Article
Environmental Sciences
Qingling Wang, Jinyu Hou, Ya Huang, Wuxing Liu, Peter Christie
Summary: A bacterial consortium called WPB was obtained from PAHs-contaminated soil and showed efficient degradation ability. Metagenomic sequencing and analysis revealed the mechanisms of pollutant degradation and the contribution of different bacteria.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Xingjie Wu, Christopher Rensing, Dongfei Han, Ke-Qing Xiao, Yuexiu Dai, Zhixi Tang, Werner Liesack, Jingjing Peng, Zhenling Cui, Fusuo Zhang
Summary: Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability. This study investigated the microbial mechanisms involved in phosphorus cycling under different agricultural and reforestation treatments. The findings revealed distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils, with phosphate solubilization dominating in agricultural soils and phosphate transport prevailing in reforestation soils.
Article
Environmental Sciences
Xingjie Wu, Pengfei Liu, Carl-Eric Wegner, Yu Luo, Ke-Qing Xiao, Zhenling Cui, Fusuo Zhang, Werner Liesack, Jingjing Peng
Summary: The study shows that organic material amendments significantly influence the link between microbial life history strategies and soil organic carbon storage, with a one-time peat-vermiculite application notably increasing organic carbon storage efficiency.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Microbiology
Ifeoma R. Ugwuanyi, Marilyn L. Fogel, Roxane Bowden, Andrew Steele, Giuseppe De Natale, Claudia Troise, Renato Somma, Monica Piochi, Angela Mormone, Mihaela Glamoclija
Summary: In this study, metagenomes were used to investigate the ecology of different substrates in the Solfatara and Pisciarelli regions. The results showed that the substrates in Solfatara had similar chemistry, while those in Pisciarelli varied. Species alpha diversity differed between locations but not across substrates, and pH was found to be the most important driver of diversity and microbial community composition. Carbon fixation and sulfur oxidation were the most important metabolic pathways at both locations.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Jannie Munk Kristensen, Caitlin Singleton, Lee-Ann Clegg, Francesca Petriglieri, Per Halkjaer Nielsen
Summary: Microbial communities in Danish full-scale activated sludge wastewater treatment plants are rich in Acidobacteriota taxa, which show high metabolic diversity and potential involvement in nitrogen and phosphorus removal and iron reduction. Genome annotation and metabolic reconstruction of Acidobacteriota metagenome-assembled genomes reveal their potential to be polyphosphate-accumulating organisms (PAOs) with intracellular storage of key compounds.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Adrien Vigneron, Perrine Cruaud, Frederic Ducellier, Ian M. Head, Nicolas Tsesmetzis
Summary: Metagenomic studies have shown the impact of oil production on microbial ecology in petroleum reservoirs, with a particular focus on microbial activities during decommissioning. Analysis of planktonic microbial communities in the aqueous phase of a subsea oil-storage structure reveals a unique microbiome dominated by Dethiosulfatibacter and Cloacimonadetes, showing potential for degradation of low molecular weight aromatic hydrocarbons. Genomic data informs decommissioning strategies in marine environments and highlights differences in hydrocarbon-degrading community composition between man-made structures and natural marine environments rich in hydrocarbons.
Article
Engineering, Environmental
Jiangtao Qiao, Jingyu Liu, Alejandro Palomo, Benjamin C. C. Bostick, Kongkea Phan, Yan Zheng, Fangbai Li
Summary: Microbially mediated inorganic-methylated arsenic transformation is crucial to rice safety. Bacteria harbor the most genes related to arsenic biotransformation, and some bacteria contain both arsM and arsI genes. The presence of the methylated arsenic pool and the arsenic methylation-demethylation cycle should be considered in paddy fields for rice safety.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Environmental Sciences
Meng Zhou, Zishu Liu, Baofeng Zhang, Jiawen Yang, Baolan Hu
Summary: Microorganisms responsible for arsenic metabolism were identified and their metabolism pathways were constructed. The study showed that arsenic reduction genes played a dominant role in arsenic metabolism and had significant impacts on microbial energy metabolism, DNA replication and repair, and membrane transport. This research is of great importance for understanding the migration and transformation behavior of arsenic in soil.
ENVIRONMENTAL POLLUTION
(2022)
Article
Environmental Sciences
Lifang Hu, Yating Qian, Manting Ci, Yuyang Long, Haozhe Zheng, Ke Xu, Yuqian Wang
Summary: This study reveals the temperature influence on arsenic methylation behavior in the leachate-saturated zone (LSZ) of landfills. By analyzing microbial diversity and functional gene quantification, nine potential species that can independently complete methylation processes were identified. These findings have significant implications for the management of arsenic contamination in landfills.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Davide Albanese, Claudia Coleine, Omar Rota-Stabelli, Silvano Onofri, Susannah G. Tringe, Jason E. Stajich, Laura Selbmann, Claudio Donati
Summary: The study generated the first bacterial genomes from rocks collected in Continental Antarctica, clustering 269 candidate species, with Actinobacteria being the most abundant and Candidatus Jiangella antarctica being recorded in all samples. Most of these new species belong to monophyletic bacterial clades that are functionally distinct from known related taxa.
Article
Biology
Jagdish Parihar, Suraj P. Parihar, Prashanth Suravajhala, Ashima Bagaria
Summary: This study presents a systematic investigation of microbial communities in arid and semi-arid regions of Thar Desert in India. The study evaluates their response to multiple environmental stresses and assesses their biotechnological potential. The results provide a detailed understanding of the abundance of microbial communities in these regions, associated with stress-related biogeochemical and biotechnological processes. This work is important for the development of effective strategies for the use of extremophiles in complex environments.
Article
Biochemistry & Molecular Biology
Fernando Puente-Sanchez, Matthias Hoetzinger, Moritz Buck, Stefan Bertilsson
Summary: Microorganisms exhibit high adaptability at the genome level, with heritable traits emerging in response to environmental niches. The pangenome concept, which partitions genomes into core and accessory regions, is valuable for studying microbial ecology and evolution. In this study, SuperPang, an algorithm that generates pangenome assemblies from input genomes, is presented. SuperPang provides a modular view of the pangenome, allowing the analysis of allelic and gene content variation. The algorithm is demonstrated through an analysis of intra-species diversity in the Polynucleobacter genus.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Microbiology
Avishek Dutta, Elizabeth Connors, Rebecca Trinh, Natalia Erazo, Srishti Dasarathy, Hugh W. W. Ducklow, Deborah K. K. Steinberg, Oscar M. M. Schofield, Jeff S. S. Bowman
Summary: The study investigates the genetic and metabolic diversity of Antarctic marine microbes through sequencing DNA samples collected in the western Antarctic Peninsula. A metagenomics pipeline was developed to process the data and construct metagenome-assembled genomes (MAGs). The study shows that microbial community functions vary based on depth, with bacteria carrying diverse genes for carbohydrate transformation. The research provides valuable insights for future Antarctic genomics research.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Agronomy
Richard Allen White, Aaron Garoutte, Emily E. Mclachlan, Lisa K. Tiemann, Sarah Evans, Maren L. Friesen
Summary: The rhizosphere microbiome plays a critical role in nitrogen cycling and overall plant nutrient uptake for switchgrass. Nitrogen fertilizer has little effect on the microbial community, but it depletes the metabolic potential of carbohydrate-active enzymes. The study also suggests that the rhizosphere microbiome may provide associative nitrogen fixation to switchgrass through a novel diazotroph Janthinobacterium.
Article
Genetics & Heredity
Arunmozhi Bharathi Achudhan, Priya Kannan, Lilly M. Saleena
Summary: Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. Metagenome assembled genomes (MAGs) were used to identify the CRISPR sequence and study the interactions between bacteria and phages. Through computational analysis of metagenomic data from a coal mine, the study identified 78 non-redundant MAGs containing CRISPR elements. By searching against the VIROblast database, the study found that these MAGs have interactions with uncultured Caudovirales phages. This unconventional metagenomics workflow provides insights into bacteria and phage interactions.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Soil Science
Barbara Fuentes, Francisco Gomez, Catalina Valdez, Anael Videla, Juan Castro-Severyn, Sergio Barahona, Roland Bol, Rodrigo Riquelme, Javier Quispe, Francisco Remonsellez
Summary: This study examined the effects of coastal fog on soil properties and microbial diversity in different altitudes of Morro Moreno National Park in Chile. The results showed that coastal fog influences the temperature, humidity, and chemical characteristics of the soil. It also affects the microbial communities, with different microbial groups dominating at different altitudes.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2022)
Article
Respiratory System
Yoshihiko Raita, Marcos Perez-Losada, Robert J. Freishtat, Andrea Hahn, Eduardo Castro-Nallar, Ignacio Ramos-Tapia, Nathaniel Stearrett, Yury A. Bochkov, James E. Gern, Jonathan M. Mansbach, Zhaozhong Zhu, Carlos A. Camargo, Kohei Hasegawa
Summary: Through transcriptome and clustering analysis, we identified biologically distinct metatranscriptome profiles with differential risks of asthma in infant bronchiolitis.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Forestry
Antonio Varas-Myrik, Francisco Sepulveda-Espinoza, Alex Fajardo, Diego Alarcon, Oscar Toro-Nunez, Eduardo Castro-Nallar, Rodrigo Hasbun
Summary: Understanding adaptive genetic variation is crucial for predicting species response to climate change. By analyzing the genomic structure and environmental relationships, researchers can predict genetic risks in different populations. This study found that populations in low elevation regions of the Andes face higher risk of maladaptation compared to those in high elevation areas.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Article
Microbiology
Barbara Fuentes, Alessandra Choque, Francisco Gomez, Jaime Alarcon, Eduardo Castro-Nallar, Franko Arenas, Daniel Contreras, Ramona Moerchen, Wulf Amelung, Claudia Knief, Ghazal Moradi, Erwin Klumpp, Claudia P. Saavedra, Joerg Prietzel, Wantana Klysubun, Francisco Remonsellez, Roland Bol
Summary: This study analyzed microbial communities in the hyperarid Yungay region of the Atacama Desert, down to a depth of 3.4m, and found that different depth intervals had specific physicochemical features and microbial composition. Moisture content, total carbon, pH, and electric conductivity were the most predictive factors for microbial richness and diversity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Jun Wu, David Danko, Ebrahim Afshinnekoo, Daniela Bezdan, Malay Bhattacharyya, Eduardo Castro-Nallar, Agnieszka Chmielarczyk, Nur Hazlin Hazrin-Chong, Youping Deng, Emmanuel Dias-Neto, Alina Frolova, Gabriella Mason-Buck, Gregorio Iraola, Soojin Jang, Pawel Labaj, Patrick K. H. Lee, Marina Nieto-Caballero, Olayinka O. Osuolale, Christos A. Ouzounis, Michael H. Perlin, Bharath Prithiviraj, Nicolas Rascovan, Anna Rozanska, Lynn M. Schriml, Torsten Semmler, Haruo Suzuki, Juan A. Ugalde, Ben Young, Johannes Werner, Maria Mercedes Zambrano, Yongxiang Zhao, Christopher Mason, Tieliu Shi
Summary: Microbes play a crucial role in maintaining ecological functions that support human health and city life in urban ecosystems. However, knowledge about the species and functions in urban environments is limited. In this study, we identified 732 novel bacterial species from 4728 samples collected from the mass transit system in 60 cities. The number of novel species was positively correlated with city population, and more species were found in skin-associated samples. We also discovered an increased presence of biosynthetic gene clusters in novel species.
ENVIRONMENTAL RESEARCH
(2022)
Article
Environmental Sciences
Yoelvis Sulbaran-Bracho, Matias Orellana-Saez, Juan Castro-Severyn, Cristobal Galban-Malagon, Eduardo Castro-Nallar, Ignacio Poblete-Castro
Summary: More than 21,000 tons of diesel oil were accidentally released into the environment in 2020, with water bodies being the most contaminated. Sustainable technologies are urgently needed to clean up rivers and oceans in order to protect wildlife and human health. Bacterial consortia, especially those from Antarctic microorganisms, show promise in diesel degradation, but their effectiveness at higher temperatures compared to their natural habitats remains uncertain.
ENVIRONMENTAL POLLUTION
(2023)
Article
Microbiology
Marcos Perez-Losada, Eduardo Castro-Nallar, Jose Laerte Boechat, Luis Delgado, Tiago Azenha Rama, Valentin Berrios-Farias, Manuela Oliveira
Summary: Allergic rhinitis and asthma lead to dysbiosis of nasal bacteriome, which can be potential biomarkers for diagnostics and therapeutics. This study provides insights into the distinct bacteriota in the nose during health and respiratory diseases.
Article
Microbiology
Sergio Guajardo-Leiva, Katterinne N. Mendez, Claudio Meneses, Beatriz Diez, Eduardo Castro-Nallar
Summary: While progress has been made in studying microbial and viral communities in the oceans, the coastal waters of Northern Patagonia, particularly the Comau Fjord, remain understudied despite high-density salmon farming and other disturbances. In this study, the researchers found that the microbial and viral communities in the Comau Fjord were distinct from global surveys but shared similarities with cosmopolitan marine microbes and known viral members from North America and the southern oceans. They also discovered functional enrichment of antibiotic resistance genes (ARGs), indicating the potential impact of salmon farming and anthropogenic activities. These findings highlight the importance of further research on the diversity, resilience, and resistance of these communities.
Article
Microbiology
Eduardo Castro-Nallar, Valentin Berrios-Farias, Beatriz Diez, Sergio Guajardo-Leiva
Summary: This study provides 48 viral metagenomes and 5,656 viral operational taxonomic units (vOTUs) from Comau Fjord, Patagonia (42 degrees S), to understand viral-mediated processes in coastal and estuarine waters.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Eduardo Castro-Nallar, Valentin Berrios-Farias, Beatriz Diez, Sergio Guajardo-Leiva
Summary: This article presents a study on 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42 degrees S) to explore the microbial dynamics and their response to anthropogenic disturbances.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Sergio Guajardo-Leiva, Valentin Berrios-Farias, Felipe G. Bermudez, Eduardo Castro-Nallar
Summary: Sentinel species can be used to monitor environmental disturbances. In this study, 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of South American sea lions were analyzed to assess whether changes in gut microbiome composition and gene content could indicate environmental disturbances from salmon farming.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Review
Environmental Sciences
Claudia Egas, Cristobal Galban-Malagon, Eduardo Castro-Nallar, Marco A. Molina-Montenegro
Summary: The Arctic and the Antarctic Continent are two eco-regions with extreme climatic conditions. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in these polar ecosystems has been well-documented since the 1960s and continues to pose a threat to biodiversity and the ecosystem. Microorganisms in polar environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes, making bioremediation by native microorganisms a feasible strategy to mitigate SVOCs presence. A comprehensive approach at the molecular and ecological level is required to address the slow degradation and accumulation of SVOCs in polar ecosystems, with implications for the preservation of these ecosystems at a global level.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Microbiology
Valentina B. Pavez, Nicolas Pacheco, Juan Castro-Severyn, Coral Pardo-Este, Javiera Alvarez, Phillippi Zepeda, Gabriel Kruger, Karem Gallardo, Francisco Melo, Rolando Vernal, Carlos Aranda, Francisco Remonsellez, Claudia P. Saavedra
Summary: In this study, the capacity of Exiguobacterium strains isolated from the Salar de Huasco in Chile to form biofilms in the presence of arsenic was assessed to understand their resistance mechanisms to this heavy metal. The results showed that these strains exhibit a significant ability to form biofilms when exposed to arsenic, shedding light on the underlying mechanisms. These findings enhance our understanding of biofilm formation, its role in arsenic resistance, and the adaptive strategies employed by bacteria in extreme environments.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biology
A. C. Briones, D. Lorca, A. Cofre, C. E. Cabezas, G. I. Krueger, C. Pardo-Este, M. S. Baquedano, C. R. Salinas, M. Espinoza, J. Castro-Severyn, F. Remonsellez, A. A. Hidalgo, E. H. Morales, C. P. Saavedra
Summary: Our study evaluated the transcriptional and post-transcriptional regulation of ompX under H2O2 stress in Salmonella Typhimurium. We found that ompX expression is induced at the transcriptional level, but unexpectedly, increased gene transcript and promoter activity do not lead to elevated protein levels, suggesting post-transcriptional regulation of ompX mRNA under oxidative stress. Through sequence analysis and inhibitory experiments, we demonstrated that sRNAs CyaR, MicA, OxyS, and the sRNA:mRNA chaperone Hfq positively modulate ompX mRNA levels in response to H2O2 stress.
BIOLOGICAL RESEARCH
(2022)