230
metagenomics with metaproteomics therefore has the most potential to decipher
microbial community dynamics and function. The rapidly developing field of metaproteomics has had increasing application within marine systems to better understand microbial communities and their roles in biogeochemical functions (Wang
et al. 2014; Williams and Cavicchioli 2014).
Two early studies by Sowell et al. (2009, 2011) elegantly demonstrated the
utility of metaproteomics for microbial oceanography. Sowell et al. (2009)
explored changes in protein expression under contrasting oceanographic conditions to examine how microbes inhabiting the upper ocean respond to their environmental conditions. Under stratified conditions in the oligotrophic Sargasso
Sea, the heterotrophic marine bacterium SAR11 expressed high-affinity transporters for limiting nutrients (e.g. phosphate), providing a possible explanation for the
dominance of this organism during nutrient-deplete summer months (Sowell et al.
2009). On the other hand, in the upwelling influenced and nutrient-rich coastal
regions of the Oregon shelf, SAR11 alternatively displayed a higher expression of
transporters associated with carbon and nitrogen uptake (Sowell et al. 2011).
These comparative proteomic approaches therefore delivered a new understanding of how the ocean’s most abundant bacterium adjusts its metabolic machinery
according to resource availability, allowing it to succeed in both nutrient-limited
and nutrient-replete conditions.
Morris et al. (2010) utilised metaproteomics to explore how nutrient utilisation strategies shape marine bacterial community structure along an oceanic
nutrient gradient. They focussed on membrane proteins that were identified both
functionally and taxonomically to provide insight into changes in both the composition of the community and the proteins they expressed. TonB-dependent
transporters, which are membrane proteins that transport diverse nutrients across
the outer membrane of Gram-negative bacteria using a proton motive force, were
found to be more abundant in nutrient-rich coastal waters, whereas other transporters such as porins, permeases and major facilitator superfamily transporters,
which transport a diverse range of substrates, were highly expressed in the nutrient-poor open ocean. Taxonomic assignment of these proteins highlighted that
diverse taxa expressed TonB-dependent transporters whilst porins were mostly
associated with the dominant open ocean microbes Prochlorococcus and SAR11
(Morris et al. 2010).
Proteomic approaches have also been used to examine microbial processes
over time. Teeling et al. (2012) coupled metatranscriptomics and metagenomics to
examine temporal dynamics of bacterioplankton substrate utilisation during the
progression of a phytoplankton bloom. During the early stages of the bloom, there
was a high expression of TonB-dependent transporters, which enable the utilisation of complex organic matter available at the start of the bloom and was linked
to an initial dominance of Bacteroidetes (Ulvibacter and Formosa). Progression
of the bloom and a change in algal exudate composition led to the dominance of
copiotrophic opportunists that expressed transporters with broad substrate spectra, including members of the gammaproteobacteria, Reinekea spp. and alphaproteobacteria Roseobacter spp. This was followed by the rise of lineages of
D.R. Varkey and M.A. Doblin
metagenomics with metaproteomics therefore has the most potential to decipher
microbial community dynamics and function. The rapidly developing field of metaproteomics has had increasing application within marine systems to better understand microbial communities and their roles in biogeochemical functions (Wang
et al. 2014; Williams and Cavicchioli 2014).
Two early studies by Sowell et al. (2009, 2011) elegantly demonstrated the
utility of metaproteomics for microbial oceanography. Sowell et al. (2009)
explored changes in protein expression under contrasting oceanographic conditions to examine how microbes inhabiting the upper ocean respond to their environmental conditions. Under stratified conditions in the oligotrophic Sargasso
Sea, the heterotrophic marine bacterium SAR11 expressed high-affinity transporters for limiting nutrients (e.g. phosphate), providing a possible explanation for the
dominance of this organism during nutrient-deplete summer months (Sowell et al.
2009). On the other hand, in the upwelling influenced and nutrient-rich coastal
regions of the Oregon shelf, SAR11 alternatively displayed a higher expression of
transporters associated with carbon and nitrogen uptake (Sowell et al. 2011).
These comparative proteomic approaches therefore delivered a new understanding of how the ocean’s most abundant bacterium adjusts its metabolic machinery
according to resource availability, allowing it to succeed in both nutrient-limited
and nutrient-replete conditions.
Morris et al. (2010) utilised metaproteomics to explore how nutrient utilisation strategies shape marine bacterial community structure along an oceanic
nutrient gradient. They focussed on membrane proteins that were identified both
functionally and taxonomically to provide insight into changes in both the composition of the community and the proteins they expressed. TonB-dependent
transporters, which are membrane proteins that transport diverse nutrients across
the outer membrane of Gram-negative bacteria using a proton motive force, were
found to be more abundant in nutrient-rich coastal waters, whereas other transporters such as porins, permeases and major facilitator superfamily transporters,
which transport a diverse range of substrates, were highly expressed in the nutrient-poor open ocean. Taxonomic assignment of these proteins highlighted that
diverse taxa expressed TonB-dependent transporters whilst porins were mostly
associated with the dominant open ocean microbes Prochlorococcus and SAR11
(Morris et al. 2010).
Proteomic approaches have also been used to examine microbial processes
over time. Teeling et al. (2012) coupled metatranscriptomics and metagenomics to
examine temporal dynamics of bacterioplankton substrate utilisation during the
progression of a phytoplankton bloom. During the early stages of the bloom, there
was a high expression of TonB-dependent transporters, which enable the utilisation of complex organic matter available at the start of the bloom and was linked
to an initial dominance of Bacteroidetes (Ulvibacter and Formosa). Progression
of the bloom and a change in algal exudate composition led to the dominance of
copiotrophic opportunists that expressed transporters with broad substrate spectra, including members of the gammaproteobacteria, Reinekea spp. and alphaproteobacteria Roseobacter spp. This was followed by the rise of lineages of
D.R. Varkey and M.A. Doblin