Marine Microbial Bioprospecting References 319
Part B | 11
environmental biotechnology field and may lead to the
discovery of genes or processes with biotechnological
potential [11.148, 149]. For instance, in a recent study,
a combination of omics approaches that included metatranscriptomic analysis was able to elucidate which
hydrocarbon degradation pathways were actively expressed in the deep sea after an oil spill and to ascribe
these pathways to particular taxa [11.154].
Another approach that can be used for the identification of novel enzymes is to directly analyze the
proteins of a microbial community using metaproteomics. This approach consists in the extraction of
the proteins from an environmental sample, followed
by the separation of the proteins (or peptides) by twodimensional polyacrylamide gel electrophoresis or liquid chromatography, and lastly MS analysis and the
identification of the proteins by in silico spectral matching against sequence databases [11.159]. The main challenges of metaproteomics are the large complexity of
protein species expressed by the members of the microbial community and the large dynamic range of protein levels [11.159]. However, faster and more sensitive mass spectrometers and advances in omics datasets
and data handling facilitate the analysis of increasingly complex environments [11.160]. Most marine
metaproteomic studies performed so far have focused
on the analysis of planktonic microorganisms, providing clues concerning key metabolic processes such as
those involved in ocean biogeochemical cycles [11.161–
164]. More recently, Kleiner and collaborators [11.165]
used metaproteomics and metabolomics to investigate
metabolic interactions in the association between a gutless marine worm and its bacterial symbionts, revealing
highly efficient pathways for the uptake, recycling, and
conservation of energy and carbon sources.
Molecular systems biology at the ecosystem level,
also known as eco-systems biology, attempts to build
models that are able to predict the behavior of a community, through the integration of omics, meta-omics, and
single-cell approaches, as well as the use of mathematical models [11.166–168]. Although still in its infancy,
this discipline has the potential to provide a comprehensive understanding of the functioning of microbial
communities, and, therefore, to facilitate their management, which is a long-term goal of environmental
biotechnology [11.168]. For example, improving the
mechanistic understanding of biodegradation processes
may facilitate the development of knowledge-based
bioremediation strategies and the design of biosensors
for the detection of pollutants [11.169].
11.4 Conclusions
Over the last years, the development of a broad array of methodologies for the analysis of environmental
microorganisms has profoundly altered bioprospecting
efforts, thus significantly increasing our access to the
genetic potential contained in microbial communities.
However, finding properties of interest in the prospected
environments is only the first stage in a series of valueadding steps, which ends in the development of products
or services with applications in human health, industry, renewable energy, etc. Importantly, strategies that
are able to maximize the biotechnological potential of
environmental microorganisms, for example, microbial
engineering and synthetic biology, have been matching
the evolution of bioprospecting tools.
As microorganisms from marine habitats are increasingly being recognized as particularly promising resources for bioprospecting, both academia and
biotechnology industry sectors are increasing their investments in marine biotechnology research and development. This is evidenced by an increment in the number of publications in marine microbial bioprospecting,
as well as the development of new products from marine biodiversity. Furthermore, marine biotechnology
has been recognized in many parts of the world as
having an enormous development potential, and the furthering of this discipline is considered as strategic not
only for reaching key societal needs but also for economic growth [11.170].
References
11.1
D. de Pascale, C. De Santi, J. Fu, B. Landfald: The
microbial diversity of Polar environments is a fertile ground for bioprospecting, Mar. Genomics 8,
15–22 (2012)
11.2
A.T. Bull, A.C. Ward, M. Goodfellow: Search
and discovery strategies for biotechnology: The
paradigm shift, Microbiol. Mol. Biol. Rev. 64, 573–
606 (2000)
Part B | 11
environmental biotechnology field and may lead to the
discovery of genes or processes with biotechnological
potential [11.148, 149]. For instance, in a recent study,
a combination of omics approaches that included metatranscriptomic analysis was able to elucidate which
hydrocarbon degradation pathways were actively expressed in the deep sea after an oil spill and to ascribe
these pathways to particular taxa [11.154].
Another approach that can be used for the identification of novel enzymes is to directly analyze the
proteins of a microbial community using metaproteomics. This approach consists in the extraction of
the proteins from an environmental sample, followed
by the separation of the proteins (or peptides) by twodimensional polyacrylamide gel electrophoresis or liquid chromatography, and lastly MS analysis and the
identification of the proteins by in silico spectral matching against sequence databases [11.159]. The main challenges of metaproteomics are the large complexity of
protein species expressed by the members of the microbial community and the large dynamic range of protein levels [11.159]. However, faster and more sensitive mass spectrometers and advances in omics datasets
and data handling facilitate the analysis of increasingly complex environments [11.160]. Most marine
metaproteomic studies performed so far have focused
on the analysis of planktonic microorganisms, providing clues concerning key metabolic processes such as
those involved in ocean biogeochemical cycles [11.161–
164]. More recently, Kleiner and collaborators [11.165]
used metaproteomics and metabolomics to investigate
metabolic interactions in the association between a gutless marine worm and its bacterial symbionts, revealing
highly efficient pathways for the uptake, recycling, and
conservation of energy and carbon sources.
Molecular systems biology at the ecosystem level,
also known as eco-systems biology, attempts to build
models that are able to predict the behavior of a community, through the integration of omics, meta-omics, and
single-cell approaches, as well as the use of mathematical models [11.166–168]. Although still in its infancy,
this discipline has the potential to provide a comprehensive understanding of the functioning of microbial
communities, and, therefore, to facilitate their management, which is a long-term goal of environmental
biotechnology [11.168]. For example, improving the
mechanistic understanding of biodegradation processes
may facilitate the development of knowledge-based
bioremediation strategies and the design of biosensors
for the detection of pollutants [11.169].
11.4 Conclusions
Over the last years, the development of a broad array of methodologies for the analysis of environmental
microorganisms has profoundly altered bioprospecting
efforts, thus significantly increasing our access to the
genetic potential contained in microbial communities.
However, finding properties of interest in the prospected
environments is only the first stage in a series of valueadding steps, which ends in the development of products
or services with applications in human health, industry, renewable energy, etc. Importantly, strategies that
are able to maximize the biotechnological potential of
environmental microorganisms, for example, microbial
engineering and synthetic biology, have been matching
the evolution of bioprospecting tools.
As microorganisms from marine habitats are increasingly being recognized as particularly promising resources for bioprospecting, both academia and
biotechnology industry sectors are increasing their investments in marine biotechnology research and development. This is evidenced by an increment in the number of publications in marine microbial bioprospecting,
as well as the development of new products from marine biodiversity. Furthermore, marine biotechnology
has been recognized in many parts of the world as
having an enormous development potential, and the furthering of this discipline is considered as strategic not
only for reaching key societal needs but also for economic growth [11.170].
References
11.1
D. de Pascale, C. De Santi, J. Fu, B. Landfald: The
microbial diversity of Polar environments is a fertile ground for bioprospecting, Mar. Genomics 8,
15–22 (2012)
11.2
A.T. Bull, A.C. Ward, M. Goodfellow: Search
and discovery strategies for biotechnology: The
paradigm shift, Microbiol. Mol. Biol. Rev. 64, 573–
606 (2000)