Molecular Identification and Localization of Filamentous Symbiotic Bacteria Associated with the Hydrothermal Vent Annelid Alvinella pompejana

Alvinella pompejana is a polychaetous annelid that inhabits high-temperature environments associated with active deep-sea hydrothermal vents along the East Pacific Rise. A unique and diverse epibiotic microflora with a prominent filamentous morphotype is found associated with the worm's dorsal integument. A previous study established the taxonomic positions of two epsilon proteobacterial phylotypes, 13B and 5A, which dominated a clone library of 16S rRNA genes amplified by PCR from the epibiotic microbial community of an A. pompejana specimen. In the present study deoxyoligonucleotide PCR primers specific for phylotypes 13B and 5A were used to demonstrate that these phylotypes are regular features of the bacterial community associated with A. pompejana. Assaying of other surfaces around colonies of A. pompejana revealed that phylotypes 13B and 5A are not restricted to A. pompejana. Phylotype 13B occurs on the exterior surfaces of other invertebrate genera and rock surfaces, and phylotype 5A occurs on a congener, Alvinella caudata. The 13B and 5A phylotypes were identified and localized on A. pompejana by in situ hybridization, demonstrating that these two phylotypes are, in fact, the prominent filamentous bacteria on the dorsal integument of A. pompejana. These findings indicate that the filamentous bacterial symbionts of A. pompejana are epsilon Proteobacteria which do not have an obligate requirement for A. pompejana.     

Small trees,big problems: Comparative leaf function under extreme edaphic stress

Premise of the Study

The pygmy forest, a plant community of severely stunted conifers and ericaceous angiosperms, occurs on patches of highly acidic, nutrient‐poor soils along the coast of Northern California, USA. This system is an excellent opportunity to study the effect of severe nutrient deficiency on leaf physiology in a naturally‐occurring ecosystem. In this study, we seek to understand the physiological mechanisms stunting the plants' growth and their implications for whole plant function.

Methods

We measured 14 traits pertaining to leaf photosynthetic function or physical structure on seven species. Samples were taken from the pygmy forest community and from conspecifics growing on higher‐nutrient soils, where trees may grow over 30 m tall.

Key Results

Pygmy plants of most species maintained similar area‐based photosynthetic and stomatal conductance rates to conspecific controls, but had lower specific leaf area (leaf area divided by dry weight), lower percent nitrogen, and less leaf area relative to xylem growth. Sequoia sempervirens, a species rare in the pygmy forest, had a categorically different response from the more common plants and had remarkably low photosynthetic rates.

Conclusions

Pygmy plants were not stunted by low photosynthetic rates on a leaf‐area basis; instead, several species had restricted whole‐plant photosynthesis due to low leaf area production. Pygmy plants of all species showed signs of greater carbon investment in their leaves and higher production of nonphotosynthetic leaf tissue, further contributing to slow growth rates.     

Interdomain salt‐bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization

The Ebola virus protein VP40 is a transformer protein that possesses an extraordinary ability to accomplish multiple functions by transforming into various oligomeric conformations. The disengagement of the C‐terminal domain (CTD) from the N‐terminal domain (NTD) is a crucial step in the conformational transformations of VP40 from the dimeric form to the hexameric form or octameric ring structure. Here, we use various molecular dynamics (MD) simulations to investigate the dynamics of the VP40 protein and the roles of interdomain interactions that are important for the domain–domain association and dissociation, and report on experimental results of the behavior of mutant variants of VP40. The MD studies find that various salt‐bridge interactions modulate the VP40 domain dynamics by providing conformational specificity through interdomain interactions. The MD simulations reveal a novel salt‐bridge between D45‐K326 when the CTD participates in a latch‐like interaction with the NTD. The D45‐K326 salt‐bridge interaction is proposed to help domain–domain association, whereas the E76‐K291 interaction is important for stabilizing the closed‐form structure. The effects of the removal of important VP40 salt‐bridges on plasma membrane (PM) localization, VP40 oligomerization, and virus like particle (VLP) budding assays were investigated experimentally by live cell imaging using an EGFP‐tagged VP40 system. It is found that the mutations K291E and D45K show enhanced PM localization but D45K significantly reduced VLP formation.     

Temporal,regional and geochemical drivers of microbial community variation in the melt ponds of the Ross Sea region,Antarctica

To expand the understanding of the poorly described planktonic bacterial communities inhabiting Antarctic meltwater ponds, this study characterized the community composition and identified environmental drivers influencing community structure from a total of 41 meltwater ponds: 37 from the McMurdo Ice Shelf (Bratina Island) and four from a terrestrial locale (Miers Valley) during three austral summers. DNA fingerprinting coupled with in situ pH and conductivity was utilized to select ponds for in-depth nutrient and chemical analysis and high-throughput sequencing of the bacterial 16S rRNA gene V5–V6 hypervariable region. Conductivity was the strongest driver of community structure across all ponds and for all time points; however, other influential factors (pH, climatological, Hg, Fe, and PO₄) were also identified. Unique members of communities (sequences absent in at least one pond) represented a small percentage of total reads but also represented a large proportion of pond biodiversity that was strongly driven by differing environmental variables (Si, B and S). Significant temporal variation in community structure was also identified within the same ponds although major taxa remained present. Miers Valley ponds exhibit greater similarity to Bratina Island ponds rather than between each other, thereby suggesting regional movement of microorganisms. In summary, these data provide the first in-depth investigation of the intra-seasonal and regional variation of the microbial communities inhabiting these ponds and proved that a total of ten cosmopolitan OTUs were the dominant components of ponds throughout all sampling times and locations, their variable relative abundances driving the major dissimilarities in community structure.     

Copepod foraging and predation risk within the surface layer during night-time feeding forays

Vertical distribution data seem to indicate that certain speciesof diel vertical migrating copepods avoid the surface high chlorophyll(Chl) region within coastal and estuarine environments, evenduring the night. Copepods may avoid this layer to reduce predationmortality, avoid advective loss or to avoid consuming too muchtoxic algae. We hypothesize that copepods make several intermittentfeeding ‘forays’ into shallow surface layers duringthe night, returning to intermediate depths between forays.Using an individual-based model (IBM) of Calanus pacificus,we examined the implications of this behavior on feeding successand mortality risk, and tested whether a practical field-samplingscheme would be able to detect foray-like behavior. In somecases, mortality of the foray-foraging copepods was up to 50%less than that of randomly behaving controls, for a given amountof food ingested. The trapping scheme devised should be ableto detect the occurrence of foray behavior (FB) in the fieldand should show differences in the gut contents of copepodsentering and leaving the uppermost food-rich layer. The presenceor absence of foray-like behavior significantly altered therelative concentration of copepods within various surface strataand thus could influence the temporal availability of copepodsas prey for the larvae and juveniles of several important managedfish species. This paper is one of six on the subject of the role of zooplanktonpredator–prey interactions in structuring plankton communities.     

Metastasis-associated C4.4A, a GPI-anchored protein cleaved by ADAM10 and ADAM17

Metalloproteases play a complex role in tumor progression. While the activity of some ADAM, ADAMTS and matrix metalloproteases (MMPs) seems to be protumorigenic, the activity of others seems to prevent tumor progression. The identification of the array of substrates of a given metalloprotease (degradome) seems an adequate approach to predict the effect of the inhibition of a metalloprotease in tumors. Here, we present the proteomic identification of a novel substrate for ADAM10 and -17. We used SILAC (Stable Isotope Labeling by Amino acids in Cell culture), a proteomic technique based on the differential metabolic labeling of cells in different conditions. This was applied to MCF7 cells derived from an invasive mammary tumor, and the same cells expressing shRNAs that knock down ADAM10 or -17. Following this approach, we have identified C4.4A as a substrate to both metalloproteases. Since C4.4A is likely involved in tumor invasion, these results indicate that the cleavage of C4.4A by ADAM10 and ADAM17 contributes to tumor progression.