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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 26310

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Dr. Ipek Kurtboke

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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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Dear Colleagues,

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.

In this section of the journal, we invite researchers to contribute papers containing a microbial diversity including metagenome analysis of different microbial niches, leading to the selective culturing of key functional taxa 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. This information can also aid policymakers, with particular reference to Sustainable Development Goals (SDGs), for a timely milestone delivery of the targeted outcomes.

Dr. Ipek Kurtboke
Guest Editor

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Keywords

microbial diversity
microbial genetic resources
conservation
preservation
culture collections
unexplored microbial diversity
metagenomics
bioinformatics

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Published Papers (11 papers)

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Research

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13 pages, 5083 KiB

Open AccessArticle

Identification, Antimicrobial and Plant Growth Promoting Activities of Endophytic Fungi Associated with Cynomorium songaricum Rupr., a Traditional Medicinal Plant in Mongolia

by Enkh-Amgalan Jigjiddorj, Amarbayasgalan Maidarjav, Bumtsend Byambasuren and Daritsogzol Nyamgerel

Diversity 2024, 16(2), 122; https://doi.org/10.3390/d16020122 - 14 Feb 2024

Cited by 1 | Viewed by 1934

Abstract

Endophytic fungi colonize the inner tissues and provide direct and indirect benefits to plants. Although Mongolia is rich in medicinal plants, due to climatic and anthropogenic reasons, the resources are being depleted, and many species are under threat of gradual extinction, while the endophytic fungi of Mongolian plants are largely unknown. In this study, a total of 24 culturable endophytic fungal strains were isolated from Cynomorium songaricum (Rupr.), a medicinal and vulnerable plant species of Mongolia. Based on the morphological characteristics and the sequences of the rDNA internal transcribed spacer (ITS) region, the isolates were identified into six genera: Fusarium (8), Clonostachys (7), Penicillium (6), Alternaria (1), Aspergillus (1), and Madurella (1). The antimicrobial activity was assessed by the agar-diffusion method, revealing that 15 strains were able to inhibit the growth of at least one of the test organisms. Among them, 1 strain showed inhibitory activity against Escherichia coli, 12 against Bacillus subtilis, 13 against Staphylococcus aureus, and 8 against Aspergillus niger, respectively. The ability to solubilize complex phosphorus and zinc minerals was observed in 3 and 21 strains, respectively, and the production of indole-3-acetic acid (IAA) was detected in nine strains in the presence of tryptophan. Our study provides the first insight into the cultivable endophytic fungal composition of C. songaricum, parasitizing the roots of Nitraria sibirica growing in the Gobi Desert of Mongolia. The resulting fungi, which have antimicrobial and plant growth-promoting properties, were preserved in the national culture collection and can be used to further exploit their biotechnological potential, as well as for the propagation of endangered and vulnerable medicinal plants. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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16 pages, 4958 KiB

Open AccessArticle

Microbiological Collections in Brazil: Current Status and Perspectives

by Chirlei Glienke, Desirrê Alexia Lourenço Petters-Vandresen, Aline da Silva Soares Souto, Luciane Marinoni and Manuela da Silva

Diversity 2024, 16(2), 116; https://doi.org/10.3390/d16020116 - 9 Feb 2024

Cited by 1 | Viewed by 1906

Abstract

As part of a Ministry of Science, Technology, and Innovation initiative, the Brazilian Societies of Botany, Microbiology, Virology, and Zoology conducted a comprehensive evaluation of biological collections in Brazil. This assessment aimed to gather insights into the current state of these collections, with the goal of providing support for future public policies, including financial subsidies and prioritization policies. In this context, we present the findings related to microbiological collections, essential to ex situ biodiversity conservation and crucial in supporting research, development, and innovation. A survey was distributed to public and private institutions across Brazil, yielding responses from 168 microbiological collections representing 79 different entities. Notably, 73 of these collections are affiliated with public research institutions and universities, underscoring the State’s pivotal role in preserving and safeguarding Brazilian microbial diversity. The primary taxonomic groups encompass bacteria (found in 70.24% of collections) and fungi (comprising 52.98% of collections), sourced from diverse Brazilian ecosystems and biomes, including those that contain several type strains. Furthermore, the collections preserve microorganisms harboring biotechnological potential applicable to environmental protection, public health, industry, and agribusiness. Despite these promising economic and biotechnological prospects, our meticulous data analysis has revealed significant limitations and vulnerabilities, especially regarding physical infrastructure and human resources, emphasizing the urgent need for interventions to guarantee their sustainability. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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12 pages, 776 KiB

Open AccessArticle

Acinetobacter thutiue sp. nov. Isolated from Oil-Contaminated Soil in Motorbike Repair Workshops

by Nhan Le Thi Tuyet and Jaisoo Kim

Diversity 2023, 15(12), 1179; https://doi.org/10.3390/d15121179 - 28 Nov 2023

Cited by 1 | Viewed by 1485

Abstract

Two Acinetobacter isolates were found in soil samples from motorbike repair workshop floors in Vietnam. The two Acinetobacter isolates were Gram-stain-negative, coccobacilli-shaped, aerobic, non-motile, non-hemolytic, oxidase-negative, and catalase-positive. They were designated as strains VNH17^T and VNK23. Their growth was inhibited by NaCl concentrations of >3%, and they grew at an optimal temperature of 20–35 °C. Acidification of D-glucose and hydrolysis of gelatin were negative. They grew on β-alanine, ethanol, L-histidine, D-malate, and L-ornithine whereas L-arginine, citrate, L-glutamate, and L-phenylalanine were not utilized. Core genome-based phylogenetic analysis revealed that the two isolated strains formed a lineage within the genus Acinetobacter in the family Moraxellaceae, the closest relative was Acinetobacter pavus (91.70–91.95%), and were grouped within a hemolytic clade with other closely-related relatives. The DNA G+C content of VNH17^T and VNK23 was 42.07% and 41.75%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values (74.41–91.61% and 20.6–45.40%, respectively) between the Acinetobacter isolates and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, and phylogenomic analyses, the isolated strains represent novel species in the genus Acinetobacter, for which the name Acinetobacter thutiue sp. nov. (type strain VNH17^T = KACC 23003^T = CCTCC AB 2023063^T) is proposed. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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13 pages, 3099 KiB

Open AccessArticle

Limobrevibacterium gyesilva gen. nov., sp. nov., Isolated from Forest Soil

by Nhan Le Thi Tuyet and Jaisoo Kim

Diversity 2023, 15(5), 684; https://doi.org/10.3390/d15050684 - 19 May 2023

Viewed by 1527

Abstract

An aerobic, oxidase-positive, catalase-negative, non-motile, oval/rod-shaped, and Gram-negative strain RN2-1^T was isolated from a Korean forest soil sample. Cells grew in a pH range of 6–9 (optimum range: 7–8), in a temperature range of 20–40 °C (optimum range: 30–35 °C), and in the presence of 0–1% (w/v) NaCl. The major polar lipid profile consisted of phosphatidylglycerol, diphosphatidyl glycerol, phosphatidylethanolamine, phosphatidylcholine, and a group of phospholipids, aminolipids, and polar lipids with unidentified structures. The major quinone was ubiquinone 10. The main fatty acids were summed feature 8 (C18:1 ω7c/C18:1 ω6c), C16:0, Cyclo-C17:0, cyclo C19:0 ω8c, and C18:1 2OH. Phylogenetic similarities based on 16S rDNA sequences showed that strain RN2-1^T grouped in the family Acetobacteraceae included the genera Rhodovastum, Acidisoma, Acidisphaera, and Acidibrevibacterium. The aerobic phototrophic bacterium Rhodovastum atsumiense G2-11^T was the closest relative to RN2-1^T (96.04% sequence similarity). Genomic DNA revealed 68.7% G+C content. Whole genome analysis and phenotypic data of the strain RN2-1^T confirmed its distinctive phylogenetic location within the family Acetobacteraceae. Because of these results, strain RN2-1^T represents the novel species of a new genus for which the name Limobrevibacterium gyesilva gen. nov., sp. nov. was proposed. The type of strain was strain RN2-1^T (KACC 23001 = JCM 35944). Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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13 pages, 1691 KiB

Open AccessArticle

Expanding Actinomycetota Diversity in the TBRC Culture Collection through Metabarcoding and Simulated In Situ Cultivation of Thailand’s Mekong River Microbiota

by Supattra Kitikhun, Paopit Siriarchawattana, Suwanee Chunhametha, Chanwit Suriyachadkun, Pattaraporn Rattanawaree, Chitwadee Phithakrotchanakoon, Piyanun Harnpicharnchai, Lily Eurwilaichitr and Supawadee Ingsriswang

Diversity 2023, 15(5), 663; https://doi.org/10.3390/d15050663 - 13 May 2023

Cited by 3 | Viewed by 1978

Abstract

Culture-independent and culture-dependent approaches were employed to investigate the taxonomic diversity and biosynthetic gene cluster potential of Actinomycetota in the Mekong River. Through 16S rRNA gene metabarcoding, 21,103 OTUs were revealed to represent 190 genera and at least 595 species of Actinomycetota, including putatively novel taxa. Conventional and in situ cultivation (IC) methods provided 75 Actinomycetota isolates representing 72 species from 21 genera. Of these, 45 species in 4 genera were new to the Thailand Bioresource Research Center (TBRC), a collection of 20,079 Actinomycetota strains from 660 species. Applying both culture-independent and culture-dependent approaches to the same sample revealed greater diversity among the Actinomycetota in the Mekong River than one approach alone. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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14 pages, 2277 KiB

Open AccessArticle

Application of Wheat Straw Compost Mixed with Chemical Fertilizer Regulates Soil Bacterial Community Diversity in Tea (Camellia sinensis) Plantation

by Haiyan Fu, Dapeng Song, Kunpeng Wang, Fengxiang Fang, Shunying Han, Fengshan Yang and Shibo Ding

Diversity 2023, 15(4), 580; https://doi.org/10.3390/d15040580 - 20 Apr 2023

Cited by 2 | Viewed by 2274

Abstract

Biofertilizers have been suggested as alternatives to synthetic fertilizers, which could reduce soil degradation brought on by excessive chemical fertilization and have an impact on the bacterial diversity and community in the soil. The diversity and community of soil bacteria in tea plantations treated with wheat straw compost have, however, received relatively little attention. In this research, a two-year field trial was run to examine the effects of applying wheat straw compost on the characteristics of the soil and the quality of the tea. We also used high-throughput sequencing to investigate the response of the soil bacterial community, and Spearman’s rank correlation was used to estimate the relationship between the soil bacterial community, soil characteristics, and tea quality. It was noticed that applying chemical fertilizer along with compost increased the fertility of the soil and the quality of the tea. Based on a two-year thorough data analysis, the T4 treatment (compost fertilizers 15,000 kg ha⁻¹ + chemical fertilizers 1050 kg ha⁻¹, chemical fertilizer reduction 30%) was determined to be the best group. The diversity and community makeup of soil bacteria were impacted by fertilization management. After the initial compost replacement, soils with compost had a greater bacterial richness than soils with inorganic fertilizers. After the second compost substitution, PCoA analysis revealed that compost fertilizer could be easily differentiated from chemical fertilizer. In 2019, Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Patescibacteria were the most prevalent bacterial phyla. In 2020, Firmicutes and Chloroflexi overtook Bacteroidetes and Patescibacteria as the two major bacterial phyla. In addition to increasing the diversity of soil bacteria and having an impact on the bacterial population, the application of wheat straw compost mixed with chemical fertilizers can also control the soil’s characteristics and the quality of the tea produced in tea plantations. So, as a fertilization way with less environmental impact, wheat straw compost fertilization can be used in tea plantations. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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12 pages, 1248 KiB

Open AccessArticle

The Effect of Long-Term Agricultural Use on the Bacterial Microbiota of Chernozems of the Forest-Steppe Zone

by Konstantin S. Boyarshin, Valeria V. Adamova, Zheng Wentao, Olga Y. Obuhova, Marina V. Kolkova, Vitaliy A. Nesterenko, Olga S. Bespalova, Violetta V. Kluyeva, Kristina A. Degtyareva, Yulia N. Kurkina, Olesia A. Makanina and Irina V. Batlutskaya

Diversity 2023, 15(2), 191; https://doi.org/10.3390/d15020191 - 30 Jan 2023

Cited by 4 | Viewed by 2025

Abstract

The structure of soil microbial communities and the factors that control it are still poorly understood and cause ongoing interest. The diversity of soil bacteria reflects the diversity of existing ecological niches and trophic connections between them and with other components of the ecosystem. The presence of certain taxa with their own characteristic properties depends on the specific environmental conditions. Analysis of the composition of soil microbiota in various physicochemical conditions allows identify landmarks for understanding the principles by which it is formed. Of particular interest in this regard are the features of cultivated fertile soils that assist agricultural production. In this paper, we have assessed the occurrence of representatives of different families of bacteria in arable and nonarable chernozems of three subtypes. The methodology of 16S microbial profiling was used. The general features of the taxonomic structure of bacterial communities of chernozem remain similar, with a high occurrence of the families Sphingomonadaceae, Xanthobacteraceae, Rubrobacteraceae and Chitinophagaceae. Notably, Gemmatimonadaceae, one of the most commonly occurring families, is approximately twice as represented in arable soils as in nonarable ones. Differences between subtypes of chernozem and between arable and nonarable areas concerned different sets of bacterial families. Among others, the occurrence of representatives of families characterized by nitrogen fixation, nitrite oxidation and reduction, ethanol oxidation, biodegradation and microbial predation is touched upon. The obtained results raise the question of the factors limiting the number of certain groups of bacteria in various soil conditions and so limiting their contribution to the properties of the ecosystem. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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15 pages, 1993 KiB

Open AccessArticle

Life Science—Microbial Culture Collections Data Integration Tasks

by Alexander Vasilenko, Galina Kochkina, Natalya Ivanushkina and Svetlana Ozerskaya

Diversity 2023, 15(1), 17; https://doi.org/10.3390/d15010017 - 22 Dec 2022

Viewed by 1639

Abstract

This paper presents interconnections between catalogs of microbial culture collections and biological databases inspected. Microbial Biological Resources Centers (mBRCs) provide Life Science (LS) and biotechnology with fit-for-use microbiological resources and related data of consistent quality. To optimize the services, facilitate cumulative research, make crosschecks, and avoid duplication of efforts, must ensure that the databases developed and maintained are interconnected with mBRC data. This research shows that, at present, connections are minimal. It proposes ways to plug the mBRC databases into the Life Science community. Such connections could open dialogue by making the mBRC data visible and accessible from the Life Science databases, and reciprocally making the Life Science database records visible and accessible from the mBRC-aggregated catalog. For this purpose, we inspected most of the databases discovered on the Internet. Each database was characterized by name, acronym, year of the last correction, uniform resource location (URL), area of practical use (health system, agriculture, etc.), presence of microbial data and database producer. The databases with microbial data were inspected in more detail in terms of the lists of the partner databases, the lists of ontologies used, the access format from computer programs, and database subjects. Our new metabase has collected 2667 Life Science databases, from which 1123 databases have microbial data. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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9 pages, 1423 KiB

Open AccessArticle

Biogeography of Black Mold Aspergillus niger: Global Situation and Future Perspective under Several Climate Change Scenarios Using MaxEnt Modeling

by Dalal Hussien M. Alkhalifah, Eman Damra, Sameh M. H. Khalaf and Wael N. Hozzein

Diversity 2022, 14(10), 845; https://doi.org/10.3390/d14100845 - 7 Oct 2022

Cited by 5 | Viewed by 4476

Abstract

Climate change impacts represent one of the most important ecological and medical issues during this century. Several fungal species will change their distribution through space and time as a response to climate changes. This will rearrange many fungal diseases throughout the world. One of the most important and very common fungi is the black mold Aspergillus niger. The COVID-19 pandemic reforms the way in which mycologists think about this fungus as an emerging healthy issue. Through this work, about one thousand records of Aspergillus niger were used to model its current and future global distribution using 19 bioclimatic variables under several climate change scenarios. Maximum entropy implemented in Maxent was chosen as the modeling tool, especially with its accuracy and reliability over the other modeling techniques. The annual mean temperature (bio 1) forms the most contributed climatological parameter to black mold distribution. The produced current distribution model came compatible with the real distribution of the species with a cosmopolitan range. The rise of temperature due to global warming will form a limitation to Aspergillus niger through several parts of its range. The generated maps of the future status of this fungus under two different RCPs for 2050 and 2070, indicate several parts that become free from black mold due to temperature limitations. The present results need more intensive future evaluation using data science and GIS, especially on a local scale including more ecological parameters other than climatological data. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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Review

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15 pages, 1633 KiB

Open AccessEditor’s ChoiceReview

Selected Case Studies on Fastidious Eukaryotic Microorganisms: Issues and Investigation Strategies

by Benedetta Turchetti, Annamaria Bevivino, Patrizia Casella, Claudia Coleine, Giovanna E. Felis, Carolina Elena Girometta, Antonio Molino, Iolanda Perugini, Antonino Pollio, Valeria Prigione, Laura Selbmann, Giovanna Cristina Varese and Pietro Buzzini

Diversity 2023, 15(7), 862; https://doi.org/10.3390/d15070862 - 16 Jul 2023

Cited by 1 | Viewed by 2798

Abstract

The concept of fastidious microorganisms currently found in scientific literature is mainly related to the difficulty of isolating/culturing/preserving bacteria. Eukaryotes are investigated much less in this respect, although they represent a fundamental part of the microbial world. Furthermore, not only isolation, but also identification and culturing (in the perspective of long-term preservation) should be considered key aspects often impacting on the study of fastidious microorganisms, especially in terms of preservation in culture collections and biotechnological exploitation. The present review aimed to investigate the current state of the art on fastidious eukaryotes, with special emphasis on the efforts to improve their isolation, identification, culturing and long-term preservation in culture collections practices. A few case studies focused on some fastidious eukaryotic microorganisms (including possible customized solutions to overcome specific issues) are also presented: isolation and preservation of slow-growing fungi, culturing of Haematococcus lacustris, isolation of unialgal strains of Cyanidiophytina (Rhodophyta), identification of Metschnikowia pulcherrima clade yeasts, isolation and preservation of Pyricularia species, preservation of Halophytophtora spp. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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10 pages, 867 KiB

Open AccessOpinion

The Future of Access and Benefit-Sharing: What Next after the Adoption of the Global Biodiversity Framework and Decision on Digital Sequence Information?

by Amber Hartman Scholz, Genuar Nunez-Vega, Lily Weissgold and Konstantin Wussmann

Diversity 2024, 16(1), 27; https://doi.org/10.3390/d16010027 - 31 Dec 2023

Viewed by 2764

Abstract

Recent decisions at the Convention on Biological Diversity's (CBD) 15th Conference of the Parties (COP15) on access and benefit-sharing (ABS) fundamentally shift how ABS will work in the future. The key ABS challenges that now lie ahead will be to integrate digital sequence information into a functioning benefit-sharing mechanism compatible with the Nagoya Protocol, to address the difficult task of measuring benefit-sharing now required by the Global Biodiversity Framework, and ultimately to address the long-term challenges of the Nagoya Protocol’s bilateral ABS approach. The relevant COP15 decisions do not provide simple and quick answers to these challenges. However, they do lay the groundwork for change and could form the basis for the further development of effective access and benefit-sharing. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Diversity and Culture Collections)

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