Molecular biology techniques and applications for ocean sensing

Zehr, Jonathan P.; Hewson, Ian; Moisander, Pia H.

doi:10.5194/os-5-101-2009

Cited by 10 publications

(6 citation statements)

References 123 publications

(91 reference statements)

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“…Automated ribosomal intergenic sequence analysis (ARISA) has proven to be a valuable tool for describing the bacterial community structure in marine ecosystems (Borin et al, 2009a, b;Fuhrman et al, 2008;Hewson et al, 2006;Zehr et al, 2009), and it was applied here to depict the bacterial community structure of epi-, mesoand bathypelagic waters. The aims of the present study were (i) to identify distinct or common patterns of bacterial community structure in epipelagic and deep waters sampled at 23 stations along a longitudinal transect in the whole Mediterranean Sea, and (ii) to describe the microbiome composition of seawater collected throughout the water column at eight stations located in the eastern and the western Mediterranean basins.…”

Section: Introductionmentioning

confidence: 99%

Biogeography of planktonic bacterial communities across the whole Mediterranean Sea

Mapelli

Varela²,

Barbato

et al. 2013

Ocean Sci.

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Bacterial population distribution in the Mediterranean Sea has been mainly studied by considering small geographical areas or specific phylogenetic groups. The present study is a molecular microbiology investigation aimed to identify the environmental factors driving total bacterioplankton community composition of seawater samples collected along a transect covering the whole Mediterranean Sea. We performed automated ribosomal intergenic sequence analysis (ARISA) and microscope evaluation of prokaryotic abundance of seawater sampled across both vertical profiles and longitudinal transects in the whole basin. Prokaryotic abundance decreased with depth at all the stations and presented similar values in epi-, meso- and bathypelagic layers across the whole Mediterranean Sea. However, peculiar bacterial assemblages were selected along a longitudinal transect in the epipelagic layers of the eastern and western sub-basins. Vertical differences of the bacterial communities were observed only when considering the epi- and bathypelagic waters, while the study of the structure of bacterial communities at a finer scale across the water column displayed higher variability at the intermediate layers. Nonetheless, different physico-chemical factors were significantly related to the distribution of bacterial populations, both according to geographic position and down the water column in the whole Mediterranean Sea. These results demonstrated that bacterial assemblages are putatively correlated to different water masses of the complex hydrographical systems of the eastern and western Mediterranean sub-basins

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Section: Introductionmentioning

confidence: 99%

Biogeography of planktonic bacterial communities across the whole Mediterranean Sea

Mapelli

Varela²,

Barbato

et al. 2013

Ocean Sci.

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“…2 In the footsteps of biomedicine: the quest for ecogenomic sensors Zehr et al (2009) provide a comprehensive summary of the application of molecular analytical techniques for environmental research. Other useful, recent reviews that serve as background information for this article include Devereux (2006), Metfies et al (2006), Paul et al (2007), Goodwin and Litaker (2008), Scholin et al (2008) and De-Long (2009).…”

Section: Molecular Markers As Sensing Elementsmentioning

confidence: 99%

“…Methods that rely on nucleic acid amplification offer the most sensitive assays for detecting low levels of target sequences (e.g., see Zehr et al, 2009;Frias-Lopez. 2008).…”

Section: The Case For Microfluidics and Sample Homogenizationmentioning

confidence: 99%

What are "ecogenomic sensors?" A review and thoughts for the future

Scholin

2010

Ocean Sci.

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Abstract. The OceanSensors08 workshop held 31 March–4 April 2008 in Warnemünde, Germany, brought together an international group of marine scientists, sensor developers and technologists with a common interest in shaping the future of ocean sensing. In preparation for that meeting a series of review papers was commissioned, one of which was meant to cover Sensors for Ocean-omics. The "ocean-omics" topic was cast very broadly. The notion was to review use of genetic techniques for assessing presence and diversity of organisms, their genomic capacity and gene expression, and to provide a prospectus of how such methods could be applied in an autonomous capacity. I chose "ecogenomic sensor" as a descriptor to convey the essence of such a system – a device that integrates genetic level sensing with larger scale environmental characterization. This phrase is derived from workshops refining the US's Ocean Observatories Initiative (OOI) and visions for instrument systems that could be deployed on such a network. But what exactly are ecogenomic sensors? A clear definition is lacking and conceptualizations far outweigh actual hardware that can be deployed in the ocean. This prospectus builds from that point. I advance a definition of "ecogenomic sensor" and outline the opportunities and challenges associated with developing such instruments. Suggestions as to how this technology may be further refined and applied are offered against the backdrop of the Autonomous Microbial Genosensor (AMG) and Environmental Sample Processor (ESP). Applications that center on detection of DNA and RNA are emphasized. The word "review" appears in the title at the request of the editors.

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“…Biotechnology applied to taxonomy and biochemical analysis (genomics) has improved in recent years, but we still need to demonstrate that these tools can be applied to resolve key questions and that they can be inexpensive and easy to use (Zehr et al, 2008;Scholin, 2009). (Kroger et al, 2009).…”

Section: Impacts Of New Pollutants On Ecosystemsmentioning

confidence: 99%