4.6 Article

A First Insight into the Microbial and Viral Communities of Comau Fjord-A Unique Human-Impacted Ecosystem in Patagonia (42° S)

Related references

Note: Only part of the references are listed.
Article Microbiology

Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis

Kento Tominaga et al.

Summary: There is little doubt that viral infection is prevalent among abundant marine prokaryotes. However, evaluating viral infections in natural prokaryotic communities is technically difficult. This study examined viral infection in abundant prokaryotes by monitoring their monthly dynamics, indicating that viral infection is prevalent regardless of host taxa or temporal dynamics.

MSYSTEMS (2023)

Review Microbiology

Antibiotic resistance in the environment

D. G. Joakim Larsson et al.

Summary: Antibiotic resistance is a global health challenge, with factors driving evolution and transmission being important to quantify and identify. The environment plays a crucial role, and understanding and managing the resistance crisis can be achieved through implementing monitoring and assessment methods to reduce risks.

NATURE REVIEWS MICROBIOLOGY (2022)

Article Microbiology

Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Neza Orel et al.

Summary: This study investigated the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators in a coastal ecosystem subjected to different anthropogenic pressures. The results showed that the coastal microbiome was primarily influenced by seasonal changes, while fecal bacterial indicators were not affected by seasons. Riverine water was found to be an important vector for the transmission of allochthonous microbes into the marine system, including potential pathogenic bacteria. Molecular analysis combined with statistical and oceanographic models can provide new insights into the potential sources and presence of microbial indicators that are overlooked by cultivation methods.

FRONTIERS IN MICROBIOLOGY (2022)

Article Biotechnology & Applied Microbiology

Responses of the Soil Bacterial Community, Resistome, and Mobilome to a Decade of Annual Exposure to Macrolide Antibiotics

Liam P. Brown et al.

Summary: This study evaluated the effects of long-term and repeated exposure to macrolide antibiotics on the diversity of soil bacterial community, resistome, and mobilome. At unrealistically high concentrations, macrolide antibiotics altered the overall diversity of resistome and mobilome, enriching for antibiotic resistance genes and mobile genetic elements of concern to human health. However, at realistic antibiotic concentrations, no effect on these endpoints was observed, suggesting that current biosolids land management practices are unlikely to pose a risk to human health due to macrolide antibiotic contamination alone.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2022)

Article Environmental Sciences

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes

Andres E. Marcoleta et al.

Summary: The Antarctic Peninsula soil hosts a wide range of microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. These bacteria show resistance to a variety of antibiotics, with some isolates demonstrating resistance to multiple compounds. Genome analysis revealed the presence of efflux pump genes and unknown mechanisms for resistance to certain antibiotics, suggesting a potential source of novel resistance genes.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Review Fisheries

Use of antimicrobials in Chilean Salmon farming: Facts, myths and perspectives

Ruben Avendano-Herrera et al.

Summary: Chile, the second largest producer of salmon, is facing concerns over the intensive use of antimicrobials in its salmon farming industry. This review provides a comprehensive analysis of the historical and current use of antimicrobials in Chilean salmonid farming, as well as the impacts on the environment and antibiotic resistance. It aims to clarify outdated or poorly supported information in existing literature and offers recommendations for reducing antimicrobial use and controlling bacterial fish pathogens.

REVIEWS IN AQUACULTURE (2022)

Article Infectious Diseases

Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon

Marilia Salgado-Caxito et al.

Summary: This study evaluated the risk perception of antimicrobial resistance (AMR) through consuming salmon fillets that have been treated with antibiotics. Results showed that the overall probability of acquiring AMR through consuming treated salmon fillets was low. However, there were slight variations in risk perception between different production stages, possibly due to bacterial infections and the use of antibiotics.

ANTIBIOTICS-BASEL (2022)

Article Environmental Sciences

Long-term airborne particle pollution assessment in the city of Coyhaique, Patagonia, Chile

Rafael Solis et al.

Summary: An assessment of air pollution in a small city in the Chilean Patagonia was conducted using PM concentration data from two monitoring stations over a period of seven years. The study analyzed the city's pollution variability, the impact of meteorological factors, and long-term trends. The results showed that the high PM concentrations observed during the coldest months were mainly due to the use of firewood for heating and cooking. The most polluted days were associated with low temperatures, low wind speed, and high PM2.5/PM10 ratios, indicating a dominance of local firewood sources. Despite a decrease in PM concentrations over time, the annual average PM levels in Coyhaique exceeded national and international air quality thresholds, highlighting the severity of the air pollution problem in the city.

URBAN CLIMATE (2022)

Article Engineering, Environmental

Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments

Cheng Chen et al.

Summary: Both traditional petroleum-based and emerging biodegradable microplastics promote N2O production in sediment, but the pathways vary. Biodegradable polylactic acid (PLA) microplastics have a greater promotion of N2O production compared to petroleum-based polyvinyl chloride (PVC) and polyethylene (PE), with PLA promoting it through nitrifier nitrification and heterotrophic denitrification, PE through nitrifier denitrification and heterotrophic denitrification, and PVC through nitrifier nitrification. Different nitrogen cycling microbes' response to microplastics leads to the differences in N2O increase pathways, with nitrifying bacteria significantly enriched in all microplastic treatments, while part of denitrifying bacteria significantly enriched in treatments containing PLA and PE microplastics.

WATER RESEARCH (2022)

Article Microbiology

Supercarriers of antibiotic resistome in a world's large river

Jiawen Wang et al.

Summary: By studying the Yangtze River, it was found that human pathogen bacteria are the major hosts of antibiotic resistance genes in the river, rather than conventional supercarriers that are prevalent in the human gut. This discovery not only explains the inconsistency between the spatial distribution of antibiotic resistance genes and their hosts, but also emphasizes the importance of controlling terrestrial pathogenic bacteria in the global riverine ecosystems.

MICROBIOME (2022)

Article Environmental Sciences

Antibiotic resistant genes in the environment-exploring surveillance methods and sustainable remediation strategies of antibiotics and ARGs

Amy R. Nava et al.

Summary: Antibiotic resistant genes are a growing environmental threat, with the potential to change the human microbiome and select for antibiotic resistant bacteria. There are multiple sources of antibiotics and antibiotic resistant genes in the environment, and it is important to assess their dissemination and develop effective surveillance and remediation strategies. Global interdisciplinary efforts are required to address this problem.

ENVIRONMENTAL RESEARCH (2022)

Review Microbiology

Role of pollution on the selection of antibiotic resistance and bacterial pathogens in the environment

Elena Buelow et al.

Summary: Research indicates that human activities causing pollution contribute to the selection of bacterial pathogens in the environment. Specifically, pollutants associated with human waste are believed to lead to genetic selection in bacterial populations, resulting in the emergence of bacterial pathogens. Scientists have identified key pollutants linked to antibiotic resistance and are discussing ways to prevent their release into the environment.

CURRENT OPINION IN MICROBIOLOGY (2021)

Article Environmental Sciences

Spatial and temporal distribution of Persistent Organic Pollutants and current use pesticides in the atmosphere of Argentinean Patagonia

Karina S. B. Miglioranza et al.

Summary: XAD-based passive air samplers were used to evaluate pollutants in the atmosphere of Argentine Patagonia, showing variable concentrations of pesticides and industrial contaminants. Higher levels of pollutants were observed along the Patagonian coast, with the highest values recorded in an industrial area downwind of intensively agriculturally used areas.

CHEMOSPHERE (2021)

Article Microbiology

Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats

Sergio Guajardo-Leiva et al.

Summary: The study reveals that viruses in hot springs exert diverse impacts on their host community through lytic and lysogenic replicative cycles, with different virus types associated with specific host taxa with varying metabolic capacities. Lytic viruses primarily infect cyanobacteria, while lysogenic viruses are linked to chemoheterotrophic bacteria, possessing accessory genes to regulate stress-related processes in their hosts. The observations suggest a connection between the ecological role of the host and the type of viral lifestyle in thermophilic microbial mats.

MICROBIOLOGY SPECTRUM (2021)

Article Microbiology

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

Mengqi Sun et al.

Summary: This study is the first systematic investigation of the spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. The results show a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, with genomes only available thanks to single-cell genomics or single-molecule sequencing. The study highlights the importance of these methods for viral discovery and reveals significant distinctions between estuarine and open ocean viromes.

MSYSTEMS (2021)

Article Biochemistry & Molecular Biology

A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko et al.

Summary: This study establishes a global metagenomic atlas of urban microbial ecosystems, revealing a vast number of unknown microbial species and genetic elements, highlighting the distribution of antibiotic resistance genes in cities, and indicating the influence of geographical and climatic characteristics on urban microbial composition.
Article Engineering, Environmental

Shotgun metagenomics assessment of the resistome, mobilome, pathogen dynamics and their ecological control modes in full-scale urban wastewater treatment plants

Popi Karaolia et al.

Summary: Both full-scale UWTPs significantly reduced BOD5 (99.4-99.9%), COD (97.6-99.4%) and TSS (98.9-99.9%). MBR was more effective in reducing the abundance and diversity of pathogen-containing taxa, with 4 and 30 taxa enriched in MBR and CAS effluents, respectively.

JOURNAL OF HAZARDOUS MATERIALS (2021)

Article Microbiology

Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities

Tomas Alarcon-Schumacher et al.

Summary: The viral communities in the Southern Ocean show high diversity and adaptability, with unique genomic features that provide insights into how viruses thrive and adapt in extreme polar marine environments. Through the study of novel viral genomes, this research expands our understanding of viral diversification and specific adaptations in the Southern Ocean.

MSYSTEMS (2021)

Review Geochemistry & Geophysics

GEOTRACES: Accelerating Research on the Marine Biogeochemical Cycles of Trace Elements and Their Isotopes

Robert F. Anderson

ANNUAL REVIEW OF MARINE SCIENCE, VOL 12 (2020)

Review Microbiology

Tara Oceans: towards global ocean ecosystems biology

Shinichi Sunagawa et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemistry & Molecular Biology

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Kern Rei Chng et al.

NATURE MEDICINE (2020)

Article Environmental Sciences

Aberrations in the microbiome of cyanobacteria from a tropical estuary polluted by heavy metals

C. Jasmin et al.

MARINE POLLUTION BULLETIN (2020)

Article Environmental Sciences

Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes

Yuyi Yang et al.

ENVIRONMENT INTERNATIONAL (2019)

Article Microbiology

Choice of assembly software has a critical impact on virome characterisation

Thomas D. S. Sutton et al.

MICROBIOME (2019)

Article Biochemistry & Molecular Biology

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Ann C. Gregory et al.

Article Microbiology

Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula

Tomas Alarcon-Schumacher et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Pharmacology & Pharmacy

Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance

Kimberley Sukhum et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2019)

Article Ecology

A horizon scan of priorities for coastal marine microbiome research

Stacey M. Trevathan-Tackett et al.

NATURE ECOLOGY & EVOLUTION (2019)

Article Environmental Sciences

Microplastic pollution in estuaries across a gradient of human impact

James N. Hitchcock et al.

ENVIRONMENTAL POLLUTION (2019)

Article Biochemistry & Molecular Biology

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

David Paez-Espino et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments

Antti Karkman et al.

NATURE COMMUNICATIONS (2019)

Article Environmental Sciences

Arctic antibiotic resistance gene contamination, a result of anthropogenic activities and natural origin

Lu Tan et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2018)

Review Microbiology

Current Status of the Use of Antibiotics and the Antimicrobial Resistance in the Chilean Salmon Farms

Claudio D. Miranda et al.

FRONTIERS IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

Benjamin J. Tully et al.

SCIENTIFIC DATA (2018)

Article Microbiology

Occurrence and abundance of antibiotic resistance genes in agricultural soil receiving dairy manure

Chad W. McKinney et al.

FEMS MICROBIOLOGY ECOLOGY (2018)

Article Multidisciplinary Sciences

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Adriana Alberti et al.

SCIENTIFIC DATA (2017)

Article Microbiology

Continental-scale pollution of estuaries with antibiotic resistance genes

Yong-Guan Zhu et al.

NATURE MICROBIOLOGY (2017)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Simon Roux et al.

NATURE (2016)

Article Computer Science, Interdisciplinary Applications

ggfortify: Unified Interface to Visualize Statistical Results of Popular R Packages

Yuan Tang et al.

R JOURNAL (2016)

Article Biotechnology & Applied Microbiology

Mash: fast genome and metagenome distance estimation using MinHash

Brian D. Ondov et al.

GENOME BIOLOGY (2016)

Article Multidisciplinary Sciences

Patterns and ecological drivers of ocean viral communities

Jennifer R. Brum et al.

SCIENCE (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Ross Overbeek et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Biochemistry & Molecular Biology

The role of aquatic ecosystems as reservoirs of antibiotic resistance

Elisabet Marti et al.

TRENDS IN MICROBIOLOGY (2014)

Article Microbiology

The Comprehensive Antibiotic Resistance Database

Andrew G. McArthur et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2013)

Article Multidisciplinary Sciences

Diverse and abundant antibiotic resistance genes in Chinese swine farms

Yong-Guan Zhu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

The oceanic biological pump modulates the atmospheric transport of persistent organic pollutants to the Arctic

Cristobal Galban-Malagon et al.

NATURE COMMUNICATIONS (2012)

Review Microbiology

Fundamentals of microbial community resistance and resilience

Ashley Shade et al.

FRONTIERS IN MICROBIOLOGY (2012)

Article Biochemical Research Methods

Quality control and preprocessing of metagenomic datasets

Robert Schmieder et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

Hanbo Chen et al.

BMC BIOINFORMATICS (2011)

Article Multidisciplinary Sciences

Antibiotic resistance is ancient

Vanessa M. D'Costa et al.

NATURE (2011)

Article Statistics & Probability

ggplot2

Hadley Wickham

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Public, Environmental & Occupational Health

Detection of the floR Gene in a Diversity of Florfenicol Resistant Gram-Negative Bacilli from Freshwater Salmon Farms in Chile

C. Fernandez-Alarcon et al.

ZOONOSES AND PUBLIC HEALTH (2010)

Article Biochemistry & Molecular Biology

ARDB-Antibiotic Resistance Genes Database

Bo Liu et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Ecology

The coasts of our world:: Ecological, economic and social importance

M. L. Martinez et al.

ECOLOGICAL ECONOMICS (2007)

Article Fisheries

Bacterial resistance to oxytetracycline in Chilean salmon farming

CD Miranda et al.

AQUACULTURE (2002)