3-11, their growth was hindered by NaCl concentrations exceeding 0.5%, while their optimal growth conditions were observed at temperatures ranging from 25 °C to 30 °C and pH levels between 7.0 and 9.0. Both strains exhibited positive results for the hydrolysis of Tween 80 and DNA, but tested negative for starch, casein, chitin, and gelatin hydrolysis. Additionally, they assimilated L-Arabinose, D-mannitol, and D-Maltose, while exhibiting negative results for the fermentation of D-glucose, esculin ferric citrate, D-mannose, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. The DNA G+C content of strain R3-3T was measured at 67.5 mol%. Comparative analysis revealed that the average nucleotide identity (ANI) values between R3-3T and the Roseateles type strains ranged from 75.14% to 78.30% while the digital DNA-DNA hybridization (dDDH) values ranged from 20.70% to 22.70%. Consequently, based on comprehensive genomic, chemotaxonomic, phenotypic, and phylogenomic evaluations, the isolated strains have been designated as a new species within the genus Roseateles, named Roseateles agri sp. nov. (with type strain R3-3T = KACC 23678T = NBRC 116681T). Full article
(This article belongs to the Special Issue Microbial Diversity and Culture Collections Hotspots in 2024)
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