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Microbiological Reviews Sep 1990The ecology of hydrocarbon degradation by microbial populations in the natural environment is reviewed, emphasizing the physical, chemical, and biological factors that... (Review)
Review
The ecology of hydrocarbon degradation by microbial populations in the natural environment is reviewed, emphasizing the physical, chemical, and biological factors that contribute to the biodegradation of petroleum and individual hydrocarbons. Rates of biodegradation depend greatly on the composition, state, and concentration of the oil or hydrocarbons, with dispersion and emulsification enhancing rates in aquatic systems and absorption by soil particulates being the key feature of terrestrial ecosystems. Temperature and oxygen and nutrient concentrations are important variables in both types of environments. Salinity and pressure may also affect biodegradation rates in some aquatic environments, and moisture and pH may limit biodegradation in soils. Hydrocarbons are degraded primarily by bacteria and fungi. Adaptation by prior exposure of microbial communities to hydrocarbons increases hydrocarbon degradation rates. Adaptation is brought about by selective enrichment of hydrocarbon-utilizing microorganisms and amplification of the pool of hydrocarbon-catabolizing genes. The latter phenomenon can now be monitored through the use of DNA probes. Increases in plasmid frequency may also be associated with genetic adaptation. Seeding to accelerate rates of biodegradation has been shown to be effective in some cases, particularly when used under controlled conditions, such as in fermentors or chemostats.
Topics: Bacteria; Biodegradation, Environmental; Environmental Pollution; Fungi; Hydrocarbons; Soil Microbiology; Water Microbiology
PubMed: 2215423
DOI: 10.1128/mr.54.3.305-315.1990 -
NPJ Biofilms and Microbiomes Apr 2021Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly...
Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.
Topics: Air Microbiology; Biomass; Ecosystem; Environmental Microbiology; Environmental Monitoring; Metagenome; Metagenomics; Microbiota; Soil Microbiology; Water Microbiology
PubMed: 33863892
DOI: 10.1038/s41522-021-00209-4 -
Clinical Microbiology and Infection :... Jul 2017
Topics: Anti-Bacterial Agents; Antimicrobial Stewardship; Disease Management; Humans; Laboratories; Mentors; Microbiology
PubMed: 28625573
DOI: 10.1016/j.cmi.2017.06.007 -
Nihon Saikingaku Zasshi. Japanese... 2021
Topics: Authorship; Bibliographies as Topic; Humans; Microbiology; Periodicals as Topic; Research Personnel; Societies, Scientific
PubMed: 33627528
DOI: 10.3412/jsb.76.129 -
The American Journal of the Medical... Jan 2012Explorations of the vaginal microbiota (VMB) began over 150 years ago. Using light microscopy and bacterial cultures, the concept of normal versus abnormal microbiota in... (Review)
Review
Explorations of the vaginal microbiota (VMB) began over 150 years ago. Using light microscopy and bacterial cultures, the concept of normal versus abnormal microbiota in women began to emerge. The latter became known by the term "bacterial vaginosis" (BV). BV microbiota is dominated by Gardnerella vaginalis and includes a number of anaerobic organisms. In contrast, normal flora is dominated by various Lactobacilli. BV microbiota is associated with vaginal discharge, poor pregnancy outcomes, pelvic inflammatory disease, postoperative wound infections and endometritis after elective abortions. In addition, BV flora predisposes women to infection by human immunodeficiency virus and sexually transmitted diseases. Application of molecular techniques over the past decade has significantly advanced our understanding of the VMB. It is far more complex than previously recognized and is composed of many previously unknown organisms in addition to those already identified by culture. Analyses using high-throughput sequencing techniques have revealed unique microbial communities not previously recognized within the older, established vaginal flora categories. These new findings will inform the design of future clinical investigations of the role of the VMB in health and disease.
Topics: Female; History, 19th Century; History, 20th Century; History, 21st Century; Humans; Metagenome; Microbiology; Molecular Biology; Vagina; Women's Health
PubMed: 22143133
DOI: 10.1097/MAJ.0b013e31823ea228 -
Comptes Rendus Biologies May 2011Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have... (Review)
Review
Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the taxonomic diversity and functioning of the indigenous microbial communities. As a consequence, the functional significance of these losses/modifications of biodiversity, in terms of the capacity of ecosystems to maintain the functions and services on which humanity depends, is now of pivotal importance. In this context, one of the main challenges in soil microbial ecology is to better understand and predict the processes that drive soil microbial diversity and the link between diversity and ecosystem process. This review describes past, present and ongoing conceptual and methodological strategies employed to better assess and understand the distribution and evolution of soil microbial diversity with the aim of increasing our capacity to translate such diversity into soil biological functioning and, more widely, into ecosystem services.
Topics: Agriculture; Bacteria; Biodiversity; Ecosystem; Environment; France; Microbiology; Soil Microbiology
PubMed: 21640949
DOI: 10.1016/j.crvi.2010.12.003 -
Nihon Saikingaku Zasshi. Japanese... 2018
Topics: Humans; Japan; Microbiology; Republic of Korea; Societies, Scientific
PubMed: 29479021
DOI: 10.3412/jsb.73.156 -
Nihon Saikingaku Zasshi. Japanese... 2018
Topics: Bacteriology; Education; Humans; Interdisciplinary Communication; International Cooperation; Intersectoral Collaboration; Japan; Microbiology; Mycobacterium Infections; Republic of Korea; Research Personnel; Societies, Scientific
PubMed: 29479022
DOI: 10.3412/jsb.73.21 -
Antimicrobial Agents and Chemotherapy Jul 2014
Topics: Anti-Infective Agents; History, 20th Century; History, 21st Century; Humans; Microbiology
PubMed: 24798286
DOI: 10.1128/AAC.03199-14 -
FEMS Microbiology Reviews Jul 2000The beginning of modern microbiology can be traced back to the 1870s, and it was based on the development of new concepts that originated during the two preceding...
The beginning of modern microbiology can be traced back to the 1870s, and it was based on the development of new concepts that originated during the two preceding centuries on the role of microorganisms, new experimental methods, and discoveries in chemistry, physics, and evolutionary cell biology. The crucial progress was the isolation and growth on solid media of clone cultures arising from single cells and the demonstration that these pure cultures have specific, inheritable characteristics and metabolic capacities. The doctrine of the spontaneous generation of microorganisms, which stimulated research for a century, lost its role as an important concept. Microorganisms were discovered to be causative agents of infectious diseases and of specific metabolic processes. Microscopy techniques advanced studies on microorganisms. The discovery of sexuality and development in microorganisms and Darwin's theory of evolution contributed to the founding of microbiology as a science. Ferdinand Cohn (1828-1898), a pioneer in the developmental biology of lower plants, considerably promoted the taxonomy and physiology of bacteria, discovered the heat-resistant endospores of bacilli, and was active in applied microbiology.
Topics: Bacteria; Bacterial Physiological Phenomena; Biological Evolution; History, 17th Century; History, 18th Century; History, 19th Century; Microbiology; Poland
PubMed: 10841971
DOI: 10.1111/j.1574-6976.2000.tb00540.x