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Special Issue "Feature Papers in Microbial Diversity and Culture Collections"

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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: 31 December 2023 | Viewed by 4889

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Dr. Ipek Kurtboke

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School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, 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

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 2000 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
microbial genetic resources
conservation
preservation
culture collections
unexplored microbial diversity
metagenomics
bioinformatics

Published Papers (6 papers)

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Research

Open AccessArticle

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

Nhan Le Thi Tuyet

and

Jaisoo Kim

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

Viewed by 323

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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Open AccessArticle

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

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

Viewed by 302

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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Open AccessArticle

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

and

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

Viewed by 524

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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Open AccessArticle

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

Konstantin S. Boyarshin

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

Viewed by 673

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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Open AccessArticle

Life Science—Microbial Culture Collections Data Integration Tasks

and

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

Viewed by 808

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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Open AccessArticle

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

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 - 07 Oct 2022

Cited by 2 | Viewed by 1550

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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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Microbiological Collections in Brazil: current status and perspectives
Authors: Aline Souto, Chirlei Glienke, Manuela da Silva et al.
Affiliation: /
Abstract: Microbiological collections play a fundamental role in the ex-situ conservation of biodiversity, aiming to support preservation, research, epidemiological studies, and the development of bioproducts. An assessment of Brazilian microbiological collections was conducted to obtain data on the current state of these collections to propose and motivate policies of financial support and prioritization. A questionnaire was developed by researchers from different Brazilian institutions with experience in microbiological culture collections. The tool addressed issues related to identification, characterization, personnel and physical infrastructures, accessibility, digitization, collection quality and management. This questionnaire was sent to public and private institutions in Brazil and was answered by 164 microbiological collections from 78 different institutions. Among these, 73 comprise public research institutions and universities, demonstrating the importance of the State in the preservation and safeguarding of Brazilian microbial diversity. The main taxonomic groups are bacteria (70.7%) and fungi (51.8%) from different Brazilian ecosystems and biomes, including several type strains. Furthermore, the collections preserve microorganisms with biotechnological potential for application in the environmental protection, public health, industry, and agribusiness. However, despite all these economic and biotechnological potentials, the data analysis showed serious limitations and fragilities, especially in terms of physical infrastructure and human resources, and raises alerts about the risk that Brazilian collections are subjected to.

Title: Identification, antimicrobial and plant growth promoting activities of endophytic fungi associated with traditional medicinal plants in Mongolia
Authors: Enkh-Amgalan Jigjiddorj*, Amarbayasgalan Maidarjav and Bumtsend Byambasuren
Affiliation: Institute of Biology, Mongolian Academy of Sciences, Enkhtaivan avenue 54b, Ulaanbaatar 13330, Mongolia
Abstract: Endophytic fungi colonise the inner tissues of plants and provide direct and indirect benefits to the plant. Although Mongolia is rich in medicinal plants, due to climatic and anthropogenic reasons the resources are being depleted and many species are under the threat of gradual extinction, while the endophytic fungi of Mongolian plants are largely unknown. Understanding the diversity and metabolic potential of endophytic fungi is of great signifcance in terms of the utilization of benefcial fungal strains in plant propagation and the discovery of bioactive compounds. In this study, a total of 36 culturable endophytic fungal strains were isolated from Saussurea involucrata (Kar. et Kir.), Cynomorium songaricum (Rupr.) and Glycyrrhiza uralensis (Fisch. ex DC), medicinal, endangered 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 to 6 genera: Clonostachys, Fusarium, Helminthosporium, Mucor, Neocosmospora, and Penicillium. The antimicrobial activity was assessed by agar-diffusion method, revealing that 20 strains were able to inhibit the growth of at least one of the test organisms. Among them, 2 strains showed inhibitory activity against Escherichia coli, 19 against Bacillus subtilis and Staphylococcus aureus, 12 against Aspergillus niger, respectively. All fungal strains were screened for their ability to solubilize complex phosphorus and zinc minerals and for their production of indole-3-acetic acid (IAA). The two best zinc solubilizing and IAA producing strains were further processed for quantitative estimation of IAA and gibberellic acid production as well as in vitro seed germination. The culture filtrate of the fungal strains significantly enhanced germination of seeds of Sophora alopecuroides L.

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