226
gene for prokaryotes (Pace et al. 1986), 18S and 28S rRNA genes for eukaryotes
(Moon-van der Staay et al. 2000; Gong et al. 2013) and the internal transcribed
spacer (ITS) region for both (Brown and Fuhrman 2005; Santoferrara et al. 2014).
Such markers generally resolve taxa to family or genus level, but more specific
genetic markers that provide higher taxonomic resolution have also been developed
(e.g. petB that encodes the cytochrome b6 subunit of the cytochrome b6f complex
(Mazard et al. 2012), rbcL that encodes the large subunit of the carbon fixation
enzyme RuBisCO (Hamsher et al. 2011), hsp90 that encodes a major heat shock
protein (Hoppenrath and Leander 2010) and nifH that encodes the iron protein of
nitrogenase enzyme (Zehr and Turner 2001). Amplicon sequencing has been applied
to a range of marine environments across temporal and spatial scales and has been
most insightful to microbial oceanographers when diversity of a specific microbial
group has been assessed, coupled with investigations of their biogeochemical transformations (e.g. diversity of diazotrophs estimated using nifH, with measured rates
of N 2 fixation; Messer et al. 2016).
To date, many studies have explored microbial community composition changes
in response to oceanographic processes such as ocean currents, upwelling, estuarine
outflows and the formation of mesoscale eddies (Treusch et al. 2009; Villar et al.
2015; Doblin et al. 2016; Zielinski et al. 2016). For example, Malviya et al. (2016)
used the hypervariable V9 region of the 18S ribosomal marker gene to characterise
the distribution and diversity of diatoms in the global ocean. Over 33,000 OTUs
could be assigned at least down to genus level, with over 90% of assigned sequences
belonging to known planktonic genera. Diatoms were less abundant in the oligotrophic open ocean compared to coastal locations, but had comparable diversity, suggesting a large reservoir of taxa that respond to changes in the environment. There
was a significant drop in diversity across Cape Agulhas (separating the Indian and
Atlantic Ocean) and the Drake Passage (separating the Atlantic and Southern
Ocean), indicating areas of restricted oceanographic circulation constrain diatom
diversity and distribution (Malviya et al. 2016).
Examining temporal dynamics in microbial diversity, Gilbert et al. (2012) used
16S rRNA sequencing to discover strong seasonal patterns in bacterial diversity (i.e.
consistent winter peaks in diversity over 6 years) at a temperate coastal location off
Plymouth, UK. They showed that environmental parameters explained most of the
variation (49–91%) in bacterial community composition compared to biological
parameters (18–51%), suggesting that bottom-up processes were potentially more
important drivers of bacteria than the temporal dynamics of coexisting eukaryotes.
Chow et al. (2013) conducted a similar study at the San Pedro Ocean Time-series
(SPOT) station off the California coast, determining that the bacterial community
comprised persistent (>75% of months), intermittent (25–75%) and ephemeral
(<25%) taxa. There was a relatively stable core microbial community at both the
surface and subsurface chlorophyll-a maximum (~30 m) such that OTUs were similar between samples taken days, weeks, months or years apart, with most pairs of
samples having on average at least 36% similarity.
Shotgun metagenomics sequencing is another approach used to characterise
microbial communities. No specific gene is targeted but rather the whole community
DNA is fragmented and sequenced (Fig. 11.1), yielding thousands of sequences for
D.R. Varkey and M.A. Doblin
gene for prokaryotes (Pace et al. 1986), 18S and 28S rRNA genes for eukaryotes
(Moon-van der Staay et al. 2000; Gong et al. 2013) and the internal transcribed
spacer (ITS) region for both (Brown and Fuhrman 2005; Santoferrara et al. 2014).
Such markers generally resolve taxa to family or genus level, but more specific
genetic markers that provide higher taxonomic resolution have also been developed
(e.g. petB that encodes the cytochrome b6 subunit of the cytochrome b6f complex
(Mazard et al. 2012), rbcL that encodes the large subunit of the carbon fixation
enzyme RuBisCO (Hamsher et al. 2011), hsp90 that encodes a major heat shock
protein (Hoppenrath and Leander 2010) and nifH that encodes the iron protein of
nitrogenase enzyme (Zehr and Turner 2001). Amplicon sequencing has been applied
to a range of marine environments across temporal and spatial scales and has been
most insightful to microbial oceanographers when diversity of a specific microbial
group has been assessed, coupled with investigations of their biogeochemical transformations (e.g. diversity of diazotrophs estimated using nifH, with measured rates
of N 2 fixation; Messer et al. 2016).
To date, many studies have explored microbial community composition changes
in response to oceanographic processes such as ocean currents, upwelling, estuarine
outflows and the formation of mesoscale eddies (Treusch et al. 2009; Villar et al.
2015; Doblin et al. 2016; Zielinski et al. 2016). For example, Malviya et al. (2016)
used the hypervariable V9 region of the 18S ribosomal marker gene to characterise
the distribution and diversity of diatoms in the global ocean. Over 33,000 OTUs
could be assigned at least down to genus level, with over 90% of assigned sequences
belonging to known planktonic genera. Diatoms were less abundant in the oligotrophic open ocean compared to coastal locations, but had comparable diversity, suggesting a large reservoir of taxa that respond to changes in the environment. There
was a significant drop in diversity across Cape Agulhas (separating the Indian and
Atlantic Ocean) and the Drake Passage (separating the Atlantic and Southern
Ocean), indicating areas of restricted oceanographic circulation constrain diatom
diversity and distribution (Malviya et al. 2016).
Examining temporal dynamics in microbial diversity, Gilbert et al. (2012) used
16S rRNA sequencing to discover strong seasonal patterns in bacterial diversity (i.e.
consistent winter peaks in diversity over 6 years) at a temperate coastal location off
Plymouth, UK. They showed that environmental parameters explained most of the
variation (49–91%) in bacterial community composition compared to biological
parameters (18–51%), suggesting that bottom-up processes were potentially more
important drivers of bacteria than the temporal dynamics of coexisting eukaryotes.
Chow et al. (2013) conducted a similar study at the San Pedro Ocean Time-series
(SPOT) station off the California coast, determining that the bacterial community
comprised persistent (>75% of months), intermittent (25–75%) and ephemeral
(<25%) taxa. There was a relatively stable core microbial community at both the
surface and subsurface chlorophyll-a maximum (~30 m) such that OTUs were similar between samples taken days, weeks, months or years apart, with most pairs of
samples having on average at least 36% similarity.
Shotgun metagenomics sequencing is another approach used to characterise
microbial communities. No specific gene is targeted but rather the whole community
DNA is fragmented and sequenced (Fig. 11.1), yielding thousands of sequences for
D.R. Varkey and M.A. Doblin