39 research outputs found
Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria
No full textMyxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities
Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: Two novel representatives of reductive sulfur cycle from soda lakes
No full textAnaerobic enrichments with H2 as electron donor and thiosulfate/polysulfide as electron acceptor at pH 10 and 0.6 M total Na+ yielded two non sulfate-reducing representatives of reductive sulfur cycle from soda lake sediments. Strain AHT 1 was isolated with thiosulfate as the electron acceptor from north–eastern Mongolian soda lakes and strain AHT 2—with polysulfide as the electron acceptor from Wadi al Natrun lakes in Egypt. Both isolates represented new phylogenetic lineages: AHT 1—within Clostridiales and AHT 2—within the Deltaproteobacteria. Both bacteria are obligate anaerobes with respiratory metabolism. Both grew chemolithoautotrophically with H2 as the electron donor and can use thiosulfate, elemental sulfur and polysulfide as the electron acceptors. AHT 2 also used nitrate as acceptor, reducing it to ammonia. During thiosulfate reduction, AHT 1 excreted sulfite. dsrAB gene was not found in either strain. Both strains were moderate salt-tolerant (grow up to 2 M total Na+) true alkaliphiles (grow between pH 8.5 and 10.3). On the basis of the phenotypic and phylogenetic data, strains AHT 1 and AHT 2 are proposed as new genera and species Dethiobacter alkaliphilus and Desulfurivibrio alkaliphilus, respectively.Department of BiotechnologyApplied Science
Insights into the genome of large sulfur bacteria revealed by analysis of single filaments
No full textMarine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments
Sedimentary Sulfides
No full textSedimentary sulfides constitute over 95% of the sulfide on the surface of the planet, and their formation, preservation and destruction largely determines the surface environment. The sulfide in sediments is mainly derived from the products of sulfate-reducing bacteria, which are currently responsible for oxidizing over half the organic matter flux reaching sediments. Pyrite is the mineral overwhelmingly produced. The geochemistry of pyrite, both in terms of its isotopic composition and its trace-element loading, has varied dramatically over geologic time. As such, it is a major source of our current understanding about the nature of the early Earth and of the Earth's subsequent geochemical and biological evolution
CARD-FISH Images from Incubations of Deep-Sea Hydrothermal Vent Fluid and Testing of Novel Probes for Arcobacter, Sulfurimonas, and Sulfurovum
No full textCARD-FISH Images from Incubations of Deep-Sea Hydrothermal Vent Fluid and Testing of Novel Probes for Arcobacter, Sulfurimonas, and Sulfurovum
No full textDesulfuromonas svalbardensis sp nov and Desulfuromusa ferrireducens sp nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard
No full textTwo psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112(T) and 102(T)) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to -2 degrees C, with respective temperature optima of 14 degrees C and 14-17 degrees C for strains 112(T) and 102(T). The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S-0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112(T) was most closely related to Desulfuromonas acetoxidans (97.0%) and Desulfuromonas thiophila NZ27(T) (95.5 %), and strain 102(T) to Malonomonas rubra Gra Mal 1(T) (96.3%) and Desulfuromusa succinoxidans Gylac(T) (95.9%) within the Deltaproteobacteria. Strains 112(T) and 102(T) therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112(T) = DSM 16958(T) = JCM 12927(T)) and Desulfuromusa ferrireducens sp. nov. (type strain 102(T) = DSM 16956 (T) = JCM 12926(T)) are proposed
Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa
No full textMethane oxidation coupled to denitrification is mediated by 'Candidatus methylomirabilis oxyfera', which belongs to the candidate phylum NC10. The distribution of putative denitrifying methane oxidizing bacteria related to "M. oxyfera" was investigated in a freshwater lake, Lake Biwa, Japan. In the surface layer of the sediment from a profundal site, a phylotype closely related to "M. oxyfera" was most frequently detected among NC10 bacteria in PCR analysis of the 16S rRNA gene. In the sediment, sequences related to "M. oxyfera" were also detected in a pmoA gene library. The presence of NC10 bacteria was also confirmed by catalyzed reporter deposition fluorescence in situ hybridization. Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR indicated that the abundance of "M. oxyfera"-related phylotype was higher in the upper layers of the profundal sediment. The horizontal distribution of the putative methanotrophs in sediment of the lake was also analyzed by DGGE, which revealed that their occurrence was restricted to deep water areas. These results agreed with those in a previous study of another freshwater lake, and suggested that the upper layer of the profundal sediments is major the habitat for denitrifying methanotrophs
Clinical application of EOS imaging system: a scoping review protocol
No full textOBJECTIVE: The objective of this scoping review is to examine and map the existing literature on the clinical application of the EOS imaging system and to identify related evidence gaps. INTRODUCTION: The EOS imaging system was originally developed to conduct imaging for medical conditions, such as scoliosis and anisomelia. However, recent research suggests that the modality has other clinical uses that may benefit patients via reduced radiation dose and, thus, improve patient safety. INCLUSION CRITERIA: This scoping review will consider all quantitative study designs, including systematic reviews and meta-analyses. Imaging phantom studies and conference abstracts will be excluded. METHODS: Databases that will be searched include Embase, MEDLINE, CINAHL Complete, Scopus, Cochrane Library, Academic Search Premier, and OpenGrey. Relevant secondary material will be identified using citation searching (backwards and forwards) of included studies through Google Scholar. In addition, we will search by author name where more than 3 included studies from the same first author are identified. Articles published from 2003 in English, Danish, Norwegian, Swedish, French, and German will be included. Two independent reviewers will perform title/abstract screening, followed by full-text screening. Data extraction will include study type and design, age of participants, anatomical/physiological region, pathology, clinical endpoint, outcome measures, sample size, and clinical application. Data will be presented in tabular format and as a narrative summary. DETAILS OF THE REVIEW AVAILABLE AT: Open Science Framework https://osf.io/yc85j/.</p
Genus-specific carbon fixation activity measurements reveal distinct responses to oxygen among hydrothermal vent campylobacteria
No full textAuthor Posting. © American Society for Microbiology, 2022. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 88(2),(2022): e02083-21, https://doi.org/10.1128/AEM.02083-21.Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, Arcobacter, Sulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances.This research was funded by the U.S. National Science Foundation grants OCE-1131095 (S.M.S.) and OCE-1136727 (S.M.S., J.S.S.). Further support was provided by the WHOI Investment in Science Fund (S.M.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office
