Lake Fryxell is a perennially ice-covered lake in the McMurdo Dry Valleys, Antarctica, with a sharp oxycline in a water column that is density stabilized by a gradient in salt concentration. Dissolved oxygen falls from 20 mg liter ؊1 to undetectable over one vertical meter from 8.9-to 9.9-m depth. We provide the first description of the benthic mat community that falls within this oxygen gradient on the sloping floor of the lake, using a combination of micro-and macroscopic morphological descriptions, pigment analysis, and 16S rRNA gene bacterial community analysis. Our work focused on three macroscopic mat morphologies that were associated with different parts of the oxygen gradient: (i) "cuspate pinnacles" in the upper hyperoxic zone, which displayed complex topography and were dominated by phycoerythrin-rich cyanobacteria attributable to the genus Leptolyngbya and a diverse but sparse assemblage of pennate diatoms; (ii) a less topographically complex "ridge-pit" mat located immediately above the oxic-anoxic transition containing Leptolyngbya and an increasing abundance of diatoms; and (iii) flat prostrate mats in the upper anoxic zone, dominated by a green cyanobacterium phylogenetically identified as Phormidium pseudopriestleyi and a single diatom, Diadesmis contenta. Zonation of bacteria was by lake depth and by depth into individual mats. Deeper mats had higher abundances of bacteriochlorophylls and anoxygenic phototrophs, including Chlorobi and Chloroflexi. This suggests that microbial communities form assemblages specific to niche-like locations. Mat morphologies, underpinned by cyanobacterial and diatom composition, are the result of local habitat conditions likely defined by irradiance and oxygen and sulfide concentrations.

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

Soil C sequestration has been proposed as a tool for addressing climate change. However, models used to predict soil C sequestration do not account for C saturation and functional differences among soil C pools. In this study, we examined differences in soil C pool content of a forest soil in Pennsylvania following 20 yr of detrital manipulation (i.e., control, no roots, no leaf litter, no inputs, double leaf litter). Detrital input treatments had a highly significant (ANOVA, F = 10.6, p < 0.0001) effect on soil C in the 0‐ to 5‐cm soil depth. However, soil C pools responded differently to the different treatments: the intra‐microaggregate silt + clay, intra‐microaggregate particulate organic matter (POM), and silt + clay within large macroaggregates in plots receiving no detrital inputs had significantly lower C concentrations (1.1, 2.5, and 0.4 g C kg−1 soil, respectively) than the control, double‐leaf‐litter, and no‐roots plots. Carbon in coarse POM within small macroaggregates was significantly lower in double‐leaf‐litter (4.5 g C kg−1 soil) and no‐leaf‐litter plots (6.6 g C kg−1 soil) than all other treatments (15.3–28 g C kg−1 soil). The intra‐microaggregate fractions in double‐leaf‐litter plots had greater C concentrations than in the control plots; along with moderate C concentrations in all bulk soil samples, this suggests that the soil is not yet approaching C saturation. This study reinforces the use of microaggregates within large macroaggregates as a diagnostic fraction for changes in soil C content and demonstrates that altering the organic matter source and quantity significantly affects soil C sequestration dynamics. Consideration of these factors will enable improved assessment of soil C sequestration capacity and management.

Here, we present the draft genome sequences for Pseudoalteromonas sp. strain UCD-33C and Pseudoalteromonas lipolytica UCD-48B. Pseudoalteromonas sp. UCD-33C was isolated from Zostera marina roots and P. lipolytica UCD-48B from Z. marina leaf blades, both collected in Woods Hole, MA. These assemblies contain 4,479,285 bp and 4,592,435 bp, respectively.