Remarkably coherent population structure for a dominant Antarctic Chlorobium species

Background In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. Results A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml−1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. Conclusion The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.

Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems

Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.

Tracing boundaries in Eastern Antarctica: Multi-scale drivers of soil microbial communities across the hyperarid Vestfold Hills

Microorganisms are key to sustaining core ecosystem processes across terrestrial Antarctica but they are rarely considered in conservation frameworks. Whilst greater advocacy has been made towards the inclusion of microbial data in this context, there is still a need for better tools to quantify multispecies responses to environmental change. Here, we extend the scope of Gradient Forest modelling beyond macroorganisms and small datasets to the comprehensive polar soil microbiome encompassing >17, 000 sequence variants for bacteria, micro-eukarya and archaea throughout the hyperarid Vestfold Hills of Eastern Antarctica. Quantification of microbial diversity against 79 physiochemical variables revealed that whilst rank-order importance differed, predictors were broadly consistent between domains, with greatest sharing occurring between bacteria and micro-eukarya. Moisture was identified as the most robust predictor for shaping the regional soil microbiome, with highest compositional turnover or “splits” occurring within the 10 – 12 % moisture content range. Often the most responsive taxa were rarer lineages of bacteria and micro-eukarya with phototrophic and nutrient-cycling capacities such as Cyanobacteria (up to 61.81 % predictive capacity), Chlorophyta (62.17 %) and Ochrophyta (57.81 %). These taxa groups are thus at greater risk of biodiversity loss or gain to projected climate trajectories, which will inevitably disturb current ecosystem dynamics. Better understanding of these threshold tipping points will positively aid conservation efforts across Eastern Antarctica. Furthermore, the successful implementation of an improved Gradient Forest model also presents an exciting opportunity to broaden its use on microbial systems globally.

Evaluation of Coliform and Faecal Coliform Bacteria in the Lakes of Broknes & Grovnes Peninsula at Larsemann Hills, East Antarctica

Purpose: More than 150 lakes on different peninsulas and islands are situated in the Larsemann Hills. The Larsemann Hills are an ice-free area and are located halfway between the Vestfold Hills and the Amery Ice Shelf on the south-eastern coast of Prydz Bay, Princess Elizabeth Land, East Antarctica. Antarctic lakes water is being polluted due to anthropogenic activities caused by various research activities and tourism. Methods: During 34th Indian Scientific Expedition to Antarctica (ISEA) in 2014 to 2015, twenty lake water samples in triplicates were collected from the Broknes & Grovnes peninsula. Coliform and faecal coliform bacteria were analyzed in these samples. Results: Out of twenty, eleven lake water samples were found to be contaminated with coliform bacteria. However, faecal coliform bacteria were absent in all the lake water samples. Coliforms are found in the lakes of Broknes peninsula (P2 Lake & P3 Lake) and Grovnes peninsula (L1C NG, L1D NG, L1E NG, L7 NG, L7A NG, L7B NG, L2 SG, L4 SG & L5 SG). Conclusion: The present study confirms the presence of coliform bacteria in the lakes of East Antarctica which indicates an alarming situation and needs to be investigated further.

Geochemical and paleomagnetic characteristics of Vestfold Hills mafic dykes in Prydz Bay region: implications on the Paleoproterozoic connection between East Antarctica and proto-India

The Archean age granite gneiss basement along the Prydz Bay coastline in East Antarctica hosts N-S, E-W, NE-SW, and NW-SE trending mafic dyke swarms in the Vestfold Hills region that intruded between 2420 and 1250 Ma. The dyke trends do not show a direct correlation with the dyke geochemistry but can be broadly discriminated into high-Mg and Fe-rich tholeiites. The former type being more siliceous, LILE, HFSE, and LREE enriched, crystallized from a fractionated melt with a notable crustal component or fluid enrichment through the previous subduction process. The Fe-rich tholeiites are less siliceous, have lower abundances of LILE and REE, and were derived from an undifferentiated, primitive melt. The geochemical characteristics of both types underline a shallow level and a high degree of melting in the majority of cases, and a broadly Island Arc Basalt (IAB) affinity. Paleomagnetic analysis of hand samples shows directional groups consistent with geochemical groupings. The Vestfold Hills dykes show a possible linkage with the coeval mafic dykes in Eastern Dharwar and Bastar cratons of the South Indian Block, based on the similarity in the Paleoproterozoic paleolatitudes.

Mantle rocks in East Antarctica

Only three localities of mantle xenoliths are known from all of East Antarctica, occurring at the Jetty Peninsula (Lambert-Amery Rift), Vestfold Hills and Gaussberg volcano. The latter two are spinel-facies peridotites, whereas the Jetty Peninsula rocks also include garnet-spinel lherzolites; all come from Indo-Antarctica. The mantle xenoliths of Jetty Peninsula and Vestfold Hills contain abundant geochemical and mineralogical evidence for multiple enrichment events that are attributed to infiltration of melts and their fluid products. Many of these episodes are spatially related to precursory activity along major trans-lithospheric structures that eventually led to the separation of India from Antarctica. Mantle rocks also occur at Schirmacher Oasis (Dronning Maud Land) and Haskard Highlands (Shackleton Ranges) as blocks tectonically emplaced in high-grade crustal rocks. These show varying degrees of alteration due to reaction with silicic crustal rocks or hydrous fluids: none correspond to unchanged mantle compositions. Geophysical surveys are our only information on the mantle lithosphere beneath the inland ice, and these can be used to infer the locations of thicker lithosphere probably related to cratons by southward extrapolation of coastal geological correlations. Intense local modification of the mantle lithosphere by melt infiltration and fluid movements may influence the large-scale images derived from geophysical data, and may be incorrectly interpreted as homogeneous compositions.

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community

Background Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. Results The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. Conclusion Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems.

Sabbea gen. nov., a new diatom genus (Bacillariophyta) from continental Antarctica

The non-marine diatom flora of the Antarctic Continent includes several endemic taxa recorded over the past 100 years. One of these taxa, Navicula adminensis D.Roberts & McMinn, was described from the Vestfold Hills, East Antarctica. Detailed light and scanning electron microscopy observations have shown that based on its morphological features, the species does not belong to the genus Navicula sensu stricto. To determine the most closely related genera to N. adminensis, the morphological features of Adlafia, Kobayasiella, Envekadea, Stenoneis, Berkeleya, Climaconeis, and Parlibellus were compared with those of N. adminensis. Although each of these genera shows one or more similar features, none of them accommodates the salient morphological characteristics of N. adminensis. Therefore, a new genus, Sabbea gen. nov., is herein described, and Navicula adminensis is formally transferred to the new genus as Sabbea adminensis comb. nov. The genus Sabbea is characterized by uniseriate striae composed of small, rounded areolae occluded externally by individual hymenes, a rather simple raphe structure with straight, short proximal ends and short terminal raphe fissures, open girdle bands with double perforation and a very shallow mantle.