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      A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

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          Abstract

          The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants.

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          Most cited references 74

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          An integrated semiconductor device enabling non-optical genome sequencing.

          The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.
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            Solexa Ltd.

             Simon Bennett (2004)
            Solexa Ltd is developing an integrated system, based on a breakthrough single molecule sequencing technology, to address a US$2 billion market that is expected to grow exponentially alongside and as a consequence of further technological enhancements. The system, software and consumables will initially be sold to research organizations, pharmaceutical companies and diagnostic companies that will sequence large regions of genomic DNA, including whole genomes, at costs several orders of magnitude below current levels. Solexa expects to launch its first product in 2006, and as it continues to make time and cost efficiencies, additional products will be launched into the expanding markets that will have broad applications in basic research through to healthcare management.
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              Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.

              The alpha-proteobacterial lineage that contains SAR11 and related ribosomal RNA gene clones was among the first groups of organisms to be identified when cultivation-independent approaches based on rRNA gene cloning and sequencing were applied to survey microbial diversity in natural ecosystems. This group accounts for 26% of all ribosomal RNA genes that have been identified in sea water and has been found in nearly every pelagic marine bacterioplankton community studied by these methods. The SAR11 clade represents a pervasive problem in microbiology: despite its ubiquity, it has defied cultivation efforts. Genetic evidence suggests that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study. Here we report the isolation of representatives of the SAR11 clade. Eighteen cultures were initially obtained by means of high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media. Eleven of these cultures have been successfully passaged and cryopreserved for future study. The volume of these cells, about 0.01 micro m(3), places them among the smallest free-living cells in culture.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                23 March 2018
                2018
                : 9
                Affiliations
                Biology Department, College of Science, Shantou University , Shantou, China
                Author notes

                Edited by: Michail M. Yakimov, Consiglio Nazionale Delle Ricerche (CNR), Italy

                Reviewed by: Martin Krüger, Federal Institute for Geosciences and Natural Resources, Germany; Tony Gutierrez, Heriot-Watt University, United Kingdom

                *Correspondence: Zhong Hu hzh@ 123456stu.edu.cn

                This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2018.00520
                5876298
                29628913
                099a79ba-95f2-4ea1-9b00-4c0237f64821
                Copyright © 2018 Zhang, Hu and Wang.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 118, Pages: 13, Words: 10437
                Categories
                Microbiology
                Review

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