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 934

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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
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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

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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

Published Papers (2 papers)

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Research

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 347
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
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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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