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11.1 Introduction
Whilst oceanographers have been interested in microbially mediated ocean processes for more than a century, our understanding of the diversity and functional
capacity of these organisms has really only been delivered since the development of
molecular approaches in the 1980s. Prior to this, our knowledge about their roles in
the ocean was primarily derived from culture-dependent approaches, whereby
microbes were isolated and grown under different conditions and subsequently
tested for their chemical and biological activity. However, as a consequence of the
difficulty in cultivating many microbial species, these approaches only afforded
insights into a very small proportion of the microbes in the ocean (Rappé and
Giovannoni 2003).
In general, molecular methodologies rely on the fact that microbes share common genes that have changed relatively little throughout the evolutionary history of
life on Earth. Analysing the differences in these conservative genes enables organisms to be classified into different species or operational taxonomic units (OTUs) in
a way that reflects their evolutionary history (Giovannoni and Cary 1993). Moreover,
DNA codes for a large variety of proteins which can then be used to infer microbial
metabolism and function (DeLong 2009). The techniques that sequence DNA,
examine its transcription, and the subsequent expression of proteins are known as
genomics, transcriptomics and proteomics, respectively. Collectively, these methodologies are referred to as ‘omic approaches.
Various ‘omic techniques have been applied in broadscale ocean surveys such as
the Global Ocean Sampling expedition (GOS), International Census of Marine
Microbes (ICoMM) and Tara Oceans expedition, as well as long-term microbial
observatories such as the Bermuda Atlantic Time-Series and Hawaii Ocean Timeseries (BATS and HOT, respectively). Here we provide a focussed, but deliberately
not exhaustive, set of laboratory and field-based examples which demonstrate the
use of such ‘omic approaches to characterise microbial processes in the ocean.
11.2 Influence of Oceanographic Processes on Microbial
Distribution and Diversity
Early investigations of the diversity of marine microbial samples involved fingerprinting techniques (Avaniss-Aghajani et al. 1994) which separated ribosomal RNA
(rRNA) fragments according to their length or nucleotide composition (e.g. terminal restriction fragment length polymorphism (T-RFLP), automated rRNA intergenic spacer analysis (ARISA)). Such methods provided no significant details on
the identity of organisms, simply patterns of similarity between samples (Dorigo
et al. 2005; Zinger et al. 2012). Alternatively, researchers identified microbes within
natural samples by microscopy using fluorescence in situ hybridisation or created
clone libraries using rRNA gene fragments, involving PCR amplification of a
D.R. Varkey and M.A. Doblin
11.1 Introduction
Whilst oceanographers have been interested in microbially mediated ocean processes for more than a century, our understanding of the diversity and functional
capacity of these organisms has really only been delivered since the development of
molecular approaches in the 1980s. Prior to this, our knowledge about their roles in
the ocean was primarily derived from culture-dependent approaches, whereby
microbes were isolated and grown under different conditions and subsequently
tested for their chemical and biological activity. However, as a consequence of the
difficulty in cultivating many microbial species, these approaches only afforded
insights into a very small proportion of the microbes in the ocean (Rappé and
Giovannoni 2003).
In general, molecular methodologies rely on the fact that microbes share common genes that have changed relatively little throughout the evolutionary history of
life on Earth. Analysing the differences in these conservative genes enables organisms to be classified into different species or operational taxonomic units (OTUs) in
a way that reflects their evolutionary history (Giovannoni and Cary 1993). Moreover,
DNA codes for a large variety of proteins which can then be used to infer microbial
metabolism and function (DeLong 2009). The techniques that sequence DNA,
examine its transcription, and the subsequent expression of proteins are known as
genomics, transcriptomics and proteomics, respectively. Collectively, these methodologies are referred to as ‘omic approaches.
Various ‘omic techniques have been applied in broadscale ocean surveys such as
the Global Ocean Sampling expedition (GOS), International Census of Marine
Microbes (ICoMM) and Tara Oceans expedition, as well as long-term microbial
observatories such as the Bermuda Atlantic Time-Series and Hawaii Ocean Timeseries (BATS and HOT, respectively). Here we provide a focussed, but deliberately
not exhaustive, set of laboratory and field-based examples which demonstrate the
use of such ‘omic approaches to characterise microbial processes in the ocean.
11.2 Influence of Oceanographic Processes on Microbial
Distribution and Diversity
Early investigations of the diversity of marine microbial samples involved fingerprinting techniques (Avaniss-Aghajani et al. 1994) which separated ribosomal RNA
(rRNA) fragments according to their length or nucleotide composition (e.g. terminal restriction fragment length polymorphism (T-RFLP), automated rRNA intergenic spacer analysis (ARISA)). Such methods provided no significant details on
the identity of organisms, simply patterns of similarity between samples (Dorigo
et al. 2005; Zinger et al. 2012). Alternatively, researchers identified microbes within
natural samples by microscopy using fluorescence in situ hybridisation or created
clone libraries using rRNA gene fragments, involving PCR amplification of a
D.R. Varkey and M.A. Doblin