Article
Virology
Leora Busse, Mike Tisza, Jocelyne DiRuggiero
Summary: This study characterizes the diversity and genetic complexity of viruses in endolithic microbial communities inhabiting rocks in hyper-arid deserts. The viral genome maps show a high level of protein diversity and the presence of virus-encoded auxiliary metabolic genes. Potential phage-host relationships were predicted between viruses and primary producers as well as heterotrophic bacteria. Furthermore, viral diversity was found not to be correlated with microbial diversity across rock substrates.
Article
Microbiology
Maria Cristina Casero, Carmen Ascaso, Antonio Quesada, Hanna Mazur-Marzec, Jacek Wierzchos
Summary: Cyanobacteria exposed to high solar radiation utilize defense mechanisms such as avoidance, antioxidant systems, and production of photoprotective compounds like scytonemin. Two cyanobacterial strains from the Atacama Desert were examined, with one strain showing lower acclimation capacity and higher accumulation of reactive oxygen species in response to light radiation compared to the other strain.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Yunha Hwang, Janina Rahlff, Dirk Schulze-Makuch, Michael Schloter, Alexander J. Probst
Summary: Viruses in Atacama Desert soils play essential roles in host-virus interactions, spreading stress resilience and metabolic genes to ensure host survival; the virus-host interactions are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.
Article
Microbiology
Carl-Eric Wegner, Raphaela Stahl, Irina Velsko, Alex Huebner, Zandra Fagernaes, Christina Warinner, Robert Lehmann, Thomas Ritschel, Kai U. Totsche, Kirsten Kuesel
Summary: By adapting methods from microbial archaeology and paleogenomics, we recovered sufficient DNA from seven rock specimens for metagenomic analysis. Limestones serve as archives for genetic records of past microbial communities, including those sensitive to environmental stress, due to specific conditions facilitating long-term DNA preservation.
Article
Plant Sciences
Jonathan E. Maldonado, Alexis Gaete, Dinka Mandakovic, Constanza Aguado-Norese, Melissa Aguilar, Rodrigo A. Gutierrez, Mauricio Gonzalez
Summary: The discovery and characterization of plant species adapted to extreme environmental conditions, such as Hoffmannseggia doellii in the Chilean Atacama Desert, have become important. This study found that H. doellii has a higher microbial diversity in its root soil, suggesting a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, the study provides an opportunity for future research on the climate change adaptation of crop plants.
Article
Agricultural Engineering
Rajeev K. Sukumaran, Meera Christopher, Prajeesh Kooloth-Valappil, AthiraRaj Sreeja-Raju, Reshma M. Mathew, Meena Sankar, Anoop Puthiyamadam, Velayudhanpillai-Prasannakumari Adarsh, Aswathi Aswathi, Valan Rebinro, Amith Abraham, Ashok Pandey
Summary: Fungal biomass degrading enzymes are crucial for biorefineries, but limited by the cost of biomass hydrolyzing enzymes. Current research focuses on improving the quantity and quality of enzymes secreted by fungi. Further production enhancements require modifying fungal metabolism.
BIORESOURCE TECHNOLOGY
(2021)
Article
Geosciences, Multidisciplinary
Franko Arenas-Diaz, Barbara Fuentes, Mark Reyers, Stephanie Fiedler, Christoph Boehm, Eduardo Campos, Yaping Shao, Roland Bol
Summary: The Atacama Desert is one of the driest and oldest deserts on Earth. Aerosols are the main inputs of exogenous material to this system. However, despite its aridity, large dust outbreaks from the Atacama Desert are rare.
EARTH-SCIENCE REVIEWS
(2022)
Article
Chemistry, Applied
Tianming Yao, Dane G. Deemer, Ming-Hsu Chen, Bradley L. Reuhs, Bruce R. Hamaker, Stephen R. Lindemann
Summary: It is unclear how minor fiber structural differences impact microbiome composition and organismal metabolic responses. In this study, two sorghum arabinoxylans (SAXs) with slightly different branch linkages were fermented to examine their effect on microbial diversity and metabolic outcomes. The results showed that the fine polysaccharide structure exerted a deterministic selection effect on distinct fermenting consortia, leading to differences in species diversity and metabolic pathways.
CARBOHYDRATE POLYMERS
(2023)
Article
Biochemistry & Molecular Biology
Lakshan Paudel, Bashu Dev Pardhe, So-Ra Han, Jun Hyuck Lee, Tae-Jin Oh
Summary: The genomic analysis of Streptomyces sp. KCCM12257 identified 233 CAZyme genes, with a predominant glycosyl hydrolase family. Among them, a new chitosanase (MDI5907146) of GH46 family was characterized, which showed activity towards colloidal chitosan. The enzyme hydrolyzes colloidal chitosan into monoacetyl chitobiose and exhibits optimum activity at pH 6.5 and 40 degrees C.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Microbiology
Katerina Nemeckova, Jan Mares, Lenka Prochazkova, Adam Culka, Filip Kosek, Jacek Wierzchos, Linda Nedbalova, Jan Dudak, Veronika Tymlova, Jan Zemlicka, Andreja Kust, Jan Zima, Eva Novakova, Jan Jehlicka
Summary: This study used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum from various sites in Sicily. Cyanobacteria were found to be the dominant microorganisms in these environments, forming differently pigmented zones within the gypsum. The study also revealed differences in the taxonomic composition of endoliths in different gypsum varieties and identified carotenoids as the most common pigments present. These findings provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum, highlighting the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Maria Jose Guevara-Araya, Victor M. Escobedo, Valeria Palma-Onetto, Marcia Gonzalez-Teuber
Summary: This study investigated the relationship between the diversity and community composition of root-associated fungal endophytes (FE) and aridity in the coastal areas of the Atacama Desert in Chile. The results showed that FE richness was negatively correlated with aridity, and soil water availability significantly influenced FE community composition. Our findings highlight the importance of climate-related factors in shaping changes in FE diversity, structure, and distribution in desert ecosystems.
Article
Microbiology
Samah O. Noor, Dhafer A. Al-Zahrani, Refaei M. Hussein, Mohammed N. Baeshen, Tarek A. A. Moussa, Salah M. Abo-Aba, Ahmed M. Al-Hejin, Nabih A. Baeshen, John P. Huelsenbeck
Summary: This study compared the fungal rhizosphere communities of different plants and gut mycobiota of an insect, revealing significant differences in diversity and abundance of fungi among different plants and insect gut.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Ecology
Christian Santander, Susana Garcia, Jorge Moreira, Humberto Aponte, Paola Araneda, Jorge Olave, Gladys Vidal, Pablo Cornejo
Summary: The study found that arbuscular mycorrhizal fungi are widely present in different elevation belts of the Atacama Desert, and they have a strong relationship with soil electrical conductivity and cation content.
Article
Plant Sciences
Gisela C. Stotz, Cristian Salgado-Luarte, Alonso T. Vigil, Henry J. De la Cruz, Victor Pasten-Marambio, Ernesto Gianoli
Summary: The study shows that decreased precipitation leads to lower species diversity and abundance within habitat islands. However, species loss is found to be stochastic, with functional diversity remaining stable. Species lost in drier sites were mainly those with lower functional redundancy.
Article
Environmental Sciences
Qian Zhang, Xiaoqing Xu, Junguang Duan, Roger T. Koide, Lei Xu, Jianmin Chu
Summary: Using a metagenomic approach, this study revealed that grassland degradation significantly affects the abundance and composition of carbohydrate-active enzyme (CAZYme) genes responsible for C cycling. Severely degraded grassland showed higher CAZyme abundance compared to other degradation severities. The interaction between degradation severity, soil depth, and soil carbon fractions influenced the composition of CAZyme gene families.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Bruno Francesco Rodrigues de Oliveira, Isabelle Rodrigues Lopes, Anna Luiza Bauer Canellas, Guilherme Muricy, Stephen Anthony Jackson, Alan D. W. Dobson, Marinella Silva Laport
Summary: The genome of sponge-associated microorganism Pseudoalteromonas sp. PA2MD11 contains a variety of carbohydrate-active enzymes with potential for degrading marine polysaccharides, including GHs and PLs families. The complete metabolism of agar and alginate by PA2MD11 was predicted, and structural protein analyses showed conservation of catalytic machinery and suitable industrially-relevant features in the enzymes. This bacterium is a potential source of biocatalysts for marine polysaccharide degradation and production of pharmacologically active oligosaccharides.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Editorial Material
Microbiology
Benito Gomez-Silva, Ramon Alberto Batista-Garcia
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Gerardo E. Rodea, Edgar Gonzalez-Villalobos, Oscar Medina-Contreras, Hugo G. Castelan-Sanchez, Pamela Aguilar-Rodea, Norma Velazquez-Guadarrama, Ulises Hernandez-Chinas, Carlos Alberto Eslava-Campos, Jose Luis Balcazar, Jose Molina-Lopez
Summary: This study sequenced and characterized the genomes of two lytic bacteriophages, showing their lytic activity against multidrug-resistant Escherichia coli strains and the absence of antibiotic resistance, lysogenic and virulence genes.
MICROBIAL PATHOGENESIS
(2022)
Article
Environmental Sciences
Giorgio Maria Vingiani, Serena Leone, Daniele De Luca, Marco Borra, Alan D. W. Dobson, Adrianna Ianora, Pasquale De Luca, Chiara Lauritano
Summary: Diatoms are photosynthetic organisms with potential applications in bioremediation, capable of degrading pollutants. In this study, two putative DBP hydrolases were identified in the transcriptome of a diatom species, and their structures and interactions with the substrate were analyzed. The expression levels of these hydrolases increased in response to DBP exposure, indicating their potential involvement in phthalates degradation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Clodagh M. Carr, Bruno Francesco Rodrigues de Oliveira, Stephen A. Jackson, Marinella Silva Laport, David J. Clarke, Alan D. W. Dobson
Summary: Many marine bacteria, including those from sea sponges, have the potential to produce polyesterase enzymes that can degrade PET plastic. In this study, a Brachybacterium ginsengisoli isolate from a deep-sea sponge was found to produce a polyesterase enzyme, named BgP. The enzyme showed high similarity to other well-characterized PET hydrolases and exhibited polyesterase activity when expressed in Escherichia coli.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Selene Zarate, Blanca Taboada, Jose Esteban Munoz-Medina, Pavel Isa, Alejandro Sanchez-Flores, Celia Boukadida, Alfredo Herrera-Estrella, Nelly Selem Mojica, Mauricio Rosales-Rivera, Bruno Gomez-Gil, Angel Gustavo Salas-Lais, Clara Esperanza Santacruz-Tinoco, Hector Montoya-Fuentes, Julio Elias Alvarado-Yaah, Gloria Maria Molina-Salinas, Gloria Elena Espinoza-Ayala, Jose Antonio Enciso-Moreno, Rosa Maria Gutierrez-Rios, Antonio Loza, Joaquin Moreno-Contreras, Rodrigo Garcia-Lopez, Xaira Rivera-Gutierrez, Andreu Comas-Garcia, Rosa Maria Wong-Chew, Maria-Eugenia Jimenez-Corona, Rosa Maria del Angel, Joel Armando Vazquez-Perez, Margarita Matias-Florentino, Marissa Perez-Garcia, Santiago Avila-Rios, Hugo G. Castelan-Sanchez, Luis Delaye, Leon P. Martinez-Castilla, Marina Escalera-Zamudio, Susana Lopez, Carlos F. Arias
Summary: The B.1.1.7 (Alpha) lineage of SARS-CoV-2 emerged and rapidly increased worldwide, but did not become the dominant lineage in most of Mexico. The states at the Mexico-U.S. border had the highest prevalence of B.1.1.7 and showed the highest lineage diversity, suggesting possible introductions from the United States. Community transmission of B.1.1.7 occurred in Mexico, as evidenced by localized distribution and specific mutations.
MICROBIOLOGY SPECTRUM
(2022)
Article
Agricultural Engineering
Benteng Wu, Richen Lin, Xue Ning, Xihui Kang, Chen Deng, Alan D. W. Dobson, Jerry D. Murphy
Summary: This study investigated the addition of pyrochar and graphene to improve medium-chain fatty acid production in microbial chain elongation fermentation. Results showed that adding pyrochar significantly enhanced the yield and selectivity of C6 n-caproate. The high electrical conductivity and surface redox groups of pyrochar were postulated to be the reasons for these improvements.
BIORESOURCE TECHNOLOGY
(2022)
Article
Microbiology
Bernardo Gutierrez, Hugo G. Castelan Sanchez, Darlan da Silva Candido, Ben Jackson, Shay Fleishon, Renaud Houzet, Christopher Ruis, Luis Delaye, Nuno R. Faria, Andrew Rambaut, Oliver G. Pybus, Marina Escalera-Zamudio
Summary: This study presents a phylogenetic analysis of SARS-CoV-2 lineages and identifies a recombination event between B.1.631 and B.1.634 lineages, resulting in the formation of the B.1.628 major cluster (lineage XB). The spatiotemporal distribution supports the conclusion that the recombination event originated in the USA and Mexico.
CELL HOST & MICROBE
(2022)
Article
Microbiology
Claudia Vilo, Qunfeng Dong, Alexandra Galetovic, Benito Gomez-Silva
Summary: The microbiome of edible Llayta, macrocolonies of cyanobacterial found in Andean wetlands, has been explored through a culture-independent approach. The study identified and reconstructed the metagenomic genome of Cyanocohniella sp. LLY associated with Llayta trichomes. This is the first genome available for members of this genus and provides new insights into their metabolic capabilities.
Article
Microbiology
Armando Navarro, Gerardo E. Rodea, Hugo G. Castelan-Sanchez, Hector Armando Saucedo-Pastrana, Delia Licona-Moreno, Carlos Eslava-Campos, Laura L. Tirado-Gomez, Ariel Vilchis-Reyes, Guadalupe Garcia de la Torre, Veronica Cruz-Licea
Summary: Antimicrobial resistance is a global public health problem, and microbiome bacteria may contribute to the horizontal gene transfer associated with antimicrobial resistance. Analysis of the microbiome from fecal samples of Mexican adolescents revealed the presence of common bacteria and multiple antimicrobial resistance genes. Some of these microorganisms may serve as important reservoirs for the transfer of antimicrobial resistance genes.
Review
Biochemistry & Molecular Biology
Jose Luis Villalpando-Aguilar, Gilberto Matos-Pech, Itzel Lopez-Rosas, Hugo Gildardo Castelan-Sanchez, Fulgencio Alatorre-Cobos
Summary: Phage therapy is an alternative treatment that uses bacteriophages to kill specific bacteria. It has shown positive results in improving food production in agriculture. However, finding effective bacteriophages is crucial for the success of this therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Camila Salazar-Ardiles, Alexander Perez-Arancibia, Leyla Asserella-Rebollo, Benito Gomez-Silva
Summary: Significant knowledge has been gained about the microbiome in the hyperarid Atacama Desert, but information on the Atacama free-living amoebae (FLA) is limited and more efforts are needed. The dominant presence of Acanthamoeba genus has been reported in water and sediment samples from the Loa and Salado rivers in northern Chile, indicating the need for further exploration of Atacama amoebae in other wetlands in the region.
Article
Evolutionary Biology
Marina Escalera-Zamudio, Sergei L. Kosakovsky Pond, Natalia Martinez de la Vina, Bernardo Gutierrez, Rhys P. D. Inward, Julien Theze, Lucy van Dorp, Hugo G. Castelan-Sanchez, Thomas A. Bowden, Oliver G. Pybus, Ruben J. G. Hulswit
Summary: Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Virology
Hugo G. Castelan-Sanchez, Leon P. Martinez-Castilla, Gustavo Sganzerla-Martinez, Jesus Torres-Flores, Gamaliel Lopez-Leal
Summary: This study infers the initial introduction of Omicron in Mexico and evaluates the impact of human mobility on virus spread. The study also identifies adaptive evolutionary processes in the Mexican SARS-CoV-2 genomes during the first month of Omicron circulation. The presence of diversifying natural selection and mutations related to immune evasion are found in the Omicron genomes.