Extracellular Electron Uptake by Two Methanosarcina Species

Direct electron uptake by prokaryotes is a recently described mechanism with a potential application for energy and CO2 storage into value added chemicals. Members of Methanosarcinales, an environmentally and biotechnologically relevant group of methanogens, were previously shown to retrieve electrons from an extracellular electrogenic partner performing Direct Interspecies Electron Transfer (DIET) and were therefore proposed to be electroactive. However, their intrinsic electroactivity has never been examined. In this study, we tested two methanogens belonging to the genus Methanosarcina, M. barkeri, and M. horonobensis, regarding their ability to accept electrons directly from insoluble electron donors like other cells, conductive particles and electrodes. Both methanogens were able to retrieve electrons from Geobacter metallireducens via DIET. Furthermore, DIET was also stimulated upon addition of electrically conductive granular activated carbon (GAC) when each was co-cultured with G. metallireducens. However, when provided with a cathode poised at −400 mV (vs. SHE), only M. barkeri could perform electromethanogenesis. In contrast, the strict hydrogenotrophic methanogen, Methanobacterium formicicum, did not produce methane regardless of the type of insoluble electron donor provided (Geobacter cells, GAC or electrodes). A comparison of functional gene categories between the two Methanosarcina showed differences regarding energy metabolism, which could explain dissimilarities concerning electromethanogenesis at fixed potentials. We suggest that these dissimilarities are minimized in the presence of an electrogenic DIET partner (e.g., Geobacter), which can modulate its surface redox potentials by adjusting the expression of electroactive surface proteins

Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora)

publisher: Elsevier articletitle: Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora) journaltitle: Molecular Phylogenetics and Evolution articlelink: http://dx.doi.org/10.1016/j.ympev.2016.08.019 content_type: article copyright: © 2016 Elsevier Inc. All rights reserved.The file attached is the Accepted/final draft post-refereeing version of the articl

The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The file attached is the published version of the article

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Systematic Biology 59 (2010): 518-533, doi:10.1093/sysbio/syq037.An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ‘Chromalveolata’ is rejected. Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxonrich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data

Foraminifera: New approaches to their paleobiology, biology and evolution

Both fossil and living foraminifera have been investigated in this study. Late Cretaceous age foraminiferal assemblages have been used to examine the relationship between high-frequency sea level change, biotic response and paleoceanography, in the U.S. Western Interior Sea. Living planktic foraminifera were also studied in order to test a novel hypothesis on the evolution of cellular organelles known as fibrillar bodies. The major findings of this dissertation are: (1) The third-order Greenhorn tectono-eustatic cycle (late Cenomanian-middle Turonian) in the Cretaceous Western Interior Basin is superposed by fourth-order relative sea level cycles and fifth-order parasequences that are reflected in foraminferal assemblages and carbonate content of shales and mudrocks. The study interval includes the Cenomanian/Turonian (C/T) boundary event (93.3 Ma) and the highest stand of sea level in the western interior during early Turonian time. Calcareous benthic foraminiferal assemblages show marked shifts in taxon dominance which is interpreted as ecologic replacement indicating change from a food-controlled to an oxygen-controlled environment. Acmes of the genus Gavelinella are related to the initiation of fourth-order transgressive episodes early in the third-order transgression and late highstand phases of the Greenhorn Cycle. The rapid proliferation of this taxon is thought to be a response to pulses of food. Warm, oxygen-poor Tethyan waters spread across the WIS during the late transgression and highstand phases of the Greenhorn Cycle. A rapid ecologic shift to Neobulimina dominance is the benthic foraminiferal response to this Tethyan incursion. The relative abundance of Neobulimina shows a highly significant correlation to carbonate content (p $\u3c$ 0.01), which is a proxy for warm, more normal marine water masses entering the WIS from the south. Tethyan water masses were replaced by those of Boreal affinity and agglutinated benthic foraminiferal assemblages during the regressive phase of the Greenhorn Cycle. Variations in benthic foraminiferal assemblage composition mirror changes in water mass salinity, oxygenation, circulation and productivity. Foraminiferal data from the western margin of the WIS support GCM models of estuarine circulation. (2) Fibrillar bodies are organelles present in the cytoplasm of all planktic foraminifera. I propose that they may have originated as symbiotic bacteria. Those in Pulleniatina obliquiloculata are squat to elongate ovoids and elongate rods with a length of 2-15 $\mu$m and a diameter of 2-5 $\mu$m. One, sometimes two such bodies (possibly products of binary fission) are bounded by a membrane-like vacuolar structure. They have an electron-lucent (DNA-containing?) central region, ribosome-like and storage-like granules, and are commonly enclosed within a vacuole. (Abstract shortened by UMI.

Enrichment of Geobacter Species in Response to Stimulation of Fe(III) Reduction in Sandy Aquifier Sediments

Engineered stimulation of Fe(III) has been proposed as a strategy to enhance the immobilization of radioactive and toxic metals in metal-contaminated subsurface environments. Therefore, laboratory and field studies were conducted to determine which microbial populations would respond to stimulation of Fe(III) reduction in the sediments of sandy aquifers. In laboratory studies, the addition of either various organic electron donors or electron shuttle compounds stimulated Fe(III) reduction and resulted in Geobacter sequences becoming important constituents of the Bacterial 16S rDNA sequences that could be detected with PCR amplification and denaturing gradient gel electrophoresis (DGGE). Quantification of Geobacteraceae sequences with a PCR most-probable-number technique indicated that the extent to which numbers of Geobacter increased was related to the degree of stimulation of Fe(III) reduction. Geothrix species were also enriched in some instances, but were orders of magnitude less numerous than Geobacter species. Shewanella species were not detected, even when organic compounds known to be electron donors for Shewanella species were used to stimulate Fe(III) reduction in the sediments. Geobacter species were also enriched in two field experiments in which Fe(III) reduction was stimulated with the addition of benzoate or aromatic hydrocarbons. The apparent growth of Geobacter species concurrent with increased Fe(III) reduction suggests that Geobacter species were responsible for much of the Fe(III) reduction in all of the stimulation approaches evaluated in three geographically distinct aquifers. Therefore, strategies for subsurface remediation that involve enhancing the activity of indigenous Fe(III)-reducing populations in aquifers should consider the physiological properties of Geobacter species in their treatment design