Article
Microbiology
John L. Dahl, Wayne Gatlin, Phuong M. Tran, Cody S. Sheik
Summary: The study isolated a novel species of Mycolicibacterium named Mycolicibacterium nivoides from a peat bog in northern Minnesota, which was distinct from its closest relative M. septicum in terms of 16S rRNA gene sequence, physiological and biochemical characteristics. Phylogenomic analysis and DNA-DNA hybridization supported the divergence of the new species from M. septicum.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Kumar Gaurav, Dhanesh Kumar, U. Jagadeeshwari, A. Shabbir, Ch Sasikala, Ch Ramana
Summary: Four new strains of alkaliphilic Planctomycetes were isolated from Chilika lagoon in India, with two of them identified as novel species: Tautonia marina and Tautonia rosea. These strains share similarities in characteristics but differ in genotypic and chemotaxonomic features.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Rika Kudo, Ryota Yamano, Juanwen Yu, Shotaro Koike, Alfabetian Harjuno Condro Haditomo, Mayanne A. M. de Freitas, Jiro Tsuchiya, Sayaka Mino, Fabiano Thompson, Jesus L. Romalde, Hisae Kasai, Yuichi Sakai, Tomoo Sawabe
Summary: Strain PT1(T), a rod-shaped bacterium isolated from laboratory-reared larvae of sea cucumber Apostichopus japonicus, demonstrated similarities to Neptuniibacter marinus ATR 1.1(T) and Neptuniibacter caesariensis MED92(T) with sequence similarities of 98.2% and 98.1%, respectively, based on the analysis of 16S rRNA gene nucleotide sequences. However, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values among these three strains were below 95% and 70%, confirming the novel status of PT1(T). Based on the genomic approach, a new species, Neptuniibacter victor sp. nov., is proposed for PT1(T).
Article
Multidisciplinary Sciences
Ryota Yamano, Juanwen Yu, Alfabetian Harjuno Condro Haditomo, Chunqi Jiang, Sayaka Mino, Jesus L. Romalde, Kyuhee Kang, Yuichi Sakai, Tomoo Sawabe
Summary: This study isolated a Gram-negative, aerobic bacterium named PTE2(T) from laboratory-reared Japanese sea cucumber larvae. Phylogenetic analysis revealed that PTE2(T) was closely related to Thalassotalea sediminis N211(T), but had some differences, indicating the novelty of this strain. Based on genome-based taxonomic approaches, PTE2(T) is proposed as a new species, Thalassotalea hakodatensis sp. nov.
Article
Multidisciplinary Sciences
Lyudmila Romanenko, Nadezhda Otstavnykh, Valeriya Kurilenko, Peter Velansky, Viacheslav Eremeev, Valery Mikhailov, Marina P. Isaeva
Summary: This research report describes the isolation of two novel strains, Profundicola chukchiensis, from the bottom sediments of the Chukchi Sea in the Arctic Ocean, Russia. These strains exhibit unique physiological and genetic characteristics that distinguish them from other known strains, leading to their classification as a novel genus and species.
Article
Multidisciplinary Sciences
Lyudmila Romanenko, Nadezhda Otstavnykh, Valeriya Kurilenko, Peter P. Velansky, Viacheslav Eremeev, Valery Mikhailov, Marina Isaeva
Summary: Two Gram-negative, halophilic strains, KMM 9713 and KMM 9724(T), were isolated from Chukchi Sea sediments in the Arctic Ocean, Russia. These strains belong to a novel genus and species, Profundicola chukchiensis gen. nov., sp. nov., based on phylogenetic and phenotypic characteristics. The strains showed distinct 16S rRNA gene sequence similarity to Ornithobacterium rhinotracheale DSM 15997(T) and Empedobacter genus members.
Article
Microbiology
Jiyoun Kim, Byungjo Lee, Geeta Chhetri, Inhyup Kim, Yoonseop So, Wonhee Jang, Taegun Seo
Summary: Three novel species of the genus Mucilaginibacter were isolated from seashells, soil, and foxtail, and showed high similarity among each other. These strains have the potential for industrial chitin degradation due to their chitinolytic capacity.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Chunming Dong, Lin Wei, Jianning Wang, Qiliang Lai, Zhaobin Huang, Zongze Shao
Summary: In this study, the taxonomic affiliation of Oceanobacter-related bacteria (ORB) in relation to alkane utilization was clarified through phylogenomic and comparative genomics analyses. The results showed that ORB can be divided into hydrocarbon-degrading (HD) and non-HD groups, which differ significantly in terms of genome size, G + C content, and genes involved in alkane utilization. The alkB gene encoding alkane monooxygenase was identified as a marker gene to distinguish the members of Oceanobacter and Thalassolituus genera. Additionally, pangenome analysis revealed that Thalassolituus possesses a larger accessory genome, which may enhance its ability to adapt to marine environments.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Shehzad Abid Khan, Hyung Min Kim, Byung Hee Chun, Che Ok Jeon
Summary: A new gram-negative bacterium, designated as Devosia aurantiaca sp. nov., was isolated from mountain soil in Gangwon-do, South Korea. It exhibits distinct physiological, chemotaxonomic, and molecular properties within the genus Devosia, highlighting its status as a novel species.
CURRENT MICROBIOLOGY
(2021)
Article
Microbiology
Jun-Jie Ying, Zhi-Cheng Wu, Yuan-Chun Fang, Lin Xu, Cong Sun
Summary: Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. due to its higher sequence identity with Aquisalinus flavus than with other strains in the Parvularcula genus. Additionally, the species is distinguished by the presence of unique fatty acids, setting it apart from closely related taxa.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Dong Wang, Lei Dong, Neeli Habib, Feng Liu, Sohail Ahmad Jan, Jian-Yu Jiao, Min Xiao, Nimaichand Salam, Wen-Jun Li
Summary: A novel species of the genus Sphingosinicella, designated Sphingosinicella terrae sp. nov., was isolated from a desert soil sample. It showed close phylogenetic relationships to Sphingosinicella ginsenosidimutans BS1(T), Sphingomonas deserti GL-C-18(T), and Sphingosinicella humi QZX222(T).
CURRENT MICROBIOLOGY
(2022)
Article
Microbiology
Hideomi Itoh, Zhenxing Xu, Yoko Masuda, Natsumi Ushijima, Chie Hayakawa, Yutaka Shiratori, Keishi Senoo
Summary: Three novel bacterial strains were isolated from soil in Japan, identified as new species in the genus Geomonas based on 16S rRNA gene sequences and genome-related analysis, named Geomonas silvestris sp. nov., Geomonas paludis sp. nov., and Geomonas limicola sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Tobias Eisenberg, Kristin Muehldorfer, Marcel Erhard, Ahmad Fawzy, Sabine Kehm, Christa Ewers, Torsten Semmler, Jochen Blom, Andre Lipski, Joerg Rau, Peter Kaempfer, Stefanie P. Glaeser
Summary: In this study, seven strains belonging to the genus Erysipelothrix were isolated from various animal sources, and two new species named Erysipelothrix anatis sp. nov. and Erysipelothrix aquatica sp. nov. were identified. Additionally, another new strain was isolated from fox urine and named Erysipelothrix urinaevulpis sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Shuai-Ting Yun, Zhuo Chen, Yan-Jun Yi, Ming-Jing Zhang, Shu-Kun Gao, Yan-Xia Zhou
Summary: A novel bacterium, designated as Pseudaestuariivita rosea sp. nov., was isolated from Acmaea sp. collected from Weihai, Shandong Province, China. This Gram-stain-negative, aerobic, non-motile rod-shaped bacterium was able to grow over a wide range of temperature, pH, and salt concentration. Genome analysis revealed the presence of various secondary metabolites in the strain.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ho Le Han, Dian Alfian Nurcahyanto, Neak Muhammad, Yong-Jae Lee, Tra T. H. Nguyen, Song-Gun Kim, Sook Sin Chan, Kuan Shiong Khoo, Kit Wayne Chew, Pau Loke Show, Thi Ngoc Thu Tran, Thi Dong Phuong Nguyen, Chen Yaw Chiu
Summary: In this study, a novel strain PL0132(T) belonging to the genus Spirosoma in the phylum Bacteroidetes was isolated and identified from a fallen leaf. This Gram-negative, strictly aerobic, rod-shaped strain showed optimal growth at 25 degrees C, pH 6-7, and tolerated 1% NaCl concentration. The complete genome of PL0132(T) consisted of one contig with a sequencing depth of 76x and a G + C content of 46.7%. The strain PL0132(T) is proposed as a new species, Spirosoma foliorum sp. nov.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Anastasia A. Ivanova, Igor Y. Oshkin, Olga V. Danilova, Dmitriy A. Philippov, Nikolai V. Ravin, Svetlana N. Dedysh
Summary: Rokubacteria, an unculitvated phylogenetic clade of prokaryotes, are found in diverse terrestrial habitats and are considered part of the rare biosphere. A study of bacteria populations in wetland habitats revealed that the abundance of Rokubacteriales is positively correlated with pH, total nitrogen content, and availability of Ca and Mg.
Correction
Microbiology
Svetlana E. Belova, Nikolai V. Ravin, Timofey A. Pankratov, Andrey L. Rakitin, Anastasia A. Ivanova, Alexey V. Beletsky, Andrey V. Mardanov, Jaap S. Sinninghe Damste, Svetlana N. Dedysh
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Irina S. Kulichevskaya, Anastasia A. Ivanova, Nataliya E. Suzina, Jaap S. Sinninghe Damste, Svetlana N. Dedysh
Summary: In this study, a novel freshwater planctomycete of the genus 'Anatilimnocola' was characterized and described. This new species exhibits distinct characteristics in terms of cell morphology, growth conditions, and genomic features compared to known freshwater planctomycetes. The findings of this study are significant in understanding the diversity and ecological functions of planctomycetes in freshwater environments.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Marine & Freshwater Biology
Ester M. Eckert, Tommaso Cancellario, Paul L. E. Bodelier, Steven A. J. Declerck, Liang Diwen, Sainur Samad, Monika Winder, Libin Zhou, Diego Fontaneto
Summary: This study investigates the factors contributing to the differences in microbiomes associated with rotifers, and finds that host ecology and habitat have a stronger influence than host phylogenetic distances.
Article
Microbiology
David R. Arahal, Hans-Juergen Busse, Carolee T. Bull, Henrik Christensen, Maria Chuvochina, Svetlana N. Dedysh, Pierre-Edouard Fournier, Konstantinos T. Konstantinidis, Charles T. Parker, Ramon Rossello-Mora, Antonio Ventosa, Markus Goeker
Summary: This article presents several opinions regarding the naming of organisms, including the rejection of certain requests, orthographical corrections, and evaluation and clarification of rules. All of these opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
D. G. Naumoff, I. S. Kulichevskaya, S. N. Dedysh
Summary: Planctomycetes of the class Phycisphaerae are a diverse group of aerobic and anaerobic heterotrophic bacteria that inhabit various marine and terrestrial environments. Humisphaera borealis M1803(T) is a characterized member of this class, capable of utilizing xylan, a plant cell wall polymer. The genetic determinants for xylan utilization in this bacterium were identified through whole genome sequence analysis, shedding light on the evolution of genes for glycoside hydrolases.
Article
Microbiology
Rob J. M. Van Spanning, Qingtian Guan, Chrats Melkonian, James Gallant, Lubos Polerecky, Jean-Francois Flot, Bernd W. Brandt, Martin Braster, Paul Iturbe Espinoza, Joost W. Aerts, Marion M. Meima-Franke, Sander R. Piersma, Catalin M. Bunduc, Roy Ummels, Arnab Pain, Emily J. Fleming, Nicole N. Van der Wel, Vasile D. Gherman, Serban M. Sarbu, Paul L. E. Bodelier, Wilbert Bitter
Summary: A study has found a methanotrophic Mycobacterium within the Actinobacteria, a group of bacteria not previously known to grow on methane under aerobic conditions. This Mycobacterium, named Candidatus Mycobacterium methanotrophicum, is closely related to well-known pathogens like M. tuberculosis and M. leprae. Genomic and proteomic analyses showed that Candidatus M. methanotrophicum possesses all the necessary enzymes for aerobic growth on methane. Stable isotope probing confirmed that this bacterium can use methane as its sole carbon and energy source.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Julia B. Gontijo, Fabiana S. Paula, Andressa M. Venturini, Jessica A. Mandro, Paul L. E. Bodelier, Siu M. Tsai
Summary: This study described the metagenome-assembled genome (MAG) of Methylocystis sp. from Amazonian floodplains sediments and explored its functional potential and ecological traits. The analysis revealed that it belongs to Methylocystis parvus and has the ability for methane oxidation and nitrogen fixation, as well as unique genes related to nitrogen metabolism and cell motility.
Article
Microbiology
Xiaoyu Cheng, Xing Xiang, Yuan Yun, Weiqi Wang, Hongmei Wang, Paul L. E. Bodelier
Summary: Karst ecosystems, which account for a significant portion of the global land area, have a mismatch between their global importance and the knowledge of their microbial ecology. To bridge this knowledge gap, this study analyzed the microbial communities in different niches of the Heshang Cave and the soils above it. The study found that archaeal communities were dominated by Thaumarchaeota, while Actinobacteria dominated bacterial communities. The important predictor groups inside the cave were correlated to NH4+ availability, while those outside the cave were correlated with pH, Ca2+, and NO2-. The study also identified key keystone taxa involved in nitrogen cycling and revealed the predicted ecological functions in karst soils. Overall, these findings enhance our understanding of the microbial dark matter in subsurface karst ecosystems.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Diana X. Sahonero-Canavesi, Melvin F. Siliakus, Alejandro Abdala Asbun, Michel Koenen, F. A. Bastiaan von Meijenfeldt, Sjef Boeren, Nicole J. Bale, Julia C. Engelman, Kerstin Fiege, Lora Strack van Schijndel, Jaap S. Sinninghe Damste, Laura Villanueva
Summary: Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea have membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Some bacteria can produce ether-bound membrane-spanning lipids (MSLs), which are likely precursors of relevant molecules in paleoclimatology. The enzymes responsible for their production have been discovered, and the building blocks of these lipids are branched fatty acids. Phylogenomic analyses reveal a wider diversity of potential MSL-producing bacteria than previously thought, which has important implications for the evolution of lipid membranes.
Review
Biochemistry & Molecular Biology
Anandi Tamby, Jaap Sinninghe S. Damste, Laura Villanueva
Summary: The deep-sea environment is characterized by extreme conditions, including high hydrostatic pressure and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed specific membrane lipid strategies to withstand these conditions, such as increased abundance of lipids containing unsaturated and branched-chain fatty acids with increasing hydrostatic pressure. However, not all piezophiles employ this strategy, highlighting the need for further understanding of the effects of hydrostatic pressure on microbial lipid membranes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Vania Scarlet Chavez-Rico, Stijn van den Bergh, Paul L. E. Bodelier, Miriam van Eekert, Yujia Luo, Klaas G. J. Nierop, Valentina Sechi, Adrie Veeken, Cees Buisman
Summary: Process technologies have a significant impact on the characteristics of organic amendments (OAs), even when the same raw material is used. This study aimed to investigate how these process technologies indirectly influence the effect of OAs on soil microbial activity and soil aggregation. The results showed that OAs produced under anaerobic conditions increased microbial activity, biomass, and soil micro-and macro-aggregation compared to compost and control treatments. This study suggests the potential for engineering OAs to achieve desired effects on soil properties.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2023)
Article
Environmental Sciences
Xiaoyu Cheng, Zhilin Zeng, Xiaoyan Liu, Lu Li, Hongmei Wang, Rui Zhao, Paul L. E. Bodelier, Weiqi Wang, Yiheng Wang, Olli H. Tuovinen
Summary: We reported the composition of methane-producing microbial communities and their interactions with methane-oxidizing bacteria (MOBs) in Heshang Cave to comprehensively understand methane cycling in the subsurface biosphere. MOBs were dominated by the high-affinity MOB, upland soil cluster (USC), while methanogens were dominated by Methanoregula and cluster ZC-I. However, MOBs in caves showed a comparable or higher potential methane oxidizing rate (PMOR) than those in soils, while methane produced by methanogens was undetected.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
Svetlana N. Dedysh
Summary: Despite the growing interest in poorly studied and uncultivated bacterial groups, they remain difficult objects for taxonomic studies. Describing these bacteria can take several years and routine laboratory tests are not suitable for slow-growing bacteria. Standard techniques in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. By investing time in detailed analysis and experimental verification of new microorganisms, unexpected findings can shape our understanding of their functional role in the environment.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Microbiology
Ekaterina N. Tikhonova, Ruslan Z. Suleimanov, Igor Y. Oshkin, Aleksey A. Konopkin, Diana V. Fedoruk, Nikolai V. Pimenov, Svetlana N. Dedysh
Summary: This study identified a novel methanotrophic bacteria capable of fast growth in saltwater, providing a new option for potential production of single-cell protein. The microbial consortium demonstrated stable growth in high salt concentration and achieved high biomass yield and protein content. Isolation attempts resulted in obtaining a pure culture of a salt-tolerant methanotrophic bacteria with a genome containing gene clusters explaining its ability to tolerate high salt concentration.