Despite decreasing costs, generating large-scale, well-replicated and multivariate microbial ecology investigations with sequencing remains an expensive and time-consuming option. As a result, many microbial ecology investigations continue to suffer from a lack of appropriate replication. We evaluated two fingerprinting approaches - terminal restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA) against 454 pyrosequencing, by applying them to 225 polar soil samples from East Antarctica and the high Arctic. By incorporating local and global spatial scales into the dataset, our aim was to determine whether various approaches differed in their ability and hence utility, to identify ecological patterns. Through the reduction in the 454 sequencing data to the most dominant OTUs, we revealed that a surprisingly small proportion of abundant OTUs (< 0.25%) was driving the biological patterns observed. Overall, ARISA and T-RFLP had a similar capacity as sequencing to separate samples according to distance at a local scale, and to correlate environmental variables with microbial community structure. Pyrosequencing had a greater resolution at the global scale but all methods were capable of significantly differentiating the polar sites. We conclude fingerprinting remains a legitimate approach to generating large datasets as well as a cost-effective rapid method to identify samples for elucidating taxonomic information or diversity estimates with sequencing methods.
Most seafloor communities at depths below the photosynthesis zone rely on food that sinks through the water column. However, the nature and strength of this pelagic-benthic coupling and its influence on the structure and diversity of seafloor communities is unclear, especially around Antarctica where ecological data are sparse. Here we show that the strength of pelagic-benthic coupling along the East Antarctic shelf depends on both physical processes and the types of benthic organisms considered. In an approach based on modelling food availability, we combine remotely sensed sea-surface chlorophyll-a, a regional ocean model and diatom abundances from sediment grabs with particle tracking and show that fluctuating seabed currents are crucial in the redistribution of surface productivity at the seafloor. The estimated availability of suspended food near the seafloor correlates strongly with the abundance of benthic suspension feeders, while the deposition of food particles correlates with decreasing suspension feeder richness and more abundant deposit feeders. The modelling framework, which can be modified for other regions, has broad applications in conservation and management, as it enables spatial predictions of key components of seafloor biodiversity over vast regions around Antarctica.
Abstract. Antarctic near-shore waters are amongst the most sensitive in the world to
ocean acidification. Microbes occupying these waters are critical drivers of
ecosystem productivity, elemental cycling and ocean biogeochemistry, yet
little is known about their sensitivity to ocean acidification. A six-level,
dose–response experiment was conducted using 650 L incubation tanks
(minicosms) adjusted to a gradient in fugacity of carbon dioxide
(fCO2) from 343 to 1641 µatm. The six
minicosms were filled with near-shore water from Prydz Bay, East
Antarctica,
and the protistan composition and abundance was determined by microscopy
during 18 days of incubation. No CO2-related change in the protistan
community composition was observed during the initial 8 day acclimation
period under low light. Thereafter, the response of both autotrophic and
heterotrophic protists to fCO2 was species-specific.
The response of diatoms was mainly cell size related; microplanktonic diatoms
(> 20 µm) increased in abundance with low to moderate
fCO2 (343–634 µatm) but decreased at
fCO2 ≥ 953 µatm. Similarly, the abundance
of Phaeocystis antarctica increased with increasing
fCO2 peaking at 634 µatm. Above this threshold
the abundance of micro-sized diatoms and P. antarctica fell
dramatically, and nanoplanktonic diatoms (≤ 20 µm) dominated,
therefore culminating in a significant change in the protistan community
composition. Comparisons of these results with previous experiments conducted
at this site show that the fCO2 thresholds are similar,
despite seasonal and interannual differences in the physical and biotic
environment. This suggests that near-shore microbial communities are likely
to change significantly near the end of this century if anthropogenic
CO2 release continues unabated, with profound ramifications for
near-shore Antarctic ecosystem food webs and biogeochemical cycling.
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