A paleolimnological reconstruction of mid and late holocene climate change in South Georgia

South Georgia is located at the barrier between Antarctica and the mid-latitudes which makes it a key location to determine the main drivers of past and present-day climate variability and to assess whether the climate in the South Atlantic was synchronous with Antarctica or South America. Here we performed a sedimentological, high resolution (ITRAX) geochemical, and fossil diatom and pigment analysis of a 5.41 m long, ca. 8000 cal yr BP, sediment core from Fan Lake, Annenkov Island, South Georgia (54°29’0’’S, 37°5’0’’W) in an attempt to separate the influence of Holocene palaeoclimatic variability from changes in catchment stability and glacier activity. While radiocarbon ages of events in the top 250 cm (c. 4 ka) of this core appear to be broadly in line with some other studies on South Georgia, the chronology of the lower half still poses several questions. The main lithological division in the profile is marked by the establishment of finely laminated sedimentation at c. 250 cm (4000 yrs BP) and is also picked out by the diatom and pigment analysis. This change is characterized by a reduction to low stable magnetic susceptibility values and a step-change increase in organic matter, and is most likely related to deglaciation of the lake catchment during the ‘Mid Holocene Hypsithermal’. Although the diatom composition is dominated by a single species (i.e., Cyclotella stelligera), relatively minor, but sometimes significant, fluctuations in other diatom species occur in the top 250 cm (mid-late Holocene). Interestingly, the most remarkable change in the diatom record occurs at c. 100 cm (1000 cal yr BP) and coincides with an increase in general lake productivity. We link these changes to increased catchment disturbance at c. 1000 cal yr BP, which is possibly associated with deglaciation following one of four relatively minor ‘post-cooling events’ during the late Holocene

Functional characterization of the diatom cyclin-dependent kinase A2 as a mitotic regulator reveals plant-like properties in a non-green lineage

Background: Cyclin-dependent kinases (CDKs) are crucial regulators of cell cycle progression in eukaryotes. The diatom CDKA2 was originally assigned to the classical A-type CDKs, but its cell cycle phase-specific transcription at the G2-to-M phase transition is typical for plant-specific B-type CDKs. Results: Here, we report the functional characterization of CDKA2 from the diatom Phaeodactylum tricornutum. Through a yeast two-hybrid library screen, CDKA2 was found to interact with the G2/M-specific CDK scaffolding factor CKS1. Localization of CDKA2 was found to be nuclear in interphase cells, while in cells undergoing cytokinesis, the signal extended to the cell division plane. In addition, overexpression of CDKA2 induced an overall reduction in the cell growth rate. Expression analysis of cell cycle marker genes in the overexpression lines indicates that this growth reduction is primarily due to a prolongation of the mitotic phase. Conclusions: Our study indicates a role for CDKA2 during cell division in diatoms. The functional characterization of a CDK with clear CDKB properties in a non-green organism questions whether the current definition of B-type CDKs being plant-specific might need revision

Chytridiomycosis of marine diatoms : the role of stress physiology and resistance in parasite-host recognition and accumulation of defense molecules

Little is known about the role of chemotaxis in the location and attachment of chytrid zoospores to potential diatom hosts. Hypothesizing that environmental stress parameters affect parasite-host recognition, four chytrid-diatom tandem cultures (Chytridium sp./Navicula sp., Rhizophydium type I/Nitzschia sp., Rhizophydium type IIa/Rhizosolenia sp., Rhizophydium type IIb/Chaetoceros sp.) were used to test the chemotaxis of chytrid zoospores and the presence of potential defense molecules in a non-contact-co-culturing approach. As potential triggers in the chemotaxis experiments, standards of eight carbohydrates, six amino acids, five fatty acids, and three compounds known as compatible solutes were used in individual and mixed solutions, respectively. In all tested cases, the whole-cell extracts of the light-stressed (continuous light exposure combined with 6 h UV radiation) hosts attracted the highest numbers of zoospores (86%), followed by the combined carbohydrate standard solution (76%), while all other compounds acted as weak triggers only. The results of the phytochemical screening, using biomass and supernatant extracts of susceptible and resistant host-diatom cultures, indicated in most of the tested extracts the presence of polyunsaturated fatty acids, phenols, and aldehydes, whereas the bioactivity screenings showed that the zoospores of the chytrid parasites were only significantly affected by the ethanolic supernatant extract of the resistant hosts

Accurate long read mapping using enhanced suffix arrays

With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping longer reads, which is based on chaining maximal exact matches and uses heuristics and the Needleman-Wunsch algorithm to bridge the gaps. To compute maximal exact matches we use a specialized index structure, called enhanced suffix array. The proposed algorithm is very accurate and can handle large reads with mutations and long insertions and deletions

Evaluation of the performance of HPLC-CHEMTAX analysis for determining phytoplankton biomass and composition in a turbid estuary (Schelde, Belgium)

In the upper Schelde estuary in 2002, phytoplankton biomass and community composition were studied using microscopic and pigment analyses. Chlorophyll a concentration was a good predictor of phytoplankton biomass estimated from cell counts and biovolume measurements. The phytoplankton carbon to chlorophyll a ratio, however, was often unrealistically low (<10). CHEMTAX was used to estimate the contribution of the major algal groups to total chlorophyll a. The dominant algal groups were diatoms and chlorophytes. While diatom equivalents in chlorophyll a predicted diatom biomass relatively well, chlorophyte equivalents in chlorophyll a were only weakly related to chlorophyte biomass. The pigment-based approach to study phytoplankton overestimated phytoplankton biomass in general and chlorophyte biomass in particular in late autumn and winter, when phytoplankton biomass was low. A possible explanation for this overestimation may be the presence of large amounts of vascular plant detritus in the upper Schelde estuary. Residual chlorophyll a, chlorophyll b and lutein in this detritus may result in an overestimation of total phytoplankton and chlorophyte biomass when the contribution of phytoplankton to total particulate organic matter is low

Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats : a comparison between bidirectional pyrosequencing and cultivation

The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1–22.2%) and OTU (3.5–3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1–V2 and V3–V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity

Selective silicate-directed motility in diatoms

Diatoms are highly abundant unicellular algae that often dominate pelagic as well as benthic primary production in the oceans and inland waters. Being strictly dependent on silica to build their biomineralized cell walls, marine diatoms precipitate 240 × 1012 mol Si per year, which makes them the major sink in the global Si cycle. Dissolved silicic acid (dSi) availability frequently limits diatom productivity and influences species composition of communities. We show that benthic diatoms selectively perceive and behaviourally react to gradients of dSi. Cell speed increases under dSi-limited conditions in a chemokinetic response and, if gradients of this resource are present, increased directionality of cell movement promotes chemotaxis. The ability to exploit local and short-lived dSi hotspots using a specific search behaviour likely contributes to micro-scale patch dynamics in biofilm communities. On a global scale this behaviour might affect sediment–water dSi fluxes and biogeochemical cycling