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Molecular Studies of Microbial Communities

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 December 2024 | Viewed by 2667

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Guest Editor
Department of Botany and Plant Pathology, Purdue University, 500 Oval Dr, West Lafayette, IN 47909, USA
Interests: ecology; fungal physiology; environmental sequencing; nanoparticle synthesis; ecotoxicology; chronic wasting disease
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Special Issue Information

Dear Colleagues,

Species within the kingdoms Archaea, Bacteria, and Fungi are ubiquitous in nature. They fulfil key environmental functions related to nutrient cycling, have beneficial to pathogenic associations with other macroscopic organisms, and thrive in habitats devoid of macroscopic life, such as hot acidic springs. Unfortunately, most microorganisms are unculturable using current laboratory techniques, a fact that has slowed the pace of research. However, due to the advancements in molecular sequencing and big data processing, it is now possible to investigate the unculturable microbial communities and their relationships to other organisms using environmental sequencing techniques. Using these methods, researchers can identify shifts in community structure, species composition, and investigate species distributional patterns among others. Therefore, this Special Issue focuses on using molecular techniques, including environmental sequencing, to uncover the microbial diversity associated with animals, insects, plants, and other environmental habitats. Manuscripts that focus on archaeal, bacterial, and fungal communities are welcome. This Special Issue strives to be a valuable collection of research articles that will assist future researchers, meaning that special emphasis will be placed on comprehensive and novel methods.

Dr. Daniel Raudabaugh
Guest Editor

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Keywords

  • environmental sequencing
  • Archaea
  • Fungi
  • microbiome
  • mycobiome
  • Bacteria
 
 

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Published Papers (2 papers)

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Research

22 pages, 1376 KiB  
Article
Polar-Region Soils as Novel Reservoir of Lactic Acid Bacteria from the Genus Carnobacterium
by Katarzyna Kosiorek, Jakub Grzesiak, Jan Gawor, Agnieszka Sałańska and Tamara Aleksandrzak-Piekarczyk
Int. J. Mol. Sci. 2024, 25(17), 9444; https://doi.org/10.3390/ijms25179444 - 30 Aug 2024
Viewed by 739
Abstract
Polar habitats offer excellent sites to isolate unique bacterial strains due to their diverse physical, geochemical, and biological factors. We hypothesize that the unique environmental conditions of polar regions select for distinct strains of lactic acid bacteria (LAB) with novel biochemical properties. In [...] Read more.
Polar habitats offer excellent sites to isolate unique bacterial strains due to their diverse physical, geochemical, and biological factors. We hypothesize that the unique environmental conditions of polar regions select for distinct strains of lactic acid bacteria (LAB) with novel biochemical properties. In this study, we characterized ten strains of psychrotrophic LAB isolated from hitherto poorly described sources—High Arctic and maritime Antarctic soils and soil-like materials, including ornithogenic soils, cryoconites, elephant seal colonies, and postglacial moraines. We evaluated the physiological and biochemical properties of the isolates. Based on 16S rRNA and housekeeping genes, the four LAB strains were assigned to three Carnobacterium species: C. alterfunditum, C. maltaromaticum, and C. jeotgali. The remaining strains may represent three new species of the Carnobacterium genus. All isolates were neutrophilic and halophilic psychrotrophs capable of fermenting various carbohydrates, organic acids, and alcohols. The identified metabolic properties of the isolated Carnobacterium strains suggest possible syntrophic interactions with other microorganisms in polar habitats. Some showed antimicrobial activity against food pathogens such as Listeria monocytogenes and human pathogens like Staphylococcus spp. Several isolates exhibited unique metabolic traits with potential biotechnological applications that could be more effectively exploited under less stringent technological conditions compared to thermophilic LAB strains, such as lower temperatures and reduced nutrient concentrations. Analysis of extrachromosomal genetic elements revealed 13 plasmids ranging from 4.5 to 79.5 kb in five isolates, featuring unique genetic structures and high levels of previously uncharacterized genes. This work is the first comprehensive study of the biochemical properties of both known and new Carnobacterium species and enhances our understanding of bacterial communities in harsh and highly selective polar soil ecosystems. Full article
(This article belongs to the Special Issue Molecular Studies of Microbial Communities)
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17 pages, 3495 KiB  
Article
Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil
by Chunyu Huo, Jianhui Mao, Jianlang Zhang, Xinzhu Yang, Shangkun Gao, Jiyue Li, Qian He, Guangda Tang, Xianan Xie and Zujing Chen
Int. J. Mol. Sci. 2024, 25(3), 1385; https://doi.org/10.3390/ijms25031385 - 23 Jan 2024
Cited by 2 | Viewed by 1294
Abstract
Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a [...] Read more.
Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92–47.9%), Proteobacteria (20.50–28.30%), and Chloroflexi (13.88–15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations. Full article
(This article belongs to the Special Issue Molecular Studies of Microbial Communities)
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