Final Report: Role of microbial synergies in immobilization of metals

This Subsurface Microbial Ecology and Community Dynamics project tested the following hypothesis: synergistic groups of microorganisms immobilize heavy elements more efficiently than do individual species. We focused on groundwater at several DOE FRC and their microbial communities affecting the fate of U, Tc, and Cr. While we did not obtain evidence to support the original hypothesis, we developed a platform to accessing novel species from the target environments. We implemented this technology and discovered and isolated novel species capable of immobilization of uranium and species with exceptionally high resistances to the extant toxic factors. We have sequenced their genomes are are in the process of investigating the genomic contents behind these surprising resistances

Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea)

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Phylogenetics and Evolution 66 (2012): 397-411, doi:10.1016/j.ympev.2012.06.024.The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of free-living and endocommensal species. However, their traditional morphology-based classification conflicts with 18S rRNA gene phylogenies indicating (1) a deep bifurcation of the Litostomatea into Rhynchostomatia and Haptoria + Trichostomatia, and (2) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea. To test whether 18S rRNA molecules provide a suitable proxy for litostomatean evolutionary history, we used eighteen new ITS1-5.8S rRNA-ITS2 region sequences from various free-living litostomatean orders. These single- and multiple-locus analyses are in agreement with previous 18S rRNA gene phylogenies, supporting that both 18S rRNA gene and ITS region sequences are effective tools for resolving phylogenetic relationships among the litostomateans. Despite insertions, deletions and mutational saturations in the ITS region, the present study shows that ITS1 and ITS2 molecules can be used to infer phylogenetic relationships not only at species level but also at higher taxonomic ranks when their secondary structure information is utilized to aid alignment.Financial support was provided by the Austrian Science Foundation (FWF Projects P-19699-B17 and P-20360-B17 to Wilhelm Foissner), the Slovak Scientific Grant Agency (VEGA Project 1/0600/11 to Peter Vd’ačný), and US NSF Grants (Projects MCB-0348341 and DEB-0816840 to Slava S. Epstein)

Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea

Author Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Extremophiles 13 (2009): 151-167, doi:10.1007/s00792-008-0206-2.Environmental factors restrict the distribution of microbial eukaryotes but the exact boundaries for eukaryotic life are not known. Here we examine protistan communities at the extremes of salinity and osmotic pressure, and report rich assemblages inhabiting Bannock and Discovery, two deep-sea superhaline anoxic basins in the Mediterranean. Using a rRNA-based approach, we detected 1538 protistan rRNA gene sequences from water samples with total salinity ranging from 39 g/kg to 280 g/Kg, and obtained evidence that this DNA was endogenous to the extreme habitats sampled. Statistical analyses indicate that the discovered phylotypes represent only a fraction of species actually inhabiting both the brine and the brine-seawater interface, with as much as 82% of the actual richness missed by our survey. Jaccard indices (e.g., for a comparison of community membership) suggest that the brine/interface protistan communities are unique to Bannock and Discovery basins, and share little (0.8-2.8%) in species composition with overlying waters with typical marine salinity and oxygen tension. The protistan communities from the basins’ brine and brine/seawater interface appear to be particularly enriched with dinoflagellates, ciliates and other alveolates, as well as fungi, and are conspicuously poor in stramenopiles. The uniqueness and diversity of brine and brine-interface protistan communities make them promising targets for protistan discovery.This study was supported by grant grant STO414/2-4 of the Deutsche Forschungsgemeinschaft, the EuroDEEP program of the European Science Foundation under 06-EuroDEEP-FP-004 MIDDLE project and NSF-grant MCB- 034834

The influence of left ventricular ejection fraction on the effectiveness of cardiac resynchronization therapy: MADIT-CRT (Multicenter Automatic Defibrillator Implantation Trial With Cardiac Resynchronization Therapy).

OBJECTIVES: The goal of this study was to evaluate the influence of left ventricular (LV) lead position on the risk of ventricular tachyarrhythmia in patients undergoing cardiac resynchronization therapy (CRT). BACKGROUND: Left ventricular ejection fraction (LVEF) is a surrogate marker of heart failure (HF) status and associated risk. Data on the effectiveness of cardiac resynchronization therapy with defibrillator (CRT-D) in patients with mild HF and better LVEF are limited. METHODS: In the MADIT-CRT (Multicenter Automatic Defibrillator Implantation Trial With Cardiac Resynchronization Therapy) study, the echocardiography core laboratory assessed baseline LVEF independent of the enrolling centers and identified a range of LVEFs, including those >30% (i.e., beyond the eligibility criteria). Echocardiographic response with CRT, defined as percent change in left ventricular end-diastolic volume (LVEDV), was analyzed in 3 prespecified LVEF groups: >30%, 26% to 30%, and 30% (in the range of 30.1% to 45.3%); 914 patients (50.5%) with LVEF 26% to 30%; and 199 patients with LVEF 30%: 22.3%; LVEF 26% to 30%: 20.1%; and LVEF 30% (hazard ratio [HR]: = 0.56 [95% confidence interval (CI): 0.39 to 0.82], p = 0.003), LVEF 26% to 30% (HR: 0.67: [95% CI: 0.50 to 0.90], p = 0.007), and LVEF 0.1). CONCLUSIONS: In MADIT-CRT, the clinical benefit of CRT was evident regardless of baseline LVEF, including those with LVEF >30%, whereas the echocardiographic response was increased with increasing LVEF, indicating that CRT might benefit patients with better LVEF. (Multicenter Automatic Defibrillator Implantation With Cardiac Resynchronization Therapy [MADIT-CRT]; NCT00180271)

The Laser Astrometric Test of Relativity Mission

This paper discusses new fundamental physics experiment to test relativistic gravity at the accuracy better than the effects of the 2nd order in the gravitational field strength. The Laser Astrometric Test Of Relativity (LATOR) mission uses laser interferometry between two micro-spacecraft whose lines of sight pass close by the Sun to accurately measure deflection of light in the solar gravity. The key element of the experimental design is a redundant geometry optical truss provided by a long-baseline (100 m) multi-channel stellar optical interferometer placed on the International Space Station. The geometric redundancy enables LATOR to measure the departure from Euclidean geometry caused by the solar gravity field to a very high accuracy. LATOR will not only improve the value of the parameterized post-Newtonian (PPN) parameter gamma to unprecedented levels of accuracy of 1 part in 1e8, it will also reach ability to measure effects of the next post-Newtonian order (1/c^4) of light deflection resulting from gravity's intrinsic non-linearity. The solar quadrupole moment parameter, J2, will be measured with high precision, as well as a variety of other relativistic. LATOR will lead to very robust advances in the tests of fundamental physics: this mission could discover a violation or extension of general relativity, or reveal the presence of an additional long range interaction in the physical law. There are no analogs to the LATOR experiment; it is unique and is a natural culmination of solar system gravity experiments.Comment: 8 pages, 2 figures, invited talk given at the Second International Conference on Particle and Fundamental Physics in Space (SpacePart'03), 10-12 December 2003, Washington, D

Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?

The impact of climate on biodiversity is indisputable. Climate changes over geological time must have significantly influenced the evolution of biodiversity, ultimately leading to its present pattern. Here we consider the paleoclimate data record, inferring that present-day hot and cold environments should contain, respectively, the largest and the smallest diversity of ancestral lineages of microbial eukaryotes.We investigate this hypothesis by analyzing an original dataset of 18S rRNA gene sequences from Western Greenland in the Arctic, and data from the existing literature on 18S rRNA gene diversity in hydrothermal vent, temperate sediments, and anoxic water column communities. Unexpectedly, the community from the cold environment emerged as one of the richest observed to date in protistan species, and most diverse in ancestral lineages.This pattern is consistent with natural selection sweeps on aerobic non-psychrophilic microbial eukaryotes repeatedly caused by low temperatures and global anoxia of snowball Earth conditions. It implies that cold refuges persisted through the periods of greenhouse conditions, which agrees with some, although not all, current views on the extent of the past global cooling and warming events. We therefore identify cold environments as promising targets for microbial discovery

Novel Eukaryotic Lineages Inferred from Small-Subunit rRNA Analyses of Oxygen-Depleted Marine Environments

Microeukaryotes in oxygen-depleted environments are among the most diverse, as well as the least studied, organisms. We conducted a cultivation-independent, small-subunit (SSU) rRNA-based survey of microeukaryotes in suboxic waters and anoxic sediments in the great Sippewisset salt marsh, Cape Cod, Mass. We generated two clone libraries and analyzed approximately 300 clones, which contained a large diversity of microeukaryotic SSU rRNA signatures. Only a few of these signatures were closely related (sequence similarity of >97%) to the sequences reported earlier. The bulk of our sequences represented deep novel branches within green algae, fungi, cercozoa, stramenopiles, alveolates, euglenozoa and unclassified flagellates. In addition, a significant number of detected rRNA sequences exhibited no affiliation to known organisms and sequences and thus represent novel lineages of the highest taxonomical order, most of them branching off the base of the global phylogenetic tree. This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes