High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake.

Deep Lake in Antarctica is a globally isolated, hypersaline system that remains liquid at temperatures down to -20 °C. By analyzing metagenome data and genomes of four isolates we assessed genome variation and patterns of gene exchange to learn how the lake community evolved. The lake is completely and uniformly dominated by haloarchaea, comprising a hierarchically structured, low-complexity community that differs greatly to temperate and tropical hypersaline environments. The four Deep Lake isolates represent distinct genera (∼85% 16S rRNA gene similarity and ∼73% genome average nucleotide identity) with genomic characteristics indicative of niche adaptation, and collectively account for ∼72% of the cellular community. Network analysis revealed a remarkable level of intergenera gene exchange, including the sharing of long contiguous regions (up to 35 kb) of high identity (∼100%). Although the genomes of closely related Halobacterium, Haloquadratum, and Haloarcula (>90% average nucleotide identity) shared regions of high identity between species or strains, the four Deep Lake isolates were the only distantly related haloarchaea to share long high-identity regions. Moreover, the Deep Lake high-identity regions did not match to any other hypersaline environment metagenome data. The most abundant species, tADL, appears to play a central role in the exchange of insertion sequences, but not the exchange of high-identity regions. The genomic characteristics of the four haloarchaea are consistent with a lake ecosystem that sustains a high level of intergenera gene exchange while selecting for ecotypes that maintain sympatric speciation. The peculiarities of this polar system restrict which species can grow and provide a tempo and mode for accentuating gene exchange.

Unsaturated diether lipids in the psychrotrophic archaeon Halorubrum lacusprofundi.

The major phospholipids of Halorubrum lacusprofundi grown at 25 degrees C were archaeol phosphatidylglycerol, archaeol phosphatidylglycerylsulphate and archaeol phosphatidylglycerylphosphate methyl ester. Glycolipids included a monoglycosyl archaeol and the sulphate ester of a diglycosyl archaeol. Cultures grown at 12 degrees C contained the same suite of phospho- and glycolipids, with the addition of a series of unsaturated analogues with up to six double bonds. The patterns of unsaturation were similar for all the phospholipid series, but a different pattern occurred in the glycolipids. The analytical techniques used in this study allow facile detection of unsaturated archaeal cell membrane lipids that are degraded by commonly used chemical derivatization procedures.

Distribution and diversity of soil microfauna from East Antarctica: assessing the link between biotic and abiotic factors.

Terrestrial life in Antarctica has been described as some of the simplest on the planet, and mainly confined to soil microfaunal communities. Studies have suggested that the lack of diversity is due to extreme environmental conditions and thought to be driven by abiotic factors. In this study we investigated soil microfauna composition, abundance, and distribution in East Antarctica, and assessed correlations with soil geochemistry and environmental variables. We examined 109 soil samples from a wide range of ice-free habitats, spanning 2000 km from Framnes Mountains to Bailey Peninsula. Microfauna across all samples were patchily distributed, from complete absence of invertebrates to over 1600 specimens/gram of dry weight of soil (gdw), with highest microfauna abundance observed in samples with visible vegetation. Bdelloid rotifers were on average the most widespread found in 87% of sampled sites and the most abundant (44 specimens/gdw). Tardigrades occurred in 57% of the sampled sites with an abundance of 12 specimens/gdw. Nematodes occurred in 71% of samples with a total abundance of 3 specimens/gdw. Ciliates and mites were rarely found in soil samples, with an average abundance of 1.3 and 0.04 specimens/gdw, respectively. We found that microfaunal composition and abundance were mostly correlated with the soil geochemical parameters; phosphorus, NO3 (-) and salinity, and likely to be the result of soil properties and historic landscape formation and alteration, rather than the geographic region they were sampled from. Studies focusing on Antarctic biodiversity must take into account soil geochemical and environmental factors that influence population and species heterogeneity.

An integrative study of a meromictic lake ecosystem in Antarctica.

In nature, the complexity and structure of microbial communities varies widely, ranging from a few species to thousands of species, and from highly structured to highly unstructured communities. Here, we describe the identity and functional capacity of microbial populations within distinct layers of a pristine, marine-derived, meromictic (stratified) lake (Ace Lake) in Antarctica. Nine million open reading frames were analyzed, representing microbial samples taken from six depths of the lake size fractionated on sequential 3.0, 0.8 and 0.1 µm filters, and including metaproteome data from matching 0.1 µm filters. We determine how the interactions of members of this highly structured and moderately complex community define the biogeochemical fluxes throughout the entire lake. Our view is that the health of this delicate ecosystem is dictated by the effects of the polar light cycle on the dominant role of green sulfur bacteria in primary production and nutrient cycling, and the influence of viruses/phage and phage resistance on the cooperation between members of the microbial community right throughout the lake. To test our assertions, and develop a framework applicable to other microbially driven ecosystems, we developed a mathematical model that describes how cooperation within a microbial system is impacted by periodic fluctuations in environmental parameters on key populations of microorganisms. Our study reveals a mutualistic structure within the microbial community throughout the lake that has arisen as the result of mechanistic interactions between the physico-chemical parameters and the selection of individual members of the community. By exhaustively describing and modelling interactions in Ace Lake, we have developed an approach that may be applicable to learning how environmental perturbations affect the microbial dynamics in more complex aquatic systems.

Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica.

Green sulfur bacteria (GSB) (Chlorobiaceae) are primary producers that are important in global carbon and sulfur cycling in natural environments. An almost complete genome sequence for a single, dominant GSB species ('C-Ace') was assembled from shotgun sequence data of an environmental sample taken from the O(2)-H(2)S interface of the water column of Ace Lake, Antarctica. Approximately 34 Mb of DNA sequence data were assembled into nine scaffolds totaling 1.79 Mb, representing approximately 19-fold coverage for the C-Ace composite genome. A high level ( approximately 31%) of metaproteomic coverage was achieved using matched biomass. The metaproteogenomic approach provided unique insight into the protein complement required for dominating the microbial community under cold, nutrient-limited, oxygen-limited and extremely varied annual light conditions. C-Ace shows physiological traits that promote its ability to compete very effectively with other GSB and gain dominance (for example, specific bacteriochlorophylls, mechanisms of cold adaptation) as well as a syntrophic relationship with sulfate-reducing bacteria that provides a mechanism for the exchange of sulfur compounds. As a result we are able to propose an explanation of the active biological processes promoted by cold-adapted GSB and the adaptive strategies they use to thrive under the severe physiochemical conditions prevailing in polar environments.

Antarctic terrestrial life--challenging the history of the frozen continent?

Antarctica is a continent locked in ice, with almost 99.7% of current terrain covered by permanent ice and snow, and clear evidence that, as recently as the Last Glacial Maximum (LGM), ice sheets were both thicker and much more extensive than they are now. Ice sheet modelling of both the LGM and estimated previous ice maxima across the continent give broad support to the concept that most if not all currently ice-free ground would have been overridden during previous glaciations. This has given rise to a widely held perception that all Mesozoic (pre-glacial) terrestrial life of Antarctica was wiped out by successive and deepening glacial events. The implicit conclusion of such destruction is that most, possibly all, contemporary terrestrial life has colonised the continent during subsequent periods of glacial retreat. However, several recently emerged and complementary strands of biological and geological research cannot be reconciled comfortably with the current reconstruction of Antarctic glacial history, and therefore provide a fundamental challenge to the existing paradigms. Here, we summarise and synthesise evidence across these lines of research. The emerging fundamental insights corroborate substantial elements of the contemporary Antarctic terrestrial biota being continuously isolated in situ on a multi-million year, even pre-Gondwana break-up timescale. This new and complex terrestrial Antarctic biogeography parallels recent work suggesting greater regionalisation and evolutionary isolation than previously suspected in the circum-Antarctic marine fauna. These findings both require the adoption of a new biological paradigm within Antarctica and challenge current understanding of Antarctic glacial history. This has major implications for our understanding of the key role of Antarctica in the Earth System.

Acidianus sulfidivorans sp. nov., an extremely acidophilic, thermophilic archaeon isolated from a solfatara on Lihir Island, Papua New Guinea, and emendation of the genus description.

A novel, extremely thermoacidophilic, obligately chemolithotrophic archaeon (strain JP7(T)) was isolated from a solfatara on Lihir Island, Papua New Guinea. Cells of this organism were non-motile, Gram-negative staining, irregular-shaped cocci, 0.5-1.5 microm in size, that grew aerobically by oxidation of sulfur, Fe(2+) or mineral sulfides. Cells grew anaerobically using Fe(3+) as a terminal electron acceptor and H(2)S as an electron donor but did not oxidize hydrogen with elemental sulfur as electron acceptor. Strain JP7(T) grew optimally at 74 degrees C (temperature range 45-83 degrees C) and pH 0.8-1.4 (pH range 0.35-3.0). On the basis of 16S rRNA gene sequence similarity, strain JP7(T) was shown to belong to the Sulfolobaceae, being most closely related to the type strains of Acidianus ambivalens (93.7 %) and Acidianus infernus (93.6 %). Cell-membrane lipid structure, DNA base composition and 16S rRNA gene sequence similarity data support the placement of this strain in the genus Acidianus. Differences in aerobic and anaerobic metabolism, temperature and pH range for growth, and 16S rRNA gene sequence differentiate strain JP7(T) from recognized species of the genus Acidianus, and an emendation of the description of the genus is proposed. Strain JP7(T) is considered to represent a novel species of the genus Acidianus, for which the name Acidianus sulfidivorans sp. nov. is proposed. The type strain is JP7(T) (=DSM 18786(T)=JCM 13667(T)).

Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats.

Several cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean samples formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species. The first taxon, designated Algoriphagus ratkowskyi gen. nov., sp. nov., was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0.85). The second taxon, designated Brumimicrobium glaciale gen. nov., sp. nov., isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism. The third taxon, designated Cryomorpha ignava gen. nov., sp. nov., isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells. Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with 'Microscilla aggregans var. catalatica', which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen. nov., sp. nov. It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam. nov. (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class FLAVOBACTERIA: