Antarctic Dry Valley mineral soils contain unexpectedly high levels of microbial biomass

We have applied bioluminescent ATP detection methods to microbial enumeration in Antarctic Dry Valley mineral soils, and validated our ATP data by two independent methods. We have demonstrated that ATP measurement is a valid means of determining microbial biomass in such sites, and that the desiccated surface mineral soils of the Antarctic Dry Valleys contain cell numbers over four orders of magnitude higher than previously suggested.     

Extraction of nematodes from Dry Valley Antarctic soils

Nematode density and taxonomic composition from Dry Valley soil processed by the sugar centrifugation (SC) method in Antarctica was compared to those extracted from soils shipped frozen to the USA and processed by either the SC or Baermann Funnel (BF) (at 5°C and 10°C) techniques. Soil selected for the extraction comparisons represented a wide range of soil properties found in the Dry Valleys. More nematodes were recovered from freshly collected Antarctic soil and from stored frozen soil using the SC technique than from BF at either temperature (P<0.05). Temperature had no effect on nematode densities extracted by the BF. Scottnema lindsayae was the most abundant species recovered by all extraction methods, but recovery was significantly lower from stored soils. Thus, nematodes can be extracted qualitatively following frozen storage using SC, but quantitative studies of nematode populations should be based on soils extracted following field sampling.     

Controls on the distribution of productivity and organic resources in Antarctic Dry Valley soils

The Antarctic Dry Valleys are regarded as one of the harshest terrestrial habitats on Earth because of the extremely cold and dry conditions. Despite the extreme environment and scarcity of conspicuous primary producers, the soils contain organic carbon and heterotrophic micro-organisms and invertebrates. Potential sources of organic compounds to sustain soil organisms include in situ primary production by micro-organisms and mosses, spatial subsidies from lacustrine and marine-derived detritus, and temporal subsidies ('legacies') from ancient lake deposits. The contributions from these sources at different sites are likely to be influenced by local environmental conditions, especially soil moisture content, position in the landscape in relation to lake level oscillations and legacies from previous geomorphic processes. Here we review the abiotic factors that influence biological activity in Dry Valley soils and present a conceptual model that summarizes mechanisms leading to organic resources therein.     

A halotolerantPlanococcus from Antarctic Dry Valley soil

A halotolerantPlanococcus (strain A4a) was isolated from saline Antarctic Dry Valley soil.Planococcus strain A4a grew over wide ranges of temperature (0°C–40°C) and NaCl concentrations (0–2.0M). When the NaCl concentration of the growth medium was increased, the total intracellular free amino acid concentration increased; however, the intracellular potassium concentration did not increase. This result suggested that intracellular free amino acids functioned as compatible solutes for growth ofPlanococcus strain A4a at elevated NaCl concentrations. The halotolerant and psychrotolerant nature ofPlanococcus strain A4a would appear to provide it with the capacity for growth in the saline Antarctic Dry Valley soil environment from which it was isolated.     

Stability of ATP in Antarctic mineral soils

The stability of exogenous ATP in Antarctic Ross desert soils has been assessed using bioluminescence monitoring of ATP-supplemented samples. Under typical east Antarctic dry valley summer conditions (−3 to +15°C), exogenous ATP was degraded with a half-life of between 0.5 and 30 h. The rate of degradation was affected, in order of significance, by soil biomass levels, temperature and water content. Such rapid removal of exogenous ATP strongly suggests that extracellular ATP from lysed cells in cold desiccated soils does not make a significant contribution to the standing ATP titre     

Soil Carbon Dioxide Flux in Antarctic Dry Valley Ecosystems

The Antarctic dry valleys of southern Victoria Land are extreme desert environments where abiotic factors, such as temperature gradients, parent material, and soil water dynamics, may have a significant influence on soil carbon dioxide (CO₂) flux. Previous measurements of soil respiration have demonstrated very low rates of CO₂ efflux, barely above detection limits. We employed a modified infrared gas-analyzer system that enabled detection of smaller changes in CO₂ concentration in the field than previously possible. We measured diel CO₂ fluxes and monitored soil microclimate at three sites in Taylor Valley. Soil CO₂ flux ranged from –0.1 to 0.15 mol m^–2 s^–1. At two of the three sites, we detected a physically driven flux associated with diel variability in soil temperature. At these sites, CO₂ uptake (negative flux) was associated with dropping soil temperatures, whereas CO₂ evolution (positive flux) was associated with increases in soil temperature. These observations are corroborated by laboratory experiments that suggest that CO₂ flux is influenced by physically driven processes. We discuss four potential mechanisms that may contribute to physically driven gas exchange. Our results suggest there are strong interactions between biological and abiotic controls over soil CO₂ flux in terrestrial ecosystems of the Antarctic dry valleys, and that the magnitude of either may dominate depending on the soil environment and biological activity.     

Invertebrate Biodiversity in Antarctic Dry Valley Soils and Sediments

We studied invertebrate communities across a transition zone between soils and stream sediments in the cold desert landscape of Taylor Valley, Antarctica. We hypothesized that hydrological and biogeochemical linkages in the functionally important transition zone between streams and surrounding soils should be important in structuring invertebrate communities. We compared invertebrate communities along transects beginning in the saturated sediments under flowing stream water and extending laterally through the hyporheic zone to the dry soils that characterize most of the dry valley landscape. Nematodes, rotifers, and tardigrades assembled into different communities in soils and sediments, but there was no relationship between the total abundance of invertebrates and moisture. Community diversity was, however, influenced by the moisture and salinity gradients created with distance from flowing waters. The wet, low-salinity sediments in the center of the stream contained the most invertebrates and had the highest taxonomic diversity. Adjacent to the stream, communities in the hyporheic zone were influenced strongly by salt deposition. Abundance of invertebrates was low in the hyporheic zone, but this area contained the most co-occurring nematode species (three species). In dry soils, communities were composed almost entirely of a single species of nematode, Scottnema lindsayae, an organism not found in the stream center. These results suggest spatially-partitioned niches for invertebrates in soils and sediments in the dry valley landscape based on proximity to sources of moisture and the interactive effects of salinity. Received 22 September 1998; accepted 16 April 1999.     

Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems

Microorganisms able to synthesize rhodopsins have the capacity to translocate ions through their membranes, using solar energy to generate a proton motive force. Rhodopsins are the most abundant phototrophic proteins in oceanic surface waters and are key constituents in marine bacterial ecology. However, it remains unclear how rhodopsins are used in most microorganisms. Despite their abundance in marine and fresh‐water systems, the presence of functional rhodopsin systems in edaphic habitats has never been reported. Here, we show the presence of several new putative H⁺, Na⁺ and Cl⁺ pumping rhodopsins identified by metagenomic analysis of Antarctic desert hypolithic communities. Reconstruction of two Proteobacteria genomes harboring xanthorhodopsin‐like proteins and one Bacteroidetes genome with a Na‐pumping‐like rhodopsin indicated that these bacteria were aerobic heterotrophs possessing the apparent capacity for the functional expression of rhodopsins. The existence of these protein systems in hypolithic bacteria expands the known role of rhodopsins to include terrestrial environments and suggests a possible predominant function as heterotrophic energy supply proteins, a feasible microbial adaptation to the harsh conditions prevalent in Antarctic edaphic systems.     

Distribution and abiotic influences on hypolithic microbial communities in an Antarctic Dry Valley

The Miers Valley within the McMurdo Dry Valleys of Antarctica supports abundant quartz and marble substrates for hypolithons—microbial colonists on the underside of these translucent rocks. Three physically distinct hypolithic community types have been identified: cyanobacteria dominated (Type I), fungus dominated (Type II) or moss dominated (Type III). The distribution of the three types was mapped across much of the ~75 km² area of the upper Miers Valley and correlated this with the measurements of selected micro-environmental variables. Type I hypolithons were most common and occurred at all altitudes up to 824 m, whilst Type II and Type III hypolithons were less abundant and restricted to lower altitudes on the valley floor (<415 m and <257 m, respectively). Whilst all colonized quartz effectively filtered incident UVB irradiance, transmittance levels for UVA and PAR varied markedly and were significant in determining hypolith type. Notably, the Type I hypolithons occurred under rocks with a significantly lower transmittance of photosynthetically active radiation than Type II and III hypolithons. Altitude and aspect were also significant factors determining hypolith type, and a role for altitude-related abiotic variables in determining the distribution of Type I, II and III hypolithons is proposed.     

Phylogenetic analysis of bacteria associated with Laminaria saccharina

Bacterial communities associated with the brown alga Laminaria saccharina from the Baltic Sea and from the North Sea were investigated using denaturing gradient gel electrophoresis and 16S rRNA gene clone libraries. The rhizoid, cauloid, meristem and phyloid revealed different 16S rRNA gene denaturing gradient gel electrophoresis banding patterns indicating a specific association of bacterial communities with different parts of the alga. Associations with cauloid and meristem were more specific, while less specific associations were obtained from the old phyloid. In addition, seasonal and geographical differences in the associated communities were observed. Results from 16S rRNA gene libraries supported these findings. Bacterial phylotypes associated with the alga were affiliated with the Alphaproteobacteria (nine phylotypes), Gammaproteobacteria (nine phylotypes) and the Bacteroidetes group (four phylotypes). A number of bacteria associated with other algae and other marine macroorganisms were among the closest relatives of phylotypes associated with L. saccharina.     

Life cycle of the microbivorous Antarctic Dry Valley nematode Scottnema lindsayae (Timm 1971)

The life cycle of the Antarctic Dry Valley soil nematode, Scottnema lindsayae (Timm 1971) was studied in laboratory culture at two temperatures, 10°C and 15°C. Soil yeast and bacteria isolated with the nematodes were used as the food source. The species reproduced sexually. The higher temperature had a negative effect on the life cycle. The number of eggs per female and the number of juveniles developing per female were greater at 10°C than at 15°C. Juveniles developed faster at 10°C and four juvenile stages were observed outside of the egg at both temperatures. The unusually long life cycle (218 d at 10°C) suggests that more than one austral summer may be required for successful completion. An increase in Dry Valley soil temperatures associated with potential global environmental change may have detrimental effects on soil nematodes.     

Phylogenetic and phylogeographic analysis of Iberian lynx populations

The Iberian lynx (Lynx pardinus), one of the world's most endangered cat species, is vulnerable due to habitat loss, increased fragmentation of populations, and precipitous demographic reductions. An understanding of Iberian lynx evolutionary history is necessary to develop rational management plans for the species. Our objectives were to assess Iberian lynx genetic diversity at three evolutionary timescales. First we analyzed mitochondrial DNA (mtDNA) sequence variation to position the Iberian lynx relative to other species of the genus LYNX: We then assessed the pattern of mtDNA variation of isolated populations across the Iberian Peninsula. Finally we estimated levels of gene flow between two of the most important remaining lynx populations (Do?ana National Park and the Sierra Morena Mountains) and characterized the extent of microsatellite locus variation in these populations. Phylogenetic analyses of 1613 bp of mtDNA sequence variation supports the hypothesis that the Iberian lynx, Eurasian lynx, and Canadian lynx diverged within a short time period around 1.53-1.68 million years ago, and that the Iberian lynx and Eurasian lynx are sister taxa. Relative to most other felid species, genetic variation in mtDNA genes and nuclear microsatellites were reduced in Iberian lynx, suggesting that they experienced a fairly severe demographic bottleneck. In addition, the effects of more recent reductions in gene flow and population size are being manifested in local patterns of molecular genetic variation. These data, combined with recent studies modeling the viability of Iberian lynx populations, should provide greater urgency for the development and implementation of rational in situ and ex situ conservation plans.     

Phylogenetic analysis of Antarctic notothenioid fishes based on two-dimensional gel electrophoresis

There has been some controversy over the phylogeny of Antarctic notothenioid fishes among researchers. In this study, total protein constituents of cardiac muscles from six well-known notothenioid species were compared by two-dimensional gel electrophoresis to obtain comprehensive phylogenetic information to shed light on the controversial issues. Our phylogenetic analyses showed that Gymnodraco acuticeps (Bathydraconidae) and Champsocephalus gunnari (Channichthyidae) composed a sistergroup, and that the family Nototheniidae was paraphyletic, because nototheniid Gobionotothen gibberifrons was more closely related to the bathydraconid-channichthyid clade than to the clade composed of three other nototheniid species. Our data also showed that Trematomus bernacchii was more closely related to Pagothenia borchgrevinki than to congeneric T. eulepidotus, suggesting that the taxonomic status of P. borchgrevinki or T. bernacchii should be re-evaluated. Since our results were supported by nucleotide sequence data on rRNA genes, phylogenetic relationships of Antarctic notothenioids have become more entrenched by molecular approaches at both protein and DNA levels.     

Phylogenetic analysis of mutualistic filamentous bacteria associated with fungus-growing ants

The attine ant-microbe system is a quadripartite symbiosis, involving a complex set of mutualistic and parasitic associations. The symbiosis includes the fungus-growing ants (tribe Attini), the basidiomycetous fungi the ants cultivate for food, specialized microfungal parasites (in the genus Escovopsis) of the cultivar, and ant-associated mu tualistic filamentous bacteria that secrete antibiotics specifically targeted to suppress the growth of Escovopsis. In this study, we conduct the first phylogenetic analysis of the filamentous mutualistic bacteria (actinomycetes) associated with fungus-growing ants. The filamentous bacteria present on 3 genera of fungus-growing ants (Acromyrmex, Trachy myrmex, and Apterostigma) were isolated from 126 colonies. The isolated actinomycetes were grouped into 3 distinct morphological types. Each morphological type was specific to the ant genus from which it was isolated, suggesting some degree of host specificity. The phylogenetic position of the 3 morphotypes was estimated using 16S rDNA for representative strains. The 8 isolates of actinomycetes sequenced are in the family Pseudonocardiaceae (Actino mycetales) and belong to the genus Pseudonocardia. Transmission electron microscopy examination of the actino mycete associated with the cuticle of Acromyrmex sp. revealed bacterial cells with an outer electron-dense membrane, consistent with actinomycetes in the genus Pseudonocardia. Ant-associated Pseudonocardia isolates did not form a monophyletic group, suggesting multiple acquisitions of actinomycetes by fungus-growing ants over their evolutionary history.     

Molecular analysis of geographic patterns of eukaryotic diversity in Antarctic soils

We describe the application of molecular biological techniques to estimate eukaryotic diversity (primarily fungi, algae, and protists) in Antarctic soils across a latitudinal and environmental gradient between approximately 60 and 87 degrees S. The data were used to (i) test the hypothesis that diversity would decrease with increasing southerly latitude and environmental severity, as is generally claimed for "higher" faunal and plant groups, and (ii) investigate the level of endemicity displayed in different taxonomic groups. Only limited support was obtained for a systematic decrease in diversity with latitude, and then only at the level of a gross comparison between maritime (Antarctic Peninsula/Scotia Arc) and continental Antarctic sites. While the most southerly continental Antarctic site was three to four times less diverse than all maritime sites, there was no evidence for a trend of decreasing diversity across the entire range of the maritime Antarctic (60 to 72 degrees S). Rather, we found the reverse pattern, with highest diversity at sites on Alexander Island (ca. 72 degrees S), at the southern limit of the maritime Antarctic. The very limited overlap found between the eukaryotic biota of the different study sites, combined with their generally low relatedness to existing sequence databases, indicates a high level of Antarctic site isolation and possibly endemicity, a pattern not consistent with similar studies on other continents.     

European bone mineral density loci are also associated with BMD in East-Asian populations

Most genome-wide association (GWA) studies have focused on populations of European ancestry with limited assessment of the influence of the sequence variants on populations of other ethnicities. To determine whether markers that we have recently shown to associate with Bone Mineral Density (BMD) in Europeans also associate with BMD in East-Asians we analysed 50 markers from 23 genomic loci in samples from Korea (n = 1,397) and two Chinese Hong Kong sample sets (n = 3,869 and n = 785). Through this effort we identified fourteen loci that associated with BMD in East-Asian samples using a false discovery rate (FDR) of 0.05; 1p36 (ZBTB40, P = 4.3×10⁻⁹), 1p31 (GPR177, P = 0.00012), 3p22 (CTNNB1, P = 0.00013), 4q22 (MEPE, P = 0.0026), 5q14 (MEF2C, P = 1.3×10⁻⁵), 6q25 (ESR1, P = 0.0011), 7p14 (STARD3NL, P = 0.00025), 7q21 (FLJ42280, P = 0.00017), 8q24 (TNFRSF11B, P = 3.4×10⁻⁵), 11p15 (SOX6, P = 0.00033), 11q13 (LRP5, P = 0.0033), 13q14 (TNFSF11, P = 7.5×10⁻⁵), 16q24 (FOXL1, P = 0.0010) and 17q21 (SOST, P = 0.015). Our study marks an early effort towards the challenge of cataloguing bone density variants shared by many ethnicities by testing BMD variants that have been established in Europeans, in East-Asians.     

Spectral Properties of the Green Alga Trebouxia,a Phycobiont of Cryptoendolithic Lichens in the Antarctic Dry Valley

An algologically pure culture of the green alga Trebouxia, a phycobiont of cryptoendolithic lichens, was isolated from sandstone samples collected in the high-altitude polar regions of Antarctica. The absorption and second-derivative absorption spectra of acetone extract of the Antarctic phycobiont cells were studied in comparison with those of a Trebouxia phycobiont isolated recently from a Parmeliaceae lichen in the Mid-European climatic zone. The cells of the Antarctic phycobiont were characterized by a lower content of chlorophyll a and a higher ratio of chlorophyll b and carotenoids to chlorophyll a as compared to the Mid-European phycobiont. Furthermore, the carotenoids of the Antarctic phycobiont were more diverse. The low-temperature fluorescence spectra of the Antarctic phycobiont were characterized by an increased intensity of the short-wavelength fluorescence peak of chlorophyll aand a diminished intensity of fluorescence in the long-wavelength spectral region.     

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH₃) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH₃ oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH₃ oxidation rates. In addition, the enrichments provided the first direct evidence for NH₃ oxidation by an AOA from an uncharacterized Thaumarchaeota–AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.