Article
Microbiology
Shang Yang, Rong Tang, Cheng-Jie Xie, Shuang Han, Christopher Rensing, Guo-Hong Liu, Shun-Gui Zhou
Summary: A novel strictly anaerobic sulfate-reducing bacterium, designated SG60(T), was isolated from paddy soil in Fujian Province, China. Strain SG60(T) showed the highest 16S rRNA sequence similarities to the type strains of Fundidesulfovibrio magnetotacticus FSS-1(T) (97.2%) and Fundidesulfovibrio putealis DSM 16056(T) (96.4%). Phylogenetic analysis and genomic comparison confirmed that strain SG60(T) belongs to the genus Fundidesulfovibrio, but represents a new species, named Fundidesulfovibrio soli sp. nov. The findings contribute to the understanding of microbial diversity and evolution in anaerobic environments.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Microbiology
Jinjie Zhou, Cui-Jing Zhang, Meng Li
Summary: A new strain of Psychrodesulfovibrio, named Desulfovibrio mangrovi sp. nov., was isolated from mangrove sediments in Futian Mangrove Nature Reserve in Shenzhen, China. The strain is a sulfate-reducing bacterium with biogeochemical significance, and it can utilize a variety of electron donors and reduce different compounds. Phylogenetic analysis revealed its close relationship with Desulfovibrio subterraneus HN2(T), suggesting a transfer to the genus Psychrodesulfovibrio.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2023)
Article
Microbiology
Akio Ueno, Satoshi Tamazawa, Shuji Tamamura, Takuma Murakami, Tamotsu Kiyama, Hidenori Inomata, Yuki Amano, Kazuya Miyakawa, Hideyuki Tamaki, Takeshi Naganuma, Katsuhiko Kaneko
Summary: A novel mesophilic sulfate-reducing bacterium, strain HN2(T), was isolated from groundwater in Hokkaido, Japan, exhibiting unique growth conditions and diverse electron acceptor utilization patterns.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Miho Watanabe, Ayaka Takahashi, Hisaya Kojima, Naoyuki Miyata, Manabu Fukui
Summary: A novel sulfate-reducing bacterium, Desulfofustis limnaeus sp. nov., was isolated from marsh soil. This bacterium exhibited a range of physiological characteristics, including growth at a wide range of temperature and pH, and the utilization of various organic acids and sulfate as electron acceptors.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Olga V. Karnachuk, Inna A. Panova, Vasilii L. Panov, Olga P. Ikkert, Vitaly V. Kadnikov, Igor I. Rusanov, Marat R. Avakyan, Lubov B. Glukhova, Anastasia P. Lukina, Anatolii V. Rakitin, Shahjahon Begmatov, Alexey V. Beletsky, Nikolai V. Pimenov, Nikolai V. Ravin
Summary: This study aims to investigate the diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut. It reveals the presence of an abundant SRB community in the feces of Bactrian camels through 16S rRNA gene profiling, SRR measurement, and targeted cultivation. The findings shed light on the activity of SRB in the camel gut.
Article
Microbiology
Tomohiro Watanabe, Tatsuya Yabe, Jackson M. Tsuji, Manabu Fukui
Summary: A novel sulfate-reducing bacterium was isolated from sediment sampled in a brackish lake in Japan, capable of respiratory growth with various electron donors and acceptors. Based on gene sequence similarity, it is closely related to Desulfarculus baarsii 2st14(T). It belongs to the family Desulfarculaceae but does not affiliate with any existing genus.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Microbiology
Miho Watanabe, Ayaka Takahashi, Hisaya Kojima, Manabu Fukui
Summary: A novel sulfate-reducing bacterium strain ASN36(T) was isolated from sediment of a brackish lake in Japan. It can grow at a temperature range of 5-35 degrees C and pH range of 6.6-8.8. The strain utilizes various organic compounds and electron acceptors for growth. Based on its genomic and phenotypic properties, it is proposed as a new species, Desulfoluna limicola sp. nov.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Rikuan Zheng, Shimei Wu, Chaomin Sun
Summary: Sulfur cycling in marine sediments is primarily driven by sulfate-reducing bacteria, leading to the production of reduced sulfide and insoluble metal sulfides. A novel sulfate-reducing bacterium, Pseudodesulfovibrio cashew SRB007, was isolated from deep-sea cold seeps and demonstrated strong resistance and removal capabilities against various heavy metal ions. The dissimilatory sulfate reduction by P. cashew SRB007 contributes to its ability to remove heavy metals through the formation of insoluble metal sulfides.
Article
Microbiology
Inna A. Panova, Olga Ikkert, Marat R. Avakyan, Dmitry S. Kopitsyn, Andrey Mardanov, Nikolai Pimenov, Viktoria A. Shcherbakova, Nikolai Ravin, Olga Karnachuk
Summary: A novel sulfate-reducing bacterium, strain OLT, with spore-forming ability, acidophilic and metal-resistant characteristics, was isolated from a microbial mat in a tailing dam at a gold ore mining site. The bacterium grows best at pH 5.5 and utilizes various electron donors for sulfate reduction, while showing resistance to certain electron acceptors like elemental sulfur and arsenate. The draft genome of strain OLT was found to be 5.29 Mb in size and placed within the genus Desulfosporosinus in the phylum Firmicutes.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Di Wang, Chuntian Yang, Borui Zheng, Minghao Yang, Yu Gao, Yuting Jin, Yizhe Dong, Pan Liu, Mingxing Zhang, Enze Zhou, Tingyue Gu, Dake Xu, Fuhui Wang
Summary: The sulfate-reducing bacterium Desulfovibrio vulgaris promotes microbiologically influenced corrosion (MIC) of CoCrFeMnNi high entropy alloy (HEA) and leads to pitting corrosion. D. vulgaris causes the formation of metal sulfides and thinning of passive film. The relative expression of hydrogenase genes hydA and hydB in the biofilms significantly increases, indicating the importance of indirect electron transfer in promoting HEA MIC by D. vulgaris under starvation.
Article
Microbiology
A. A. Frolova, A. Y. Merkel, A. A. Kuchierskaya, E. A. Bonch-Osmolovskaya, A. Slobodkin
Summary: In this study, a novel alkaliphilic sulfate-reducing bacterium, Pseudodesulfovibrio alkaliphilus sp. nov., was isolated from a terrestrial mud volcano on the Taman peninsula in Russia. The bacterium, strain F-1(T), exhibited a diverse range of electron donors and acceptors for sulfate reduction, and showed optimal growth in alkaline conditions.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Romain Darnajoux, Keisuke Inomura, Xinning Zhang
Summary: Recent studies have shown that sulfate reducing bacteria play an important role in nitrogen cycling, especially in oligotrophic coastal and benthic environments. A cellular model was developed to study the growth of sulfate reducers under different nitrogen availabilities. The model confirmed that these bacteria prefer to use ammonium rather than fix nitrogen for growth. This study contributes to a better understanding of anaerobic heterotrophic diazotrophs in environments with fluctuating nitrogen conditions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Microbiology
Ayaka Takahashi, Hisaya Kojima, Miho Watanabe, Manabu Fukui
Summary: A new mesophilic and neutrophilic sulfate-reducing bacterium, Pseudodesulfovibrio sediminis sp. nov., was isolated from sediment of a brackish lake in Japan. The strain SF6(T) showed motility, rod-shaped cells and used lactate, ethanol, and glucose as growth substrates.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Cynthia C. Gilmour, Ally Bullock Soren, Caitlin M. Gionfriddo, Mircea Podar, Judy D. Wall, Steven D. Brown, Joshua K. Michener, Maria Soledad Goni Urriza, Dwayne A. Elias
Summary: ND132T strain, isolated from Chesapeake Bay, USA, is a sulfate-reducing and mercury-methylating bacterium with high levels of mercury methylation. It belongs to the genus Pseudodesulfovibrio and has been proposed as a new species, Pseudodesulfovibrio mercurii.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
A. A. Frolova, A. Yu. Merkel, A. A. Kuchierskaya, A. I. Slobodkin
Summary: A new alkaliphilic, sulfate-reducing, anaerobic bacterium strain H1(T) has been isolated and characterized. It can grow under a wide range of temperature, pH, and salt concentration conditions. The genome analysis and phylogenetic analysis suggest that this bacterium belongs to a novel species, Desulfobotulus pelophilus.
Article
Genetics & Heredity
Roberto Tadeu Raittz, Camilla Reginatto De Pierri, Marta Maluk, Marcelo Bueno Batista, Manuel Carmona, Madan Junghare, Helisson Faoro, Leonardo M. Cruz, Federico Battistoni, Emanuel de Souza, Fabio de Oliveira Pedrosa, Wen-Ming Chen, Philip S. Poole, Ray A. Dixon, Euan K. James
Summary: The Betaproteobacterial genus Azoarcus is significant for plant growth-promotion and remediation of petroleum waste-polluted water and soils. It consists of distinct plant-associated and petroleum-contaminated groups, with different characteristics and ecological roles.
Article
Chemistry, Analytical
Moritz Janda, Brandon K. B. Seah, Dennis Jakob, Janine Beckmann, Benedikt Geier, Manuel Liebeke
Summary: Spatial metabolomics using mass spectrometry imaging is a powerful tool to map hundreds to thousands of metabolites in biological systems. However, annotation of m/z values is a major challenge in MSI, complicated by background ions introduced during experimental procedures. Adduct formation, particularly with sodium or potassium ions, significantly increases total m/z peak counts, and current data analyses often neglect matrix adducts, leading to an overestimation of metabolite numbers.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Brandon K. B. Seah, Estienne C. Swart
Summary: Ciliates are single-celled eukaryotes that can eliminate specific DNA sequences. Long-read sequencing technologies offer the potential to reconstruct longer IESs, but require a different assembly strategy.
Article
Genetics & Heredity
Marcelo Bueno Batista, Paul Brett, Corinne Appia-Ayme, Yi-Ping Wang, Ray Dixon
Summary: The NifL-NifA regulatory system plays a crucial role in integrating signals of oxygen, carbon, and nitrogen to control transcription of nitrogen fixation genes. A single amino acid substitution in NifA disrupts the regulation of nitrogen fixation in response to carbon and nitrogen status. This may enable engineering of carbon source-dependent ammonia excretion in diverse Proteobacteria.
Article
Biochemistry & Molecular Biology
Corinne Appia-Ayme, Richard Little, Govind Chandra, Carlo de Oliveira Martins, Marcelo Bueno Batista, Ray Dixon
Summary: All diazotrophic bacteria and archaea use a nitrogenase enzyme to convert nitrogen gas into ammonia. Some nitrogen-fixing prokaryotes also express different nitrogenase enzymes called V-dependent and Fe-only nitrogenases. In this study, researchers discovered interactions between bacterial enhancer-binding proteins (bEBPs) that are important for nitrogen fixation, specifically in Azotobacter vinelandii bacteria. The findings suggest the potential for fine-tuning the expression of alternative nitrogenases in response to metal availability.
MOLECULAR MICROBIOLOGY
(2022)
Article
Microbiology
Brandon Kwee Boon Seah, Christiane Emmerich, Aditi Singh, Estienne Carl Swart
Summary: In this study, methods for growing and harvesting Loxodes cells in bulk with liquid soil extract medium were described, along with a new fixative called ZFAE that effectively fixes Loxodes cells. This allows for long-term maintenance, large-scale growth, and modern cell biology investigations of Loxodes monoclonal strains in laboratory conditions.
Article
Genetics & Heredity
Timothy Lyndon Haskett, Ramakrishnan Karunakaran, Marcelo Bueno Batista, Ray Dixon, Philip Simon Poole
Summary: In this study, the researchers successfully controlled nitrogen fixation and NH3 excretion by manipulating the regulation of glutamine synthetase (GS) under specific conditions. This has significant implications for targeted delivery of fixed nitrogen to crops and prevention of interaction with non-target plants.
Correction
Microbiology
Lizbeth Sayavedra, Tianqi Li, Marcelo Bueno Batista, Brandon K. B. Seah, Catherine Booth, Qixiao Zhai, Wei Chen, Arjan Narbad
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Brandon K. B. Seah, Minakshi Singh, Christiane Emmerich, Aditi Singh, Christian Woehle, Bruno Huettel, Adam Byerly, Naomi A. Stover, Mayumi Sugiura, Terue Harumoto, Estienne C. Swart
Summary: During sexual conjugation, ciliates eliminate internal sequences from the germline genome to produce the functional somatic genome. We assembled 40,000 Internal Eliminated Sequences (IESs) of Blepharisma stoltei to gain insight into IESs and ciliate genome editing. Contrary to expectations, the germline genome of Blepharisma contains few transposases but instead has a high abundance of a Miniature Inverted-repeat Transposable Element (MITE) derived from a Pogo-family transposon.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Minakshi Singh, Brandon K. B. Seah, Christiane Emmerich, Aditi Singh, Christian Woehle, Bruno Huettel, Adam Byerly, Naomi A. Stover, Mayumi Sugiura, Terue Harumoto, Estienne C. Swart
Summary: Ciliates are microbial eukaryotes that undergo massive DNA excision during the development of their somatic genome. In this study, the somatic genome assembly of Blepharisma stoltei was reported, revealing the presence of PiggyBac transposase homologs that were no longer associated with transposons. These homologs are subject to purifying selection, with one being a putative IES excisase with a complete catalytic triad. It is hypothesized that PiggyBac homologs were ancestral excisases that enabled extensive natural genome editing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Editorial Material
Genetics & Heredity
Brandon Kwee Boon Seah, Estienne Carl Swart
Summary: Many organisms remove DNA from their genomes during development as a defense against mobile elements. However, genome editing actually conceals these elements, allowing survival and evolution in a neutral manner, leading to an enlargement of the germline genome over time.
TRENDS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Nathaniel R. Boyer, Monika Tokmina-Lukaszewska, Marcelo Bueno Batista, Florence Mus, Ray Dixon, Brian Bothner, John W. Peters
Summary: NifL is a crucial flavoprotein responsible for regulating the transcription of nitrogen fixation genes. Understanding its structural changes under different conditions can provide insights into the regulatory mechanism of nitrogen fixation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Julia S. Martin del Campo, Jack Rigsbee, Marcelo Bueno Batista, Florence Mus, Luis M. Rubio, Oliver Einsle, John W. Peters, Ray Dixon, Dennis R. Dean, Patricia C. Dos Santos
Summary: Understanding the reduction of nitrogen gas to ammonia at ambient conditions has been a longstanding challenge. This knowledge is crucial for transferring biological nitrogen fixation to crops and developing improved synthetic catalysts. Azotobacter vinelandii has emerged as the preferred model organism for studying this process over the past 30 years. This review summarizes the current understanding and places it in historical context.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)