Article
Biochemistry & Molecular Biology
Connor D. Harris, Ellis L. Torrance, Kasie Raymann, Louis-Marie Bobay
Summary: The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. CoreCruncher is a robust and fast program that can construct core genomes across hundreds or thousands of genomes. Compared to other tools, CoreCruncher is more conservative and less sensitive to the presence of paralogs and xenologs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Xiuran Yin, Guowei Zhou, Mingwei Cai, Qing-Zeng Zhu, Tim Richter-Heitmann, David A. Aromokeye, Yang Liu, Rolf Nimzyk, Qingfei Zheng, Xiaoyu Tang, Marcus Elvert, Meng Li, Michael W. Friedrich
Summary: The study found that multiple low-abundance archaeal groups are actually catabolic protein degraders, while the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism. In addition, the catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.
Review
Biotechnology & Applied Microbiology
Laurenz Schroeer, Nico Boon, Tim De Kock, Veerle Cnudde
Summary: Microorganisms, including bacteria, archaea, algae and fungi, colonize natural building stones and impact substrates in various ways. Bacteria, with their high diversity, are among the most relevant colonizers, altering rock properties through discoloration, dissolution or precipitation. The role of archaea remains unresolved, but new technologies provide tools to better understand microbial diversity and true function.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2021)
Article
Chemistry, Medicinal
Cedric Hermans, Maarten Lieven De Mol, Marieke Mispelaere, Anne-Sofie De Rop, Jeltien Rombaut, Tesneem Nusayr, Rebecca Creamer, Sofie L. De Maeseneire, Wim K. Soetaert, Paco Hulpiau
Summary: MariClus is an online user-friendly platform for mining and visualizing marine gene clusters. It provides information on clusters and predicted molecules for over 500 marine-related prokaryotes. Users can easily search and visualize the information in table format or graphical representation.
Article
Multidisciplinary Sciences
Ronnakrit Rattanasriampaipong, Yi Ge Zhang, Ann Pearson, Brian P. Hedlund, Shuang Zhang
Summary: Archaeal membrane lipids, specifically the GDGTs, can be used to reconstruct ancient temperatures and provide insights into the ecology and evolution of marine ammonia-oxidizing archaea (AOA). The study identified thermal and nonthermal behaviors of GDGTs, which can be used as indicators of environmental temperature. The distribution of GDGTs in AOA cultures and shallow water samples followed a temperature-dependent trend, while deep water samples showed a nonthermal behavior. Statistical analysis revealed long-term trends in GDGT-2/GDGT-3 ratios, suggesting a suppression of deep water marine AOA during greenhouse climates in the Mesozoic and early Cenozoic periods.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Edward F. DeLong
Summary: In 1977, Woese and Fox discovered a new microbial domain, Archaea, and later found that they were not only limited to extreme environments but also abundant in oxygen-rich marine waters. Subsequent studies revealed the widespread presence of marine planktonic archaea, their unexpected symbiotic associations, physiologies, and global abundance.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Limnology
Giancarlo Bachi, Elisabetta Morelli, Margherita Gonnelli, Cecilia Balestra, Raffaella Casotti, Valtere Evangelista, Daniel J. Repeta, Chiara Santinelli
Summary: This study investigates the link between the biological lability and the molecular weight, fluorescence, and polarity of phytoplankton dissolved organic matter (DOM) by incubating exudates from the diatom Phaeodactylum tricornutum with a natural community of marine heterotrophic prokaryotes. The results show that freshly produced phytoplankton DOM exhibits a dynamic pattern of degradation that is likely related to changes in DOM quality. Protein-like DOM is likely a labile component of phytoplankton exudates, while humic-like substances are resistant to bacterial degradation.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Review
Biochemistry & Molecular Biology
Elena Porzio, Maria Rosaria Faraone Mennella, Giuseppe Manco
Summary: DING proteins, with their characteristic N-terminus DINGGG, are widely distributed among different organisms and share a highly conserved phosphate binding site. Despite their sequence conservation, they exhibit heterogeneity in biological activities and have been implicated in various pathologies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Jessyca Freitas-Silva, Bruno Francesco Rodrigues de Oliveira, Felipe de Mello Vigoder, Guilherme Muricy, Alan D. W. Dobson, Marinella Silva Laport
Summary: The study conducted an in-depth genomic analysis of Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, revealing a diverse range of potential biosynthetic gene clusters involved in antimicrobial activity. The strain also possesses a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes and genes responsible for adaptation to the marine habitat.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Zhen Yan, Kaifeng Du, Yunfeng Yan, Rui Huang, Fanping Zhu, Xianzheng Yuan, Shuguang Wang, James G. Ferry
Summary: Anaerobic marine environments play a significant role in the production of methane, a greenhouse gas. Methanotrophic archaea (ANME) prevent methane release by relying on a symbiotic relationship with sulfate-reducing bacteria or direct reduction of metal oxides. This study examines the growth characteristics of two marine methanogens and reveals that they can conserve energy by reducing ferrihydrite or humic acids, resulting in the production of acetate and/or formate.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Bin Wei, Gang-Ao Hu, Zhen-Yi Zhou, Wen-Chao Yu, Ao-Qi Du, Cai-Ling Yang, Yan-Lei Yu, Jian-Wei Chen, Hua-Wei Zhang, Qihao Wu, Qi Xuan, Xue-Wei Xu, Hong Wang
Summary: By analyzing the genomes of marine prokaryotes, it was found that at least 96.8% of their secondary metabolic potential remains unexplored. Metabolomics and genomics approaches of a marine-derived bacterium identified potential biosynthetic pathways of novel polyketides and known compounds. These findings provide valuable knowledge for targeted discovery and biosynthesis of novel marine prokaryotic natural products.
Article
Biochemistry & Molecular Biology
Peter T. S. van der Gulik, Martijn Egas, Ken Kraaijeveld, Nina Dombrowski, Astrid T. Groot, Anja Spang, Wouter D. Hoff, Jenna Gallie
Summary: Automated genome annotation is crucial for extracting biological information from sequence data. However, there is a pervasive error in prokaryotic tRNA gene sets on GtRNAdb, where partial, non-canonical tRNA genes are mis-categorized as standard, canonical tRNA genes. We recommend using a combination of screening input sequences, activating the automated pseudogene detection function, and scrutinizing predicted tRNA genes with low isotype scores to improve predictions.
Article
Geochemistry & Geophysics
A. El Albani, K. O. Konhauser, A. Somogyi, J. Ngwalghoubou Ikouanga, A. Lamboux, J. Blichert-Toft, E. Chi-Fru, C. Fontaine, A. Mazurier, A. Riboulleau, A. -C. Pierson-Wickmann, F. Albarede
Summary: Sediments from the Francevillian Group in Gabon contain pyritized structures that suggest the presence of colonial organisms. Through a comprehensive study, including morphology, mineralogy, and geochemistry, these structures are considered putative biogenic traces, with no association with sulfate reduction. Anomalies in organic carbon and zinc content in the fillings of these structures further indicate their biogenicity.
EARTH AND PLANETARY SCIENCE LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Alejandro Alvarez-Lugo, Arturo Becerra
Summary: Isomerases are a unique class of enzymes that perform various chemical reactions at the intramolecular level. This study analyzes individual isomerases and identifies duplication events in prokaryotes. The findings suggest that paralogous enzymes are mostly retained with original function, followed by subfunctionalization and neofunctionalization to a lesser extent.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Ecology
Goncalo Figueiredo, Margarida Gomes, Claudia Covas, Sonia Mendo, Tania Caetano
Summary: The research revealed the significant potential of Sphingobacteriaceae bacterial family as a source of new SMs, with the ability to produce unknown compounds, and some genera have the potential as plant growth promoters and bioremediators. The study found that some strains of the genera Mucilaginibacter and Sphingobacterium have a high number of biosynthetic gene clusters, indicating their potential in SMs production.
Article
Biotechnology & Applied Microbiology
C. Covas, A. Vaz, B. Almeida, J. Lourenco, G. Figueiredo, O. L. Franco, S. Mendo, T. Caetano
Summary: Secondary metabolites are bioactive compounds that are challenging to produce in the laboratory. This study used RNA-seq to investigate the cellular pathways of Pedobacter lusitanus NL19 modulated by high concentrations of peptone from casein (PC). The results showed that high PC concentrations significantly repressed the biosynthesis of biotin and the production of certain nonribosomal peptides, highlighting the effect of PC on gene expression and metabolic pathways.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Diana Dias, Carlos Fonseca, Sonia Mendo, Tania Caetano
Summary: Antimicrobial resistance is a serious global issue for public health and animal health. This study investigated the resistome of wild boar fecal microbiome, identifying a diverse set of genes conferring resistance to antibiotics, some of which are included in the WHO list of critically important antimicrobials.
ENVIRONMENTAL POLLUTION
(2022)
Article
Microbiology
Susana Serrano, Sonia Mendo, Tania Caetano
Summary: Haloarchaea are important components of saline aquatic environments and produce diverse secondary metabolites with potential ecological and biotechnological significance. This study analyzed 67 Haloarchaea genomes and identified multiple biosynthetic gene clusters involved in the production of terpenes, RiPPs, and siderophores. The findings suggest that all Haloarchaea might produce squalene and bacterioruberin, and some of them may have other carotenoid biosynthetic capabilities.
RESEARCH IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Joana C. Barbosa, Itala C. Silva, Tania Caetano, Eva Mosker, Maria Seidel, Joana Lourenco, Roderich D. Suessmuth, Nuno C. Santos, Sonia Goncalves, Sonia Mendo
Summary: Lichenicidin is a promising natural antimicrobial peptide with strong bactericidal activity and no cytotoxicity towards human cells.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Biophysics
Joana C. Barbosa, Sonia Goncalves, Marcin Makowski, Itala C. Silva, Tania Caetano, Tanja Schneider, Eva Moesker, Roderich D. Suessmuth, Nuno C. Santos, Sonia Mendo
Summary: Lantibiotics are a promising solution to antibiotic resistance, particularly against Gram-positive bacteria like MRSA and VRE. Work on lichenicidin has shown that the interaction between the two peptides, Blia and Blip, is necessary for full activity against target bacteria. The mechanism of action involves an increase in net surface charge and observed cell surface perturbations that result in leakage of internal contents.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Environmental Sciences
Diana Dias, Carlos Fonseca, Tania Caetano, Sonia Mendo
Summary: The emergence of antimicrobial resistance poses a global threat to public health, and the circulation of ARGs in the environment plays a crucial role in the development of resistance. This study found various antibiotic resistance genes in the fecal microbiome of red deer, with tetrcycline resistance genes being the most abundant. Additionally, other genes posing current and future threats to human health were identified. Although multidrug-resistant bacteria were isolated, the overall level of antibiotic resistance was low.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemical Research Methods
Goncalo Figueiredo, Carina Pedrosa Costa, Joana Lourenco, Tania Caetano, Silvia M. Rocha, Sonia Mendo
Summary: Microbial metabolomics is used to analyze and understand the metabolites produced and released by microorganisms in specific conditions. This research aims to investigate the impact of culture media changes on the metabolic profile and production of biotechnologically relevant compounds in Pedobacter lusitanus NL19 and Pedobacter himalayensis MTCC 6384. The study identified 320 metabolites belonging to different chemical families and associated 80 metabolites with various metabolic pathways. The findings provide insights into how slight changes in culture media composition can affect microbial metabolism and have potential applications in metabolomics pipeline construction and biotechnology.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biology
Thales Costa, Elena Cassin, Catarina Moreirinha, Sonia Mendo, Tania Sousa Caetano
Summary: This study investigates the transcription, antimicrobial activity, and biomolecular profile of halophilic archaea genes involved in the biosynthesis of peptide secondary metabolites. The results suggest that the ycaO and medM genes are transcriptionally active, with medM2 showing the highest transcript level. The deletion of the ycaO gene does not affect the antimicrobial activity of H. mediterranei.
Article
Biotechnology & Applied Microbiology
Joana C. Barbosa, Eva Moesker, Raquel Faria, Roderich D. Sussmuth, Sonia Mendo, Tania Caetano
Summary: This study investigated the activity of lichenicidin A2 (LicA2) trimming proteases (LicP and LicT). The presence of a negatively charged amino acid residue at the cleavage site was found to be important for the efficacy of LicP. Mutations in the lichenicidin hexapeptide and alterations in the GG-motif resulted in higher processing rates. This research is important for understanding the activity of lantibiotic-related transporters and proteases and their potential application in industrial processes.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Mariam Kholany, Nicolas Schaeffer, Ines P. E. Macario, Telma Veloso, Tania Caetano, Joana L. Pereira, Ana C. R. V. Dias, Joao A. P. Coutinho, Soinia P. M. Ventura
Summary: Haloarchaea, a class of marine microbial resources, can be a promising source of valuable compounds such as bacterioruberin. Natural and biocompatible hydrophobic eutectic solvents (HES) based on menthol and carboxylic acids were investigated for the extraction of bacterioruberin. The menthol and levulinic acid mixture showed the best results and proteins could be recovered by adding water to the extract, forming a protein-rich interfacial precipitate. The process intensification was achieved by reusing the eutectic phase over multiple extraction cycles, resulting in a bacterioruberin-rich extract.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Microbiology
Claudia Covas, Goncalo Figueiredo, Margarida Gomes, Tiago Santos, Sonia Mendo, Tania S. Caetano
Summary: Secondary metabolites from environmental bacteria provide solutions for various health and environmental challenges. The study focuses on uncovering the diversity of biosynthetic gene clusters encoded in the genomes of Pedobacter spp. The potential for the production of various secondary metabolites, including RiPPs, terpenes, hybrid SMs, PKs, NRPs, and siderophores, is revealed.