Novel Environmental Microbial Species and Genomic Characteristics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 1059

Editor

College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
Interests: microbial symbiosis; extremophiles; microbial photosensors; evolutionary microbiology; biochemistry; NGS; metagenomics; fungal genomics; algal biofuels and algal biology
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Special Issue Information

Dear Colleagues,

There are an estimated 1030 microorganisms in the world, and we depend on them, for our health and for our environment. The importance of a healthy gut microbiome on health conditions like obesity, diabetes, heart health and even mental health is well known, but microbes in every environment are crucial for waste removal and nutrient recycling on the planet.

We live in a microbial world. However, of all these bacteria, we have only discovered and studied less than 2% of the estimated number of species that are out there. Similarly, for fungi, it is estimated that 90% of species on the planet are still unknown. Even with increased genomic sequencing capabilities in the last decades, there is a large number of bacterial and fungal species, especially from less studied or more extreme environments, for which the whole genomes have not been sequenced. A larger variety of whole genome sequences of diverse species is needed to better understand the diversity and evolution of life on the planet at a molecular level.

Having more completed whole genome and metabolic analysis is also crucial to support the growing number of metagenomic studies of human, animal, plant and ecological environments. Many such metagenomic studies suffer from the lack of whole genome data to perform the taxonomic and metabolic in-depth analysis that is needed to validate these studies.

We invite the submission of high-quality whole genomes and their in-depth analysis from novel microbial (bacterial and fungal) species from interesting environments or conditions, to further understand the variety of life in general.

Dr. John Kyndt
Guest Editor

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Keywords

  • whole-genome sequencing
  • microbial diversity
  • extremophiles
  • evolution of life
  • genome data analysis

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Published Papers (2 papers)

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Research

18 pages, 4587 KB  
Article
Terrisphaera alpina gen. nov., sp. nov., a Cellulolytic Planctomycete Representing the First Described Soil-Inhabiting Member of the Class Phycisphaerae
by Anastasia A. Ivanova, Irina S. Kulichevskaya, Daniil G. Naumoff, Gennady S. Kachmazov, Natalia E. Suzina and Svetlana N. Dedysh
Life 2026, 16(8), 1222; https://doi.org/10.3390/life16081222 - 23 Jul 2026
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Abstract
A novel planctomycete, strain T20PH1T, was isolated from alpine meadow soil collected at an altitude of 1800 m in the North Caucasus Mountains, Russia. Phylogenomic analysis placed it within the family Tepidisphaeraceae of the class Phycisphaerae. The closest relatives based [...] Read more.
A novel planctomycete, strain T20PH1T, was isolated from alpine meadow soil collected at an altitude of 1800 m in the North Caucasus Mountains, Russia. Phylogenomic analysis placed it within the family Tepidisphaeraceae of the class Phycisphaerae. The closest relatives based on 16S rRNA gene sequence similarity are Fontivita pretiosa B-254T (88.9%), ‘Humisphaera borealis’ M1803T (88.6%), and Tepidisphaera mucosa 2842T (88.4%). Strain T20PH1T is the first soil-derived representative of the class Phycisphaerae. Cells of strain T20PH1T are motile, pink-pigmented cocci reproducing by binary fission. This planctomycete is an obligately aerobic chemoorganotroph with growth optima at 25–30 °C and pH 6.0–7.0. A notable functional trait of strain T20PH1T is its ability to grow on cellulose, including microcrystalline, fibrous and carboxymethyl cellulose, as well as on xylan, starch, lichenan and xanthan. The genome comprised a 5.15 Mb chromosome and a 125 kb plasmid with G + C contents of 65.97 and 66.75%, respectively. Genome analysis identified a GH5_5 subfamily cellulase as the most likely enzyme responsible for cellulose degradation by this planctomycete. Based on phenotypic and phylogenomic evidence, strain T20PH1T (=LMG 34157T = KCTC 102499T) was classified as representing a novel genus and species, Terrisphaera alpina gen. nov., sp. nov. Full article
(This article belongs to the Special Issue Novel Environmental Microbial Species and Genomic Characteristics)
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16 pages, 9864 KB  
Article
A Modern Framework for Identifying Novel Environmental Legionella Species
by Karla Vasari, Maja Kovačević, Niko Kasalo, Snježana Kazazić, Ivan Mijakovic, Göran Klobučar, Damjan Franjevic, Josip Skejo, Tomislav Domazet-Lošo, Brian G. Shelton, Marina Santic and Roberta Sauerborn Klobucar
Life 2026, 16(7), 1187; https://doi.org/10.3390/life16071187 - 17 Jul 2026
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Abstract
Accurate species-level identification of Legionella during routine environmental surveillance remains challenging, as standard proteomic screening methods like MALDI-TOF MS often lack the resolution to distinguish closely related taxa. This study introduces a novel, cost-effective, and stepwise taxonomic framework that bridges routine environmental monitoring [...] Read more.
Accurate species-level identification of Legionella during routine environmental surveillance remains challenging, as standard proteomic screening methods like MALDI-TOF MS often lack the resolution to distinguish closely related taxa. This study introduces a novel, cost-effective, and stepwise taxonomic framework that bridges routine environmental monitoring with multi-layered, genome-resolved analysis. We expanded upon our previous screening of four novel candidate lineages by focusing on the three remaining, uncharacterized environmental isolates, while using the recently validly described Legionella sheltonii (strain PATHC038) as a reference framework control. By applying nucleotide- and protein-based overall genomic relatedness indices (ANI, dDDH, AAI, and POCP) alongside core-genome phylogenomics, our framework independently confirmed the genomic distinctiveness of the three isolates, which exhibited AAI values of 94.3–96.6% and POCP values of 86.5–91.0%, with POCP values lying close to the proposed species delineation threshold. By defining clear criteria for escalating isolates from culture to targeted sequencing, this workflow prevents diagnostic misidentification during epidemiological outbreak investigations and provides public health agencies with a scalable tool to monitor hidden Legionella diversity, ultimately enhancing proactive water safety and risk assessment. Full article
(This article belongs to the Special Issue Novel Environmental Microbial Species and Genomic Characteristics)
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