Measurement of photosynthesis using PAM technology in a purple sulfur bacterium Thermochromatium tepidum (Chromatiaceae).

PubMed

Ritchie, Raymond J; Mekjinda, Nutsara

2015-01-01

We demonstrate that Blue-diode-based pulse amplitude modulation (PAM) technology can be used to measure the photosynthetic electron transport rate (ETR) of purple sulfur bacteria (Thermochromatium tepidum, Chromatiaceae). Previous studies showed that PAM technology could be used to estimate photosynthesis in purple nonsulfur bacteria and so PAM technology can be used to estimate photosynthesis of both kinds of purple photosynthetic bacteria. The absorptance of Thermochromatium films on glass fiber disks was measured and used to calculate actual ETR. ETR vs Irradiance (P vs E) curves fitted the waiting-in-line model (ETR = (ETRmax × E/Eopt) × exp (1−E/Eopt)). Yield (Y) was only ≈ 0.3–0.4. Thermochromatium saturates at 325 ± 13.8 μmol photons m(−2) s(−1) or ≈15% sunlight and shows photoinhibition at high irradiances. A pond of Thermochromatium would exhibit classic surface inhibition. Photosynthesis is extremely low in the absence of an electron source: ETR increases in the presence of acetate (5 mol m(−3)) provided as an organic carbon source and also increases in the presence of sulfite (3 mol m(−3)) but not sulfide and is only marginally increased by the presence of Fe(2+). Nonphotochemical quenching does occur in Thermochromatium but at very low levels compared to oxygenic photo-organisms or Rhodopseudomonads.

Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific

PubMed Central

Schneider, Dominik; Arp, Gernot; Reimer, Andreas; Reitner, Joachim; Daniel, Rolf

2013-01-01

On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth. PMID:23762495

Effects of Calcium Ions on the Thermostability and Spectroscopic Properties of the LH1-RC Complex from a New Thermophilic Purple Bacterium Allochromatium tepidum.

PubMed

Kimura, Yukihiro; Lyu, Shuwen; Okoshi, Akira; Okazaki, Koudai; Nakamura, Natsuki; Ohashi, Akira; Ohno, Takashi; Kobayashi, Manami; Imanishi, Michie; Takaichi, Shinichi; Madigan, Michael T; Wang-Otomo, Zheng-Yu

2017-05-18

The light harvesting-reaction center (LH1-RC) complex from a new thermophilic purple sulfur bacterium Allochromatium (Alc.) tepidum was isolated and characterized by spectroscopic and thermodynamic analyses. The purified Alc. tepidum LH1-RC complex showed a high thermostability comparable to that of another thermophilic purple sulfur bacterium Thermochromatium tepidum, and spectroscopic characteristics similar to those of a mesophilic bacterium Alc. vinosum. Approximately 4-5 Ca 2+ per LH1-RC were detected by inductively coupled plasma atomic emission spectroscopy and isothermal titration calorimetry. Upon removal of Ca 2+ , the denaturing temperature of the Alc. tepidum LH1-RC complex dropped accompanied by a blue-shift of the LH1 Q y absorption band. The effect of Ca 2+ was also observed in the resonance Raman shift of the C3-acetyl νC═O band of bacteriochlorophyll-a, indicating changes in the hydrogen-bonding interactions between the pigment and LH1 polypeptides. Thermodynamic parameters for the Ca 2+ -binding to the Alc. tepidum LH1-RC complex indicated that this reaction is predominantly driven by the largely favorable electrostatic interactions that counteract the unfavorable negative entropy change. Our data support a hypothesis that Alc. tepidum may be a transitional organism between mesophilic and thermophilic purple bacteria and that Ca 2+ is one of the major keys to the thermostability of LH1-RC complexes in purple bacteria.

Genome-Wide Transcriptional Profiling of the Purple Sulfur Bacterium Allochromatium vinosum DSM 180T during Growth on Different Reduced Sulfur Compounds

PubMed Central

Weissgerber, Thomas; Dobler, Nadine; Polen, Tino; Latus, Jeanette; Stockdreher, Yvonne

2013-01-01

The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to photoorganoheterotrophic growth on malate. Differential expression of 1,178 genes was observed, corresponding to 30% of the A. vinosum genome. Relative transcription of 551 genes increased significantly during growth on one of the different sulfur sources, while the relative transcript abundance of 627 genes decreased. A significant number of genes that revealed strongly enhanced relative transcription levels have documented sulfur metabolism-related functions. Among these are the dsr genes, including dsrAB for dissimilatory sulfite reductase, and the sgp genes for the proteins of the sulfur globule envelope, thus confirming former results. In addition, we identified new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Those four genes for hypothetical proteins that exhibited the strongest increases of mRNA levels on sulfide and elemental sulfur, respectively, were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for sulfur globule formation during the oxidation of sulfide and thiosulfate and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria. PMID:23873913

Interaction and Synergism of Microbial Fuel Cell Bacteria within Methanogenesis

NASA Technical Reports Server (NTRS)

Klaus, David

2004-01-01

Biological hydrogen production from waste biomass has both terrestrial and Martian advanced life support applications. On earth, biological hydrogen production is being explored as a greenhouse neutral form of clean and efficient energy. In a permanently enclosed space habitat, carbon loop closure is required to reduce mission costs. Plants are grown to revitalize oxygen supply and are consumed by habitat inhabitants. Unharvested portions must then be recycled for reuse in the habitat. Several biological degradation techniques exist, but one process, biophotolysis, can be used to produce hydrogen from inedible plant biomass. This process is two-stage, with one stage using dark fermentation to convert plant wastes into organic acids. The second stage, photofermentation, uses photoheterotrophic purple non-sulfur bacteria with the addition of light to turn the organic acids into hydrogen and carbon dioxide. Such a system can prove useful as a co-generation scheme, providing some of the energy needed to power a larger primary carbon recovery system, such as composting. Since butyrate is expected as one of the major inputs into photofermentation, a characterization study was conducted with the bacterium Rhodobacter sphaeroides SCJ, a novel photoheterotrophic non-sulfur purple bacteria, to examine hydrogen production performance at 10 mM-100 mM butyrate concentrations. As butyrate levels increased, hydrogen production increased up to 25 mM, and then decreased and ceased by 100 mM. Additionally, lag phase increased with butyrate concentration, possibly indicating some product inhibition. Maximal substrate conversion efficiency was 8.0%; maximal light efficiency was 0.89%; and maximal hydrogen production rate was 7.7 Umol/mg/cdw/hr (173 ul/mg cdw/hr). These values were either consistent or lower than expected from literature.

Ecologically and Geologically Relevant Isotope Signatures of C, N, and S in Okenone Producing Purple Sulfur Bacteria

NASA Astrophysics Data System (ADS)

Smith, D.; Steele, A.; Bowden, R.; Fogel, M. L.

2013-12-01

The carbon (C), nitrogen (N), and sulfur (S) cycles are linked in euxinic environments by purple sulfur bacteria (PSB). PSB could be responsible for the isotopic enrichments that have been observed in both fresh and marine anoxic basins. Okenane, the only recognized molecular fossil unique to PSB, is derived from okenone, a carotenoid pigment unique to Chromatiaceae. Since PSB have this exclusive molecular fossil and are fundamental components in the overall ecology of euxinic environments, a comprehensive study was undertaken to assess the C, N, and S metabolisms PSB carryout under precise laboratory conditions. The consequential isotopic fractionations that may be documented in modern environments and geologic record were examined. Autotrophic cultures of Marichromatium purpuratum DSMZ 1591 (Mpurp1591) were observed to have a fractionation between CO2 and biomass (Δ13Cbiomass - CO2), ranging from -16.1 to -37.6‰, dependent on growth stage. This rather large range of CO2 fractionation expands previously reported values for RuBisCO in PSB. Ammonium assimilation, controlled by glutamate dehydrogenase, was shown to have a fractionation (Δ15Nbiomass - NH4) of -15‰ in autotrophic cultures of Mpurp1591 and Thiocapsa marina 5653, documented for the first time in PSB. While it has been previously shown that phototrophic sulfur oxidizing bacteria connect sulfur and carbon cycling in euxinic ecosystems, the percentage of elemental sulfur and bulk biomass δ34S values of Mpurp1591 cells were contingent upon their carbon metabolisms. Here we show that the isotopic enrichments of S and N observed in freshwater and marine anoxic basins could be explained by the prevalence of PSB.

Carbon isotope fractionation by thermophilic phototrophic sulfur bacteria: evidence for autotrophic growth in natural populations

NASA Technical Reports Server (NTRS)

Madigan, M. T.; Takigiku, R.; Lee, R. G.; Gest, H.; Hayes, J. M.

1989-01-01

Purple phototrophic bacteria of the genus Chromatium can grow as either photoautotrophs or photoheterotrophs. To determine the growth mode of the thermophilic Chromatium species, Chromatium tepidum, under in situ conditions, we have examined the carbon isotope fractionation patterns in laboratory cultures of this organism and in mats of C. tepidum which develop in sulfide thermal springs in Yellowstone National Park. Isotopic analysis (13C/12C) of total carbon, carotenoid pigments, and bacteriochlorophyll from photoautotrophically grown cultures of C. tepidum yielded 13C fractionation factors near -20%. Cells of C. tepidum grown on excess acetate, wherein synthesis of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase ribulose bisphosphate carboxylase) was greatly repressed, were isotopically heavier, fractionation factors of ca. -7% being observed. Fractionation factors determined by isotopic analyses of cells and pigment fractions of natural populations of C. tepidum growing in three different sulfide thermal springs in Yellowstone National Park were approximately -20%, indicating that this purple sulfur bacterium grows as a photoautotroph in nature.

Characterizations of purple non-sulfur bacteria isolated from paddy fields, and identification of strains with potential for plant growth-promotion, greenhouse gas mitigation and heavy metal bioremediation.

PubMed

Sakpirom, Jakkapan; Kantachote, Duangporn; Nunkaew, Tomorn; Khan, Eakalak

2017-04-01

This study was aimed at selecting purple non-sulfur bacteria (PNSB) isolated from various paddy fields, including Cd- and Zn-contaminated paddy fields, based on their biofertilizer properties. Among 235 PNSB isolates, strain TN110 was most effective in plant growth-promoting substance (PGPS) production, releasing 3.2 mg/L of [Formula: see text] , 4.11 mg/L of 5-aminolevulinic acid (ALA) and 3.62 mg/L of indole-3-acetic acid (IAA), and reducing methane emission up to 80%. This strain had nifH, vnfG and anfG, which are the Mo, V and Fe nitrogenase genes encoded for key enzymes in nitrogen fixation under different conditions. This strain provided 84% and 55% removal of Cd and Zn, respectively. Another isolate, TN414, not only produced PGPS (1.30 mg/L of [Formula: see text] , 0.94 mg/L of ALA and 0.65 mg/L of IAA), but was also efficient in removing both Cd and Zn at 72% and 74%, respectively. Based on 16S rDNA sequencing, strain TN110 was identified as Rhodopseudomonas palustris, while strain TN414 was Rubrivivax gelatinosus. A combination of TN110 and TN414 could potentially provide a biofertilizer, which is a greener alternative to commercial/chemical fertilizers and an agent for bioremediation of heavy metals and greenhouse gas mitigation in paddy fields. Copyright © 2016 Institut Pasteur. All rights reserved.

Protein structure, electron transfer and evolution of prokaryotic photosynthetic reaction centers

NASA Technical Reports Server (NTRS)

Blankenship, R. E.

1994-01-01

Photosynthetic reaction centers from a variety of organisms have been isolated and characterized. The groups of prokaryotic photosynthetic organisms include the purple bacteria, the filamentous green bacteria, the green sulfur bacteria and the heliobacteria as anoxygenic representatives as well as the cyanobacteria and prochlorophytes as oxygenic representatives. This review focuses on structural and functional comparisons of the various groups of photosynthetic reaction centers and considers possible evolutionary scenarios to explain the diversity of existing photosynthetic organisms.

A quantum mechanical analysis of the light-harvesting complex 2 (LH2) from purple photosynthetic bacteria: insights into the electrostatic effects of transmembrane helices.

PubMed

Pichierri, Fabio

2011-02-01

We perform a quantum mechanical study of the peptides that are part of the LH2 complex from Rhodopseudomonas acidophila, a non-sulfur purple bacteria that has the ability of producing chemical energy from photosynthesis. The electronic structure calculations indicate that the transmembrane helices of these peptides are characterized by dipole moments with a magnitude of about 150D. When the full nonamer assembly made of 18 peptides is considered, then a macrodipole of magnitude 806D is built up from the vector sum of each monomer dipole. The macrodipole is oriented normal to the membrane plane and with the positive tip toward the cytoplasm thereby indicating that the electronic charge of the protein scaffold is polarized toward the periplasm. The results obtained here suggest that the asymmetric charge distribution of the protein scaffold contributes an anisotropic electrostatic environment which differentiates the absorption properties of the bacteriochlorophyll pigments, B800 and B850, embedded in the LH2 complex. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Transition of microbiological and sedimentological features associated with the geochemical gradient in a travertine mound in northern Sumatra, Indonesia

NASA Astrophysics Data System (ADS)

Sugihara, Chiya; Yanagawa, Katsunori; Okumura, Tomoyo; Takashima, Chizuru; Harijoko, Agung; Kano, Akihiro

2016-08-01

Modern travertines, carbonate deposits in Ca-rich hydrothermal water with high pCO2, often display a changing environment along the water path, with corresponding variability in the microbial communities. We investigated a travertine-bearing hot spring at the Blue Pool in northern Sumatra, Indonesia. The thermal water of 62 °C with high H2S (200 μM) and pCO2 ( 1 atm) developed a travertine mound 70 m wide. The concentrations of the gas components H2S and CO2, decrease immediately after the water is discharged, while the dissolved oxygen, pH, and aragonite saturation increase in the downstream direction. Responding to the geochemical gradient in the water, the surface biofilms change color from white to pink, light-green, dark-green, and brown as the water flows from the vent; this corresponds to microbial communities characterized by chemolithoautotrophs (Halothiobacillaceae), purple sulfur bacteria (Chromatiaceae), Anaerolineaceae, and co-occurrence of green non-sulfur bacteria (Chloroflexales)-Cyanobacteria, and green sulfur bacteria (Chlorobiales), respectively. In an environment with a certain level of H2S (> 1 μM), sulfur digestion and anoxygenic photosynthesis can be more profitable than oxygenic photosynthesis by Cyanobacteria. The precipitated carbonate mineral consists of aragonite and calcite, with the proportion of aragonite increasing downstream due to the larger Mg2 +/Ca2 + ratio in the water or the development of thicker biofilm. Where the biofilm is well developed, the aragonite travertines often exhibit laminated structures that were likely associated with the daily metabolism of these bacteria. The microbiological and sedimentological features at the Blue Pool may be the modern analogs of geomicrobiological products in the early Earth. Biofilm of anoxygenic photosynthetic bacteria had the potential to form ancient stromatolites that existed before the appearance of cyanobacteria.

Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog.

PubMed

Kulichevskaya, Irina S; Guzev, Vladimir S; Gorlenko, Vladimir M; Liesack, Werner; Dedysh, Svetlana N

2006-06-01

An isolate of purple non-sulfur bacteria was obtained from an acidic Sphagnum peat bog and designated strain RS(T). The colour of cell suspensions of this bacterium growing in the light under anaerobic conditions is purplish red. Cells of strain RS(T) are rod-shaped, 0.8-1.0 microm wide and 2.0-6.0 microm long, motile by means of polar flagella, reproduce by budding and have a tendency to form rosette-like clusters in older cultures. The cells contain lamellar intracytoplasmic membranes underlying, and parallel to, the cytoplasmic membrane. The photosynthetic pigments are bacteriochlorophyll a and carotenoids; the absorption spectrum of living cells shows maxima at 377, 463, 492, 527, 592, 806 and 867 nm. The cells grow photoheterotrophically under anaerobic or microaerobic conditions with various organic carbon sources or grow photolithoautotrophically with H(2) and CO(2). Strain RS(T) is a moderately acidophilic organism exhibiting growth at pH values between 4.8 and 7.0 (with an optimum at pH 5.2-5.5). The major fatty acids are 16 : 1omega7c and 18 : 1omega7c; the major quinones are Q-10 and Q-9. The DNA G + C content of strain RS(T) is 62.6 mol%. Analysis of the 16S rRNA gene sequence revealed that the novel isolate is most closely related (97.3 % sequence similarity) to the type strain ATCC 25092(T) of the moderately acidophilic purple non-sulfur bacterium Rhodoblastus acidophilus, formerly named Rhodopseudomonas acidophila. However, in contrast to Rbl. acidophilus, strain RS(T) is not capable of aerobic growth in the dark, has no spirilloxanthin among the carotenoids and differs in the pattern of substrate utilization. The value for DNA-DNA hybridization between strain RS(T) and Rbl. acidophilus ATCC 25092(T) is only 22 %. Thus, strain RS(T) represents a novel species of the genus Rhodoblastus, for which the name Rhodoblastus sphagnicola sp. nov. is proposed. Strain RS(T) (=DSM 16996(T) = VKM B-2361(T)) is the type strain.

Isotope effects associated with the anaerobic oxidation of sulfite and thiosulfate by the photosynthetic bacterium, Chromatium vinosum

NASA Technical Reports Server (NTRS)

Fry, B.; Gest, H.; Hayes, J. M.

1985-01-01

The purple photosynthetic bacterium Chromatium vinosum, strain D, catalyzes several oxidations of reduced sulfur compounds under anaerobic conditions in the light: e.g., sulfide --> sulfur --> sulfate, sulfite --> sulfate, and thiosulfate --> sulfur + sulfate. Here it is shown that no sulfur isotope effect is associated with the last of these processes; isotopic compositions of the sulfur and sulfate produced can differ, however, if the sulfane and sulfonate positions within the thiosulfate have different isotopic compositions. In the second process, an observed change from an inverse to a normal isotope effect during oxidation of sulfite may indicate the operation of 2 enzymatic pathways. In contrast to heterotrophic anaerobic reduction of oxidized sulfur compounds, anaerobic oxidations of inorganic sulfur compounds by photosynthetic bacteria are characterized by relatively small isotope effects.

Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Kuo-Hsiang; Barry, Kerrie; Chertkov, Olga

Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

Diversity of Total Bacterial Communities and Chemoautotrophic Populations in Sulfur-Rich Sediments of Shallow-Water Hydrothermal Vents off Kueishan Island, Taiwan.

PubMed

Wang, Li; Cheung, Man Kit; Liu, Rulong; Wong, Chong Kim; Kwan, Hoi Shan; Hwang, Jiang-Shiou

2017-04-01

Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for <2% of the total bacterial community in the vent area. These findings suggest that the rTCA cycle is the major chemoautotrophic carbon fixation pathway in sediments of the shallow-water HTVs off Kueishan Island.

A comprehensive sulfur and oxygen isotope study of sulfur cycling in a shallow, hyper-euxinic meromictic lake

NASA Astrophysics Data System (ADS)

Gilhooly, William P.; Reinhard, Christopher T.; Lyons, Timothy W.

2016-09-01

Mahoney Lake is a permanently anoxic and sulfidic (euxinic) lake that has a dense plate of purple sulfur bacteria positioned at mid-water depth (∼7 m) where free sulfide intercepts the photic zone. We analyzed the isotopic composition of sulfate (δ34SSO4 and δ18OSO4), sulfide (δ34SH2S), and the water (δ18OH2O) to track the potentially coupled processes of dissimilatory sulfate reduction and phototrophic sulfide oxidation within an aquatic environment with extremely high sulfide concentrations (>30 mM). Large isotopic offsets observed between sulfate and sulfide within the monimolimnion (δ34SSO4-H2S = 51‰) and within pore waters along the oxic margin (δ34SSO4-H2S > 50‰) are consistent with sulfate reduction in both the sediments and the anoxic water column. Given the high sulfide concentrations of the lake, sulfur disproportionation is likely inoperable or limited to a very narrow zone in the chemocline, and therefore the large instantaneous fractionations are best explained by the microbial process of sulfate reduction. Pyrite extracted from the sediments reflects the isotopic composition of water column sulfide, suggesting that pyrite buried in the euxinic depocenter of the lake formed in the water column. The offset between sulfate and dissolved sulfide decreases at the chemocline (δ34SSO4-H2S = 37‰), a trend possibly explained by elevated sulfate reduction rates and inconsistent with appreciable disproportionation within this interval. Water column sulfate exhibits a linear response in δ18OSO4-δ34SSO4 and the slope of this relationship suggests relatively high sulfate reduction rates that appear to respond to seasonal changes in the productivity of purple sulfur bacteria. Although photosynthetic activity within the microbial plate influences the δ18OSO4-δ34SSO4 relationship, the biosignature for photosynthetic sulfur bacteria is restricted to the oxic/anoxic transition zone and is apparently minor relative to the more prevalent process of sulfate reduction operative throughout the light-deprived deeper anoxic water column and sediment pore waters.

Interactions among sulfide-oxidizing bacteria

NASA Technical Reports Server (NTRS)

Poplawski, R.

1985-01-01

The responses of different phototrophic bacteria in a competitive experimental system are studied, one in which primary factors such as H2S or light limited photometabolism. Two different types of bacteria shared one limited source of sulfide under specific conditions of light. The selection of a purple and a green sulfur bacteria and the cyanobacterium was based on their physiological similarity and also on the fact that they occur together in microbial mats. They all share anoxygenic photosynthesis, and are thus probably part of an evolutionary continuum of phototrophic organisms that runs from, strictly anaerobic physiology to the ability of some cyanobacteria to shift between anoxygenic bacterial style photosynthesis and the oxygenic kind typical of eukaryotes.

Characterization and In Situ Carbon Metabolism of Phototrophic Consortia

PubMed Central

Glaeser, Jens; Overmann, Jörg

2003-01-01

A dense population of the phototrophic consortium “Pelochromatium roseum” was investigated in the chemocline of a temperate holomictic lake (Lake Dagow, Brandenburg, Germany). Fluorescence in situ hybridization revealed that the brown epibionts of “P. roseum” constituted up to 37% of the total bacterial cell number and up to 88% of all green sulfur bacteria present in the chemocline. Specific amplification of 16S rRNA gene fragments of green sulfur bacteria and denaturing gradient gel electrophoresis fingerprinting yielded a maximum of four different DNA bands depending on the year of study, indicating that the diversity of green sulfur bacteria was low. The 465-bp 16S rRNA gene sequence of the epibiont of “P. roseum” was obtained after sorting of individual consortia by micromanipulation, followed by a highly sensitive PCR. The sequence obtained represents a new phylotype within the radiation of green sulfur bacteria. Maximum light-dependent H14CO3− fixation in the chemocline in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea suggested that there was anaerobic autotrophic growth of the green sulfur bacteria. The metabolism of the epibionts was further studied by determining stable carbon isotope ratios (δ13C) of their specific biomarkers. Analysis of photosynthetic pigments by high-performance liquid chromatography revealed the presence of high concentrations of bacteriochlorophyll (BChl) e and smaller amounts of BChl a and d and chlorophyll a in the chemocline. Unexpectedly, isorenieratene and β-isorenieratene, carotenoids typical of other brown members of the green sulfur bacteria, were absent. Instead, four different esterifying alcohols of BChl e were isolated as biomarkers of green sulfur bacterial epibionts, and their δ13C values were determined. Farnesol, tetradecanol, hexadecanol, and hexadecenol all were significantly enriched in 13C compared to bulk dissolved and particulate organic carbon and compared to the biomarkers of purple sulfur bacteria. The difference between the δ13C values of farnesol, the major esterifying alcohol of BChl e, and CO2 was −7.1%, which provides clear evidence that the mode of growth of the green sulfur bacterial epibionts of “P. roseum” in situ is photoautotrophic. PMID:12839739

Tissue-Specific Accumulation of Sulfur Compounds and Saponins in Different Parts of Garlic Cloves from Purple and White Ecotypes.

PubMed

Diretto, Gianfranco; Rubio-Moraga, Angela; Argandoña, Javier; Castillo, Purificación; Gómez-Gómez, Lourdes; Ahrazem, Oussama

2017-08-20

This study set out to determine the distribution of sulfur compounds and saponin metabolites in different parts of garlic cloves. Three fractions from purple and white garlic ecotypes were obtained: the tunic (SS), internal (IS) and external (ES) parts of the clove. Liquid Chromatography coupled to High Resolution Mass spectrometry (LC-HRMS), together with bioinformatics including Principal Component Analysis (PCA), Hierarchical Clustering (HCL) and correlation network analyses were carried out. Results showed that the distribution of these metabolites in the different parts of garlic bulbs was different for the purple and the white ecotypes, with the main difference being a slightly higher number of sulfur compounds in purple garlic. The SS fraction in purple garlic had a higher content of sulfur metabolites, while the ES in white garlic was more enriched by these compounds. The correlation network indicated that diallyl disulfide was the most relevant metabolite with regards to sulfur compound metabolism in garlic. The total number of saponins was almost 40-fold higher in purple garlic than in the white variety, with ES having the highest content. Interestingly, five saponins including desgalactotigonin-rhamnose, proto-desgalactotigonin, proto-desgalactotigonin-rhamnose, voghieroside D1, sativoside B1-rhamnose and sativoside R1 were exclusive to the purple variety. Data obtained from saponin analyses revealed a very different network between white and purple garlic, thus suggesting a very robust and tight coregulation of saponin metabolism in garlic. Findings in this study point to the possibility of using tunics from purple garlic in the food and medical industries, since it contains many functional compounds which can be exploited as ingredients.

Evaluation of Lighting Systems, Carbon Sources, and Bacteria Cultures on Photofermentative Hydrogen Production.

PubMed

Hu, Chengcheng; Choy, Sing-Ying; Giannis, Apostolos

2018-05-01

Fluorescent and incandescent lighting systems were applied for batch photofermentative hydrogen production by four purple non-sulfur photosynthetic bacteria (PNSB). The hydrogen production efficiency of Rhodopseudomonas palustris, Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodospirillum rubrum was evaluated using different carbon sources (acetate, butyrate, lactate, and malate). Incandescent light was found to be more effective for bacteria cell growth and hydrogen production. It was observed that PNSB followed substrate selection criteria for hydrogen production. Only R. palustris was able to produce hydrogen using most carbon sources. Cell density was almost constant, but cell growth rate and hydrogen production were significantly varied under the different lighting systems. The kinetics study suggested that initial substrate concentration had a positive correlation with lag phase duration. Among the PNSB, R. palustris grew faster and had higher hydrogen yields of 1.58, 4.92, and 2.57 mol H 2 /mol using acetate, butyrate, and lactate, respectively. In the integrative approach with dark fermentation effluents rich in organic acids, R. palustris should be enriched in the phototrophic microbial consortium of the continuous hydrogen production system.

Incorporation of spheroidene and spheroidenone into light-harvesting complexes from purple sulfur bacteria.

PubMed

Ashikhmin, Aleksandr; Makhneva, Zoya; Bolshakov, Maksim; Moskalenko, Andrey

2017-05-01

Spheroidene and spheroidenone from the non-sulfur bacterium Rhodobacter (Rba.) sphaeroides were incorporated into diphenylamine (DPA) LH1-RC and LH2 complexes from sulfur bacteria Allochromatium (Alc.) minutissimum and Ectothiorhodospira (Ect.) haloalkaliphila in which carotenoid (Car) biosynthesis was inhibited by ~95%. A series of biochemical characteristics of the modified LH2 complexes was studied (electrophoretic mobility, absorption and CD spectra, Car composition, Car-to-BChl energy transfer and thermal stability). It was found that the electrophoretic mobility of the complexes with incorporated Cars did not change compared to that of the control and DPA-complexes, indicating the absence of any significant change in the structure of LH complexes upon DPA-treatment and subsequent incorporation of Cars. The analysis of fluorescence excitation spectra of the spheroidene-incorporated LH2 complex (LH2:sph) and the spheroidenone-incorporated LH2 complex (LH2:sph-ne) showed that spheroidene and spheroidenone exhibited relatively low efficiencies of energy transfer to BChl, when incorporated into the LH2 DPA-complexes from Alc. minutissimum and Ect. haloalkaliphila, although, they showed high efficiencies, being in their natural state in the LH2 complexes from Rba. sphaeroides. A significant increase in thermostability observed for the LH2:sph and LH2:sph-ne complexes with respect to the LH2 DPA-complexes indicated that the two incorporated Cars stabilized the structure of the LH2 complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells.

PubMed

Rago, Laura; Cristiani, Pierangela; Villa, Federica; Zecchin, Sarah; Colombo, Alessandra; Cavalca, Lucia; Schievano, Andrea

2017-08-01

Dissolved oxygen (DO) at cathodic interface is a critical factor influencing microbial fuel cells (MFC) performance. In this work, three MFCs were operated with cathode under different DO conditions: i) air-breathing (A-MFC); ii) water-submerged (W-MFC) and iii) assisted by photosynthetic microorganisms (P-MFC). A plateau of maximum current was reached at 1.06±0.03mA, 1.48±0.06mA and 1.66±0.04mA, increasing respectively for W-MFC, P-MFC and A-MFC. Electrochemical and microbiological tools (Illumina sequencing, confocal microscopy and biofilm cryosectioning) were used to explore anodic and cathodic biofilm in each MFC type. In all cases, biocathodes improved oxygen reduction reaction (ORR) as compared to abiotic condition and A-MFC was the best performing system. Photosynthetic cultures in the cathodic chamber supplied high DO level, up to 16mg O2 L -1 , which sustained aerobic microbial community in P-MFC biocathode. Halomonas, Pseudomonas and other microaerophilic genera reached >50% of the total OTUs. The presence of sulfur reducing bacteria (Desulfuromonas) and purple non-sulfur bacteria in A-MFC biocathode suggested that the recirculation of sulfur compounds could shuttle electrons to sustain the reduction of oxygen as final electron acceptor. The low DO concentration limited the cathode in W-MFC. A model of two different possible microbial mechanisms is proposed which can drive predominantly cathodic ORR. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural Characterization of the Novel and Thermal Stable Hydrogenases from the Purple Sulfur Bacteria Thiocapsa Roseopersicina and Lamprobacter Modestohalophilus

DTIC Science & Technology

2011-08-01

production activity achieved for hydrogenase encapsulated in sol–gel material doped with carbon nanotubes . J. Mater. Chem., 20, 1065 (2010). Abstract...Doping hydrogenase-containing sol-gel materials with multi-walled carbon nanotubes , polyethylene glycol and methyl viologen results in a greater than...homogeneous T. roseopersicina hydrogenase and of multi-walled carbon nanotubes in silica gel was studied. It is shown that in such material between the

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

PubMed Central

Wilbanks, Elizabeth G; Jaekel, Ulrike; Salman, Verena; Humphrey, Parris T; Eisen, Jonathan A; Facciotti, Marc T; Buckley, Daniel H; Zinder, Stephen H; Druschel, Gregory K; Fike, David A; Orphan, Victoria J

2014-01-01

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria. PMID:24428801

Metabolic flexibility revealed in the genome of the cyst-forming α-1 proteobacterium Rhodospirillum centenum

PubMed Central

2010-01-01

Background Rhodospirillum centenum is a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic N2-fixing environment. It is emerging as a genetically amenable model organism for molecular genetic analysis of cyst formation, photosynthesis, phototaxis, and cellular development. Here, we present an analysis of the genome of this bacterium. Results R. centenum contains a singular circular chromosome of 4,355,548 base pairs in size harboring 4,105 genes. It has an intact Calvin cycle with two forms of Rubisco, as well as a gene encoding phosphoenolpyruvate carboxylase (PEPC) for mixotrophic CO2 fixation. This dual carbon-fixation system may be required for regulating internal carbon flux to facilitate bacterial nitrogen assimilation. Enzymatic reactions associated with arsenate and mercuric detoxification are rare or unique compared to other purple bacteria. Among numerous newly identified signal transduction proteins, of particular interest is a putative bacteriophytochrome that is phylogenetically distinct from a previously characterized R. centenum phytochrome, Ppr. Genes encoding proteins involved in chemotaxis as well as a sophisticated dual flagellar system have also been mapped. Conclusions Remarkable metabolic versatility and a superior capability for photoautotrophic carbon assimilation is evident in R. centenum. PMID:20500872

Sedimentology, Mineralogy, Morphology, and Characterization of Purple Non-Sulfur Bacteria Communities from Modern Hypersaline Microbial Mats in Puerto Rico and the Virgin Islands

NASA Astrophysics Data System (ADS)

Rodriguez Colon, B. J.; Rivera-Lopez, E. O.; Ramirez-Martinez, W. R.; Rios-Velazquez, C.; Perez-Valentin, K. A.

2017-12-01

Microbial mats are organosedimentary structures which house complex guilds of microbial communities, held together by a gelatinous exopolymeric substance (EPS). This biofilm contributes to the formation of laminations by binding and trapping sediments, as well as in-situ organomineralization. Microbial mats commonly thrive in extreme habitats, such as the hypersaline environments, which have been studied throughout several coastal regions in the Caribbean. This project aims to study the morphology, sedimentology, and mineralogy of five different modern hypersaline microbial mats from Puerto Rico and Anegada that have not yet been studied, to assess their differences/similarities. At the same time, we intent to isolate and characterize purple non-sulfur bacteria (PNSB), which is an anoxyphototrophic microorganism that contributes to the pink pigmentation observed in the second layer of a typical microbial mat. Different layers within each mat were separated, dissected and dissolved to remove all organic material. The resulting sediment was then analyzed mineralogically using X-ray diffraction, and used to make petrographic thin sections. To isolate PNSB candidates, serial dilutions followed by filtration were performed to extracted sections from the pink layer of each mat. The samples were planted in Petri dishes with marine media and placed in Anaerobic Jars. Colonies Descriptions, Gram stain and molecular analysis using 16S rDNA gene was performed. Preliminary results show a diversity of mat morphologies throughout the ponds, similar to what has been observed in other hypersaline ponds and marshes in the Caribbean. Sedimentary analysis shows that the mats from Puerto Rico have similar allochthonous material (e.g. Halimeda sp. fragments). Microcodium fabrics, conoform structures, and hemispheroidal morphologies were observed as well. In Anegada, lithified microbialites were observed in the Red Pond location. Mineralogically, all samples were similar except for the mats in Cabo Rojo, Puerto Rico, which contained allochthonous quartz. 38 possible PNSB candidates were isolated from the mats, showing similar colonial characteristics (convex elevations, entire margins and pink pigmentations). Molecular results will be shown during the meeting.

Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov.

PubMed

Kulichevskaya, Irina S; Danilova, Olga V; Tereshina, Vera M; Kevbrin, Vadim V; Dedysh, Svetlana N

2014-08-01

A light-pink-pigmented, microaerophilic bacterium was obtained from a methanotrophic consortium enriched from acidic Sphagnum peat and designated strain Pf56(T). Cells of this bacterium were Gram-negative, non-motile, thick curved rods that contained a vesicular intracytoplasmic membrane system characteristic of some purple non-sulfur alphaproteobacteria. The absorption spectrum of acetone/methanol extracts of cells grown in the light showed maxima at 363, 475, 505, 601 and 770 nm; the peaks at 363 and 770 nm are characteristic of bacteriochlorophyll a. However, in contrast to purple non-sulfur bacteria, strain Pf56(T) was unable to grow phototrophically under anoxic conditions in the light. Best growth occurred on some sugars and organic acids under micro-oxic conditions by means of fermentation. The fermentation products were propionate, acetate and hydrogen. Slow chemo-organotrophic growth was also observed under fully oxic conditions. Light stimulated growth. C1 substrates were not utilized. Strain Pf56(T) grew at pH 4.0-7.0 (optimum pH 5.5-6.5) and at 15-30 °C (optimum 22-28 °C). The major cellular fatty acids were 19 : 0 cyclo ω8c and 18 : 1ω7c; quinones were represented by ubiquinone Q-10. The G+C content of the DNA was 70.0 mol%. Strain Pf56 displays 93.6-94.7 and 92.7-93.7% 16S rRNA gene sequence similarity to members of the families Methylocystaceae and Beijerinckiaceae, respectively, and belongs to a large cluster of environmental sequences retrieved from various wetlands and forest soils in cultivation-independent studies. Phenotypic, genotypic and chemotaxonomic characteristics of strain Pf56(T) suggest that it represents a novel genus and species of bacteriochlorophyll a-containing fermentative bacteria, for which the name Roseiarcus fermentans gen. nov., sp. nov. is proposed. Strain Pf56(T) ( = DSM 24875(T) = VKM B-2876(T)) is the type strain of Roseiarcus fermentans, and is also the first characterized member of a novel family within the class Alphaproteobacteria, Roseiarcaceae fam. nov. © 2014 IUMS.

Titanospirillum velox: a huge, speedy, sulfur-storing spirillum from Ebro Delta microbial mats

NASA Technical Reports Server (NTRS)

Guerrero, R.; Haselton, A.; Sole, M.; Wier, A.; Margulis, L.

1999-01-01

A long (20-30 micrometer), wide (3-5 micrometer) microbial-mat bacterium from the Ebro Delta (Tarragona, Spain) was grown in mixed culture and videographed live. Intracellular elemental sulfur globules and unique cell termini were observed in scanning-electron-microprobe and transmission-electron micrographs. A polar organelle underlies bundles of greater than 60 flagella at each indented terminus. These Gram-negative bacteria bend, flex, and swim in a spiral fashion; they translate at speeds greater than 10 body lengths per second. The large size of the spirillum permits direct observation of cell motility in single individual bacteria. After desiccation (i.e., absence of standing water for at least 24 h), large populations developed in mat samples remoistened with sea water. Ultrastructural observations reveal abundant large sulfur globules irregularly distributed in the cytoplasm. A multilayered cell wall, pliable and elastic yet rigid, distends around the sulfur globules. Details of the wall, multiflagellated termini, and large cytoplasmic sulfur globules indicate that these fast-moving spirilla are distinctive enough to warrant a genus and species designation: Titanospirillum velox genus nov., sp. nov. The same collection techniques at a similar habitat in the United States (Plum Island, northeast Essex County, Massachusetts) also yielded large populations of the bacterium among purple phototrophic and other inhabitants of sulfurous microbial-mat muds. The months-long survival of T. velox from Spain and from the United States in closed jars filled with mud taken from both localities leads us to infer that this large spirillum has a cosmopolitan distribution.

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

PubMed Central

Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G.; Tang, Sen-Lin

2016-01-01

Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches. PMID:26934492

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

PubMed

Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G; Tang, Sen-Lin

2016-01-01

Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

Different Metabolomic Responses to Carbon Starvation between Light and Dark Conditions in the Purple Photosynthetic Bacterium, Rhodopseudomonas palustris.

PubMed

Kanno, Nanako; Matsuura, Katsumi; Haruta, Shin

2018-03-29

Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark. After starvation for 5 d in the light, cells showed increases in the amount of ATP and the NAD + /NADH ratio. Decreases in the amounts of most metabolites related to glycolysis and the TCA cycle in energy-rich starved cells suggest the active utilization of these metabolites for the modification of cellular components. Starvation in the dark induced the consumption of cellular compounds such as amino acids, indicating that the degradation of these cellular components produced ATP in order to maintain viability under energy-poor conditions. The present results suggest that intracellular energy levels alter survival strategies under carbon-starved conditions through metabolism.

Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat

NASA Astrophysics Data System (ADS)

Decker, K.; Potter, C.

2003-12-01

The creation of a mathematical simulation model of photosynthetic microbial mats is an important step in our understanding of key biogeochemical cycles that may have altered the atmospheres of early Earth and of other terrestrial planets. A modeling investigation is presented here as a tool to utilize and integrate empirical results from research on hypersaline mats from Baja California, Mexico into a computational system that can be used to simulate biospheric inputs of trace gases to the atmosphere. An early version of our model calculates fluxes and cycling of oxygen, sulfide, and dissolved inorganic carbon (DIC) via abiotic components and via the major bacterial guilds: cyanobacteria (CYA), sulfur reducing bacteria (SRB), purple sulfur bacteria (PSB) and colorless sulfur bacteria (CSB). We used generalized monod-type equations that incorporate substrate and energy limits upon maximum rates of metabolic processes such as photosynthesis and sulfate reduction. We ran a simulation using temperature and irradiance inputs from data collected from a microbial mat in Guerrero Negro in Baja Mexico. Model oxygen, sulfide, and DIC results compared well with data collected in the field mats. A divergence from the field data was an initial large negative DIC flux early in the morning and little flux into the mat thereafter in the simulation. We hypothesize that this divergence will be reduced or eliminated if the salinity of the water surrounding the mat were used as an environmental input and as a limit to photosynthesis rates. Salinity levels, organic carbon, methane, methanogens and green nonsulfur bacteria will be added to this model before it is incorporated into a global model to simulate geological time scales.

Evolutionary and geologic consequences of organic carbon fixing in the primitive anoxic ocean

NASA Astrophysics Data System (ADS)

Berry, W. B. N.; Wilde, P.

1983-03-01

Steps leading to development of the modern photic-based marine food web are postulated as the result of modifications of the environment, enhanced by the activity of Archean sulfur chemoautotrophs. Such organisms (Anoxium) evolved in an anoxic ocean prior to 3.9 × 109 yr ago at Archean analogs of modern oceanic hydrothermal vents. At this time geothermal energy was more readily available to organisms than photic energy, given atmospheric conditions at the surface similar to Venus, where intensity is low and only middle and red visible wavelengths penetrate the cloudy CO2-rich atmosphere. Competition for the reduced sulfur developed due to oxidation and loss of sulfur to sediments. Consequently, evolutionary advantage shifted to Anoxium isolates that could use alternate energy sources such as light to supplement the diminished supplies of reduced sulfur. Initially, photo-sulfur organisms evolved similar to modern purple bacteria that absorb in the red visible spectra. Subsequent carbon fixing and oxidation improved both the quantity and range of light reaching the ocean surface. This permitted absorption in the blue visible range so that water splitting was now feasible, releasing free oxygen and accelerating oxidation. Eventually, reducing environments became restricted, completing the shift in the principal marine carbon-fixing activity from anoxic chemoautotrophic to aerobic photosynthetic organisms.

Differential staining of bacteria: acid fast stain.

PubMed

Reynolds, Jackie; Moyes, Rita B; Breakwell, Donald P

2009-11-01

Acid-fastness is an uncommon characteristic shared by the genera Mycobacterium (Section 10A) and Nocardia. Because of this feature, this stain is extremely helpful in identification of these bacteria. Although Gram positive, acid-fast bacteria do not take the crystal violet into the wall well, appearing very light purple rather than the deep purple of normal Gram-positive bacteria. (c) 2009 by John Wiley & Sons, Inc.

Characterizing the Purple Earth: Modeling the globally integrated spectral variability of the Archean Earth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanromá, E.; Pallé, E.; López, R.

2014-01-01

Ongoing searches for exoplanetary systems have revealed a wealth of planets with diverse physical properties. Planets even smaller than the Earth have already been detected and the efforts of future missions are aimed at the discovery, and perhaps characterization, of small rocky exoplanets within the habitable zone of their stars. Clearly, what we know about our planet will be our guideline for the characterization of such planets. However, the Earth has been inhabited for at least 3.8 Gyr and its appearance has changed with time. Here, we have studied the Earth during the Archean eon, 3.0 Gyr ago. At thatmore » time, one of the more widespread life forms on the planet was purple bacteria. These bacteria are photosynthetic microorganisms and can inhabit both aquatic and terrestrial environments. Here, we use a radiative transfer model to simulate the visible and near-infrared radiation reflected by our planet, taking into account several scenarios regarding the possible distribution of purple bacteria over continents and oceans. We find that purple bacteria have a reflectance spectrum that has a strong reflectivity increase, similar to the red edge of leafy plants, although shifted redward. This feature produces a detectable signal in the disk-averaged spectra of our planet, depending on cloud amount and purple bacteria concentration/distribution. We conclude that by using multi-color photometric observations, it is possible to distinguish between an Archean Earth in which purple bacteria inhabit vast extensions of the planet and a present-day Earth with continents covered by deserts, vegetation, or microbial mats.« less

Spatial distribution of Chloroflexus-like bacteria in the hypersaline artificial microbial mat

NASA Astrophysics Data System (ADS)

Bachar, A.; Polerecky, L.; Vamvakopoulos, K.; de Beer, D.; Jonkers, H. M.

An artificial microbial mat grown in a mesocosm originated from the Hypersaline Lake of La Salada de Chiprana NE Spain was examined with respect to its organism s spatial distribution via high resolution methods A special attention was given to the elucidative Chloroflexus -like bacteria on which spatial distribution data is not available We have characterized this thick 1cm and developed mat for photopigments HPLC and obtained the general pigment distribution pattern Furthermore fiberoptic and photosynthetic microsensor measurements gave inner light attenuations and flux rates of oxygen within the different layers respectively Using fluorescence and spectral imaging we were able to detect characteristic pigmentation in the different layers FISH probes targeting Chloroflexus -like bacteria confirmed the visualization techniques and showed a single hybridized layer below the cyanobacterial layer as did the HPLC fiberoptic microsensor and fluorescence imaging We conclude that Chloroflexus -like bacteria are located below the cyanobacterial layer and above the purple sulfur bacteria and for the firs time we are able to show it by different independent state of the art techniques These approaches can be important for rapid community investigations within a millimeter scale microniches

Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland.

PubMed

Abed, Raeid M M; Al-Kharusi, Samiha; Prigent, Stephane; Headley, Tom

2014-01-01

Various types of cyanobacterial mats were predominant in a wetland, constructed for the remediation of oil-polluted residual waters from an oil field in the desert of the south-eastern Arabian Peninsula, although such mats were rarely found in other wetland systems. There is scarce information on the bacterial diversity, spatial distribution and oil-biodegradation capabilities of freshwater wetland oil-polluted mats. Microbial community analysis by Automated Ribosomal Spacer Analysis (ARISA) showed that the different mats hosted distinct microbial communities. Average numbers of operational taxonomic units (OTUsARISA) were relatively lower in the mats with higher oil levels and the number of shared OTUsARISA between the mats was <60% in most cases. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities in the wetland mats were influenced by oil and ammonia levels, but to a lesser extent by plant density. In addition to oil and ammonia, redundancy analysis (RDA) showed also a significant contribution of temperature, dissolved oxygen and sulfate concentration to the variations of the mats' microbial communities. Pyrosequencing yielded 282,706 reads with >90% of the sequences affiliated to Proteobacteria (41% of total sequences), Cyanobacteria (31%), Bacteriodetes (11.5%), Planctomycetes (7%) and Chloroflexi (3%). Known autotrophic (e.g. Rivularia) and heterotrophic (e.g. Azospira) nitrogen-fixing bacteria as well as purple sulfur and non-sulfur bacteria were frequently encountered in all mats. On the other hand, sequences of known sulfate-reducing bacteria (SRBs) were rarely found, indicating that SRBs in the wetland mats probably belong to yet-undescribed novel species. The wetland mats were able to degrade 53-100% of C12-C30 alkanes after 6 weeks of incubation under aerobic conditions. We conclude that oil and ammonia concentrations are the major key players in determining the spatial distribution of the wetland mats' microbial communities and that these mats contribute directly to the removal of hydrocarbons from oil field wastewaters.

Excitonic energy transfer in light-harvesting complexes in purple bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye Jun; Sun Kewei; Zhao Yang

Two distinct approaches, the Frenkel-Dirac time-dependent variation and the Haken-Strobl model, are adopted to study energy transfer dynamics in single-ring and double-ring light-harvesting (LH) systems in purple bacteria. It is found that the inclusion of long-range dipolar interactions in the two methods results in significant increase in intra- or inter-ring exciton transfer efficiency. The dependence of exciton transfer efficiency on trapping positions on single rings of LH2 (B850) and LH1 is similar to that in toy models with nearest-neighbor coupling only. However, owing to the symmetry breaking caused by the dimerization of BChls and dipolar couplings, such dependence has beenmore » largely suppressed. In the studies of coupled-ring systems, both methods reveal an interesting role of dipolar interactions in increasing energy transfer efficiency by introducing multiple intra/inter-ring transfer paths. Importantly, the time scale (4 ps) of inter-ring exciton transfer obtained from polaron dynamics is in good agreement with previous studies. In a double-ring LH2 system, non-nearest neighbor interactions can induce symmetry breaking, which leads to global and local minima of the average trapping time in the presence of a non-zero dephasing rate, suggesting that environment dephasing helps preserve quantum coherent energy transfer when the perfect circular symmetry in the hypothetic system is broken. This study reveals that dipolar coupling between chromophores may play an important role in the high energy transfer efficiency in the LH systems of purple bacteria and many other natural photosynthetic systems.« less

Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis.

PubMed

Shimizu, Takayuki; Shen, Jiangchuan; Fang, Mingxu; Zhang, Yixiang; Hori, Koichi; Trinidad, Jonathan C; Bauer, Carl E; Giedroc, David P; Masuda, Shinji

2017-02-28

Sulfide was used as an electron donor early in the evolution of photosynthesis, with many extant photosynthetic bacteria still capable of using sulfur compounds such as hydrogen sulfide (H 2 S) as a photosynthetic electron donor. Although enzymes involved in H 2 S oxidation have been characterized, mechanisms of regulation of sulfide-dependent photosynthesis have not been elucidated. In this study, we have identified a sulfide-responsive transcriptional repressor, SqrR, that functions as a master regulator of sulfide-dependent gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus SqrR has three cysteine residues, two of which, C41 and C107, are conserved in SqrR homologs from other bacteria. Analysis with liquid chromatography coupled with an electrospray-interface tandem-mass spectrometer reveals that SqrR forms an intramolecular tetrasulfide bond between C41 and C107 when incubated with the sulfur donor glutathione persulfide. SqrR is oxidized in sulfide-stressed cells, and tetrasulfide-cross-linked SqrR binds more weakly to a target promoter relative to unmodified SqrR. C41S and C107S R. capsulatus SqrRs lack the ability to respond to sulfide, and constitutively repress target gene expression in cells. These results establish that SqrR is a sensor of H 2 S-derived reactive sulfur species that maintain sulfide homeostasis in this photosynthetic bacterium and reveal the mechanism of sulfide-dependent transcriptional derepression of genes involved in sulfide metabolism.

Cloning and heterologous expression of chlorophyll a synthase in Rhodobacter sphaeroides.

PubMed

Ipekoğlu, Emre M; Göçmen, Koray; Öz, Mehmet T; Gürgan, Muazzez; Yücel, Meral

2017-03-01

Rhodobacter sphaeroides is a purple non-sulfur bacterium which photoheterotrophically produces hydrogen from organic acids under anaerobic conditions. A gene coding for putative chlorophyll a synthase (chlG) from cyanobacterium Prochlorococcus marinus was amplified by nested polymerase chain reaction and cloned into an inducible-expression plasmid which was subsequently transferred to R. sphaeroides for heterologous expression. Induced expression of chlG in R. sphaeroides led to changes in light absorption spectrum within 400-700 nm. The hydrogen production capacity of the mutant strain was evaluated on hydrogen production medium with 15 mM malate and 2 mM glutamate. Hydrogen yield and productivity were increased by 13.6 and 22.6%, respectively, compared to the wild type strain. The results demonstrated the feasibility of genetic engineering to combine chlorophyll and bacteriochlorophyll biosynthetic pathways which utilize common intermediates. Heterologous expression of key enzymes from biosynthetic pathways of various pigments is proposed here as a general strategy to improve absorption spectra and yield of photosynthesis and hydrogen gas production in bacteria. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins

PubMed Central

Imhoff, Johannes F.; Rahn, Tanja; Künzel, Sven; Neulinger, Sven C.

2018-01-01

Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria employing this photosystem in nature. Almost complete pufLM gene sequences and the derived protein sequences from 152 type strains and 45 additional strains of phototrophic Proteobacteria employing photosystem II were compared. The results give interesting and comprehensive insights into the phylogeny of the photosynthetic apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from Caulobacterales (Brevundimonas subvibrioides). A special relationship exists between the PufLM sequences of those bacteria employing bacteriochlorophyll b instead of bacteriochlorophyll a. A clear phylogenetic association of aerobic phototrophic purple bacteria to anaerobic purple bacteria according to their PufLM sequences is demonstrated indicating multiple evolutionary lines from anaerobic to aerobic phototrophic purple bacteria. The impact of pufLM gene sequences for studies on the environmental diversity of phototrophic bacteria is discussed and the possibility of their identification on the species level in environmental samples is pointed out. PMID:29472894

How Markovian is exciton dynamics in purple bacteria?

NASA Astrophysics Data System (ADS)

Vaughan, Felix; Linden, Noah; Manby, Frederick R.

2017-03-01

We investigate the extent to which the dynamics of excitons in the light-harvesting complex LH2 of purple bacteria can be described using a Markovian approximation. To analyse the degree of non-Markovianity in these systems, we introduce a measure based on fitting Lindblad dynamics, as well as employing a recently introduced trace-distance measure. We apply these measures to a chromophore-dimer model of exciton dynamics and use the hierarchical equation-of-motion method to take into account the broad, low-frequency phonon bath. With a smooth phonon bath, small amounts of non-Markovianity are present according to the trace-distance measure, but the dynamics is poorly described by a Lindblad master equation unless the excitonic dimer coupling strength is modified. Inclusion of underdamped, high-frequency modes leads to significant deviations from Markovian evolution in both measures. In particular, we find that modes that are nearly resonant with gaps in the excitonic spectrum produce dynamics that deviate most strongly from the Lindblad approximation, despite the trace distance measuring larger amounts of non-Markovianity for higher frequency modes. Overall we find that the detailed structure in the high-frequency region of the spectral density has a significant impact on the nature of the dynamics of excitons.

New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.

PubMed

Imhoff, Johannes F

2016-05-24

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.

Peripheral Light-Harvesting LH2 Complex Can Be Assembled in Cells of Nonsulfur Purple Bacterium Rhodoblastus acidophilus without Carotenoids.

PubMed

Bol'shakov, M A; Ashikhmin, A A; Makhneva, Z K; Moskalenko, A A

2015-09-01

The effect of carotenoids on the assembly of LH2 complex in cells of the purple nonsulfur bacterium Rhodoblastus acidophilus was investigated. For this purpose, the bacterial culture was cultivated with an inhibitor of carotenoid biosynthesis - 71 µM diphenylamine (DPA). The inhibitor decreased the level of biosynthesis of the colored carotenoids in membranes by ~58%. It was found that a large amount of phytoene was accumulated in them. This carotenoid precursor was bound nonspecifically to LH2 complex and did not stabilize its structure. Thermostability testing of the isolated LH2 complex together with analysis of carotenoid composition revealed that the population of this complex was heterogeneous with respect to carotenoid composition. One fraction of the LH2 complex with carotenoid content around 90% remains stable and was not destroyed under heating for 15 min at 50°C. The other fraction of LH2 complex containing on average less than one molecule of carotenoid per complex was destroyed under heating, forming a zone of free pigments (and polypeptides). The data suggest that a certain part of the LH2 complexes is assembled without carotenoids in cells of the nonsulfur bacterium Rbl. acidophilus grown with DPA. These data contradict the fact that the LH2 complex from nonsulfur bacteria cannot be assembled without carotenoids, but on the other hand, they are in good agreement with the results demonstrated in our earlier studies of the sulfur bacteria Allochromatium minutissimum and Ectothiorhodospira haloalkaliphila. Carotenoidless LH2 complex was obtained from these bacteria with the use of DPA (Moskalenko, A. A., and Makhneva, Z. K. (2012) J. Photochem. Photobiol., 108, 1-7; Ashikhmin, A., et al. (2014) Photosynth. Res., 119, 291-303).

Flat laminated microbial mat communities

NASA Astrophysics Data System (ADS)

Franks, Jonathan; Stolz, John F.

2009-10-01

Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.

Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.

PubMed

Luedin, Samuel M; Pothier, Joël F; Danza, Francesco; Storelli, Nicola; Frigaard, Niels-Ulrik; Wittwer, Matthias; Tonolla, Mauro

2018-01-01

" Thiodictyon syntrophicum" sp. nov. strain Cad16 T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria . The type strain Cad16 T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16 T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16 T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232 T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16 T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.

Phenolic Composition and Evaluation of the Antimicrobial Activity of Free and Bound Phenolic Fractions from a Peruvian Purple Corn (Zea mays L.) Accession.

PubMed

Gálvez Ranilla, Lena; Christopher, Ashish; Sarkar, Dipayan; Shetty, Kalidas; Chirinos, Rosana; Campos, David

2017-12-01

Beneficial effects on overall gut health by phenolic bioactives-rich foods are potentially due to their modulation of probiotic gut bacteria and antimicrobial activity against pathogenic bacteria. Based on this rationale, the effect of the free and bound phenolic fractions from a Peruvian purple corn accession AREQ-084 on probiotic lactic acid bacteria such as Lactobacillus helveticus and Bifidobacterium longum and the gastric cancer-related pathogen Helicobacter pylori was evaluated. The free and bound phenolic composition was also determined by ultra-performance liquid chromatography. Anthocyanins were the major phenolic compounds (310.04 mg cyanidin-3-glucoside equivalents/100 g dry weight, DW) in the free phenolic fraction along with hydroxycinnamic acids such as p-coumaric acid derivatives, followed by caffeic and ferulic acid derivatives. The bound phenolic form had only hydroxycinnamic acids such as ferulic acid, p-coumaric acid, and a ferulic acid derivative with ferulic acid being the major phenolic compound (156.30 mg/100 g DW). These phenolic compounds were compatible with beneficial probiotic lactic acid bacteria such as L. helveticus and B. longum as these bacteria were not inhibited by the free and bound phenolic fractions at 10 to 50 mg/mL and 10 mg/mL of sample doses, respectively. However, the pathogenic H. pylori was also not inhibited by both purple corn phenolic forms at same above sample doses. This study provides the preliminary base for the characterization of phenolic compounds of Peruvian purple corn biodiversity and its potential health benefits relevant to improving human gut health. This study provides insights that Peruvian purple corn accession AREQ-084 can be targeted as a potential source of health-relevant phenolic compounds such as anthocyanins along with hydroxycinnamic acids linked to its dietary fiber fraction. Additionally, these phenolic fractions did not affect the gut health associated beneficial bacteria nor the pathogenic H. pylori. Purple corn can be targeted for design of probiotic functional foods integrated with their anthocyanin linked-coloring properties. © 2017 Institute of Food Technologists®.

Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod

PubMed Central

Ngangbam, Ajit Kumar; Baten, Abdul; Waters, Daniel L. E.; Whalan, Steve; Benkendorff, Kirsten

2015-01-01

Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita. PMID:26488885

Spectroscopic studies of two spectral variants of light-harvesting complex 2 (LH2) from the photosynthetic purple sulfur bacterium Allochromatium vinosum.

PubMed

Niedzwiedzki, Dariusz M; Bina, David; Picken, Nichola; Honkanen, Suvi; Blankenship, Robert E; Holten, Dewey; Cogdell, Richard J

2012-09-01

Two spectral forms of the peripheral light-harvesting complex (LH2) from the purple sulfur photosynthetic bacterium Allochromatium vinosum were purified and their photophysical properties characterized. The complexes contain bacteriochlorophyll a (BChl a) and multiple species of carotenoids. The composition of carotenoids depends on the light conditions applied during growth of the cultures. In addition, LH2 grown under high light has a noticeable split of the B800 absorption band. The influence of the change of carotenoid distribution as well as the spectral change of the excitonic absorption of the bacteriochlorophylls on the light-harvesting ability was studied using steady-state absorption, fluorescence and femtosecond time-resolved absorption at 77K. The results demonstrate that the change of the distribution of the carotenoids when cells were grown at low light adapts the absorptive properties of the complex to the light conditions and maintains maximum photon-capture performance. In addition, an explanation for the origin of the enigmatic split of the B800 absorption band is provided. This spectral splitting is also observed in LH2 complexes from other photosynthetic sulfur purple bacterial species. According to results obtained from transient absorption spectroscopy, the B800 band split originates from two spectral forms of the associated BChl a monomeric molecules bound within the same complex. Copyright © 2012 Elsevier B.V. All rights reserved.

Microbial characteristics of purple paddy soil in response to Pb pollution.

PubMed

Jiang, Qiu-Ju; Zhang, Yue-Qiang; Zhang, La-Mei; Zhou, Xin-Bin; Shi, Xiao-Jun

2014-05-01

The study focused on the change of microbial characteristics affected by Plumbum pollution with purple paddy soil in an incubation experiment. The results showed that low concentration of Plumbum had little effect on most of microbial amounts, biological activity and enzymatic activity. However, denitrifying activity was inhibited severely, and inhibition rate was up to 98%. Medium and high concentration of Plumbum significantly reduced the amounts and activity of all microorganisms and enzymatic activity, which increased with incubation time. Negative correlations were found between Plumbum concentrations and microbial amounts, biological activity and enzymatic activities except fungi and actinomyces. Thus they can be used to indicate the Plumbum pollution levels to some extent. LD(50) of denitrifying bacteria (DB) and ED50 of denitrifying activity were 852mg/kg and 33.5mg/kg. Across all test soil microbes, denitrifying bacteria was most sensitive to Plumbum pollution in purple paddy soil. Value of early warning showed that anaerobic cellulose-decomposing bacteria (ACDB) and actinomyces were also sensitive to Plumbum pollution. We concluded that denitrifying activity, actinomyces, ACDB or DB can be chosen as predictor of Plumbum contamination in purple paddy soil.

Effect of pH on optimization of photofermentative hydrogen production by co-culture of Rhodobacter sphaeroides-NMBL-02 and Bacillus firmus-NMBL-03.

PubMed

Pandey, A; Dolly, S; Semwal, D; Pandey, A

2017-07-31

Rhodobacter sphaeroides NMBL-02, photosynthetic purple non sulfur (PNS) bacteria and associated Bacillus firmus NMBL-03 were isolated from water sample collected from 15-20 inches beneath the surface of ponds from Northern region of India in modified Sistrom's media (120 ml) containing 3 g/L malate and 1.2 g/L ammonium sulfate. The isolation was done in air tight serum bottles (120 ml) under tungsten bulb (1.8 kLux light intensity) at 30 oC ± 2 oC. The PNS and heterotrophic bacteria associated with the culture was purified by clonal selection method and characterized by 16S rDNA sequencing. The PNS isolate was identified as Rhodobacter sphaeroides NMBL-02 (ID: 1467407, Accession BANKIT: JN256030) and associated heterotroph as Bacillus firmus NMBL-03 (Gene Bank Accession no.: JN 256029). The effect of initial medium pH on optimization of hydrogen production was investigated in batch process. The maximum hydrogen potential and hydrogen production rate was 2310 ± 55 ml/L and 4.75 ml/L culture/h respectively using glutamate (1.7 mmol/L) as nitrogen source and malate (22.38 mmol/L) as carbon source with 76.39% malate conversion efficiency at initial medium pH 5.0. This co-culture has the ability to produce significant amount of hydrogen in the pH range of 5.0 to 10.0 with 76.39% to 35.71% malate conversion respectively.

Cytoplasmic Sulfurtransferases in the Purple Sulfur Bacterium Allochromatium vinosum: Evidence for Sulfur Transfer from DsrEFH to DsrC

PubMed Central

Stockdreher, Yvonne; Venceslau, Sofia S.; Josten, Michaele; Sahl, Hans-Georg; Pereira, Inês A. C.; Dahl, Christiane

2012-01-01

While the importance of sulfur transfer reactions is well established for a number of biosynthetic pathways, evidence has only started to emerge that sulfurtransferases may also be major players in sulfur-based microbial energy metabolism. Among the first organisms studied in this regard is the phototrophic purple sulfur bacterium Allochromatium vinosum. During the oxidation of reduced sulfur species to sulfate this Gammaproteobacterium accumulates sulfur globules. Low molecular weight organic persulfides have been proposed as carrier molecules transferring sulfur from the periplasmic sulfur globules into the cytoplasm where it is further oxidized via the “Dsr” (dissimilatory sulfite reductase) proteins. We have suggested earlier that the heterohexameric protein DsrEFH is the direct or indirect acceptor for persulfidic sulfur imported into the cytoplasm. This proposal originated from the structural similarity of DsrEFH with the established sulfurtransferase TusBCD from E. coli. As part of a system for tRNA modification TusBCD transfers sulfur to TusE, a homolog of another crucial component of the A. vinosum Dsr system, namely DsrC. Here we show that neither DsrEFH nor DsrC have the ability to mobilize sulfane sulfur directly from low molecular weight thiols like thiosulfate or glutathione persulfide. However, we demonstrate that DsrEFH binds sulfur specifically to the conserved cysteine residue DsrE-Cys78 in vitro. Sulfur atoms bound to cysteines in DsrH and DsrF were not detected. DsrC was exclusively persulfurated at DsrC-Cys111 in the penultimate position of the protein. Most importantly, we show that persulfurated DsrEFH indeed serves as an effective sulfur donor for DsrC in vitro. The active site cysteines Cys78 of DsrE and Cys20 of DsrH furthermore proved to be essential for sulfur oxidation in vivo supporting the notion that DsrEFH and DsrC are part of a sulfur relay system that transfers sulfur from a persulfurated carrier molecule to the dissimilatory sulfite reductase DsrAB. PMID:22815818

Singlet-triplet fission of carotenoid excitation in light-harvesting LH2 complexes of purple phototrophic bacteria.

PubMed

Klenina, I B; Makhneva, Z K; Moskalenko, A A; Gudkov, N D; Bolshakov, M A; Pavlova, E A; Proskuryakov, I I

2014-03-01

The current generally accepted structure of light-harvesting LH2 complexes from purple phototrophic bacteria conflicts with the observation of singlet-triplet carotenoid excitation fission in these complexes. In LH2 complexes from the purple bacterium Allochromatium minutissimum, a drop in the efficiency of carotenoid triplet generation is demonstrated, which correlates with the extent of selective photooxidation of bacteriochlorophylls absorbing at ~850 nm. We conclude that singlet-triplet fission of carotenoid excitation proceeds with participation of these excitonically coupled bacteriochlorophylls. In the framework of the proposed mechanism, the contradiction between LH2 structure and photophysical properties of carotenoids is eliminated. The possibility of singlet-triplet excitation fission involving a third mediator molecule was not considered earlier.

The evolution of glutathione metabolism in phototrophic microorganisms

NASA Technical Reports Server (NTRS)

Fahey, Robert C.; Buschbacher, Ralph M.; Newton, Gerald L.

1988-01-01

The low molecular weight thiol composition of a variety of phototropic microorganisms is examined in order to ascertain how evolution of glutathione (GSH) production is related to the evolution of oxygenic photosynthesis. Cells were extracted in the presence of monobromobimane (mBBr) to convert thiols (RSH) to fluorescent derivatives (RSmB) which were analyzed by high performance liquid chromatography (HPLC). Significant levels of GSH were not found in green sulfur bacteria. Substantial levels were present in purple bacteria, cyanobacteria, and eukaryotic algae. Other thiols measured included cysteine, gamma-glutamylcysteine, thiosulfate, coenzyme A, and sulfide. Many of the organisms also exhibited a marked ability to reduce mBBr to syn-(methyl,methyl)bimane, an ability which was quenched by treatment with 2-pyridyl disulfide or 5,5 prime-bisdithio - (2-nitrobenzoic acid) prior to reaction with mBBr. These observations indicate the presence of a reducing system capable of electron transfer to mBBr and reduction of reactive disulfides. The distribution of GSH in phototropic eubacteria indicates that GSH synthesis evolved at or around the time that oxygenic photosynthesis evolved.

Potato purple top phytoplasma-induced disruption of gibberellin homeostasis in tomato plants

USDA-ARS?s Scientific Manuscript database

Phytoplasmas are phloem-inhabiting, cell wall-less bacteria that cause numerous plant diseases worldwide. Plants infected by phytoplasmas often exhibit various symptoms indicative of hormonal imbalance. In the present study, we investigated the effects of potato purple top (PPT) phytoplasma infect...

Sugar Dehydration without Sulfuric Acid: No More Choking Fumes in the Classroom!

NASA Astrophysics Data System (ADS)

Silverstein, Todd P.; Zhang, Yi

1998-06-01

Sugar is a common reagent often used in colorful classroom demonstrations. It produces a growing column of black ash when dehydrated by concentrated sulfuric acid, and it produces a brilliant purple flame when combusted with potassium chlorate. Unfortunately, both of these reactions also produce copious quantities of noxious fumes which make them problematic as lecture demonstrations. We have modified and combined these two reactions. Our demonstration uses no sulfuric acid, yields relatively little smoke, and produces an exciting and unpredictable growing column of black carbon.

Oxygen and sulfur isotope fractionation during sulfide oxidation by anoxygenic phototrophic bacteria

NASA Astrophysics Data System (ADS)

Brabec, Michelle Y.; Lyons, Timothy W.; Mandernack, Kevin W.

2012-04-01

Sulfide-mediated anoxygenic photosynthesis (SMAP) carried out by anaerobic phototrophic bacteria may have played an important role in sulfur cycling, formation of sulfate, and, perhaps, primary production in the Earth’s early oceans. Determination of ε34SSO4-Sulfide- and ε18OSO4-H2O values for bacterial sulfide oxidation will permit more refined interpretation of the δ34S and δ18OSO4 values measured in modern anoxic environments, such as meromictic lakes where sulfide commonly extends into the photic zone, and in the ancient rock record, particularly during periods of the Precambrian when anoxic and sulfidic (euxinic) conditions were believed to be more pervasive than today. Laboratory experiments with anaerobic purple and green sulfur phototrophs, Allochromatium vinosum and Chlorobaculum tepidum, respectively, were conducted to determine the sulfur and oxygen isotope fractionation during the oxidation of sulfide to sulfate. Replicate experiments were conducted at 25 °C for A. vinosum and 45 °C for C. tepidum, and in duplicate at three different starting oxygen isotope values for water to determine sulfate-water oxygen isotope fractionations accurately (ε18OSO4-H2O). ε18OSO4-H2O values of 5.6 ± 0.2‰ and 5.4 ± 0.1‰ were obtained for A. vinosum and C. tepidum, respectively. Temperature had no apparent effect on the ε18OSO4-H2O values. By combining all data from both cultures, an average ε18OSO4-H2O value of 5.6 ± 0.3‰ was obtained for SMAP. This value falls between those previously reported for bacterial oxidation of sphalerite and elemental sulfur (7-9‰) and abiotic and biotic oxidation of pyrite and chalcopyrite (2-4‰). Sulfur isotope fractionation between sulfide and sulfate formed by A.vinosum was negligible (0.1 ± 0.2‰) during all experiments. For C. tepidum an apparent fractionation of -2.3 ± 0.5‰ was observed during the earlier stages of oxidation based on bulk δ34S measurements of sulfate and sulfide and became smaller (-0.7 ± 0.3‰) when sulfate concentrations rose above 0.5 mM and sulfide concentrations had became negligible.

CaCO3 Precipitation in Multilayered Cyanobacterial Mats: Clues to Explain the Alternation of Micrite and Sparite Layers in Calcareous Stromatolites

PubMed Central

Kaźmierczak, Józef; Fenchel, Tom; Kühl, Michael; Kempe, Stephan; Kremer, Barbara; Łącka, Bożena; Małkowski, Krzysztof

2015-01-01

Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near the base of living cyanobacterial layers, and (ii) through precipitation of a variety of mixed Mg calcite/aragonite morphs in layers of degraded cyanobacteria dominated by purple sulfur bacteria. The δ13C values were about 2‰ heavier in carbonates from the living cyanobacterial zones as compared to those generated in the purple bacterial zones. Saturation indices calculated with respect to calcite, aragonite, and dolomite inside the mats showed extremely high values across the mat profile. Such high values were caused by high pH and high carbonate alkalinity generated within the mats in conjunction with increased concentrations of calcium and magnesium that were presumably stored in sheaths and extracellular polymer substances (EPS) of the living cyanobacteria and liberated during their post-mortem degradation. The generated CaCO3 morphs were highly similar to morphs reported from heterotrophic bacterial cultures, and from bacterially decomposed cyanobacterial biomass emplaced in Ca-rich media. They are also similar to CaCO3 morphs precipitated from purely inorganic solutions. No metabolically (enzymatically) controlled formation of particular CaCO3 morphs by heterotrophic bacteria was observed in the studied mats. The apparent alternation of in vivo and post-mortem generated calcareous layers in the studied cyanobacterial mats may explain the alternation of fine-grained (micritic) and coarse-grained (sparitic) laminae observed in modern and fossil calcareous cyanobacterial microbialites as the result of a probably similar multilayered mat organization. PMID:25761263

Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr's Lake, the Bahamas

NASA Astrophysics Data System (ADS)

Paul, Varun G.; Wronkiewicz, David J.; Mormile, Melanie R.; Foster, Jamie S.

2016-04-01

Microbialites found in the low-light-intensity, hypersaline waters of Storr's Lake (SL), San Salvador Island, the Bahamas, were investigated with respect to their morphology, mineralogy, and microbial diversity. Previously described microbialite morphologies, as well as a newly identified "multi-cuspate" morphology, were observed at various depths. Electron microscopy analysis revealed the presence of angular, blocky, and needle-shaped crystals with mineralized cyanobacterial filaments and remains of exopolymeric substances. X-ray diffraction studies confirmed the presence of both Mg-calcite and aragonite in the plateau-mushroom and pinnacle mound microbialites, whereas only Mg-calcite was identified in the other microbialite morphotypes. A comprehensive molecular analysis using barcoded pyrosequencing of five different microbial mat communities identified at least 12 dominant bacterial phyla. Cyanobacteria were generally low in abundance and ranged from ˜0.01% in the deeper pinnacle mounds to ˜3.2% in the shallow calcareous knobs. Other photosynthetic members included green nonsulfur bacteria of the phylum Chloroflexi and purple sulfur bacteria of the class Gammaproteobacteria. All mat types contained significant amounts of sulfate-reducing and dehalogenating bacteria. The low light intensity reaching the deeper microbialites, the lack of dominant cyanobacteria, and the abundance of sulfate reducers and Chloroflexi collectively suggest that sulfate reduction and anoxygenic photosynthetic processes influence the carbonate biomineralization process in these systems.

Phototrophic bacteria and their role in the biogeochemical sulfur cycle

NASA Technical Reports Server (NTRS)

Trueper, H. G.

1985-01-01

An essential step that cannot be bypassed in the biogeochemical cycle of sulfur today is dissimilatory sulfate reduction by anaerobic bacteria. The enormous amounts of sulfides produced by these are oxidized again either anaerobically by phototrophic bacteria or aerobically by thiobacilli and large chemotrophic bacteria (Beggiatoa, Thiovulum, etc.). Phototrophic bacteria use sulfide, sulfur, thiosulfate, and sulfite as electron donors for photosynthesis. The most obvious intermediate in their oxidative sulfur metabolism is a long chain polysulfide that appears as so called sulfur globules either inside (Chromatiaceae) or outside (Ectothiorhodospiraceae, Chlorobiaceae, and some of the Rhodospirillaceae) the cells. The assimilation of sulfur compounds in phototrophic bacteria is in principle identical with that of nonphototrophic bacteria. However, the Chlorobiaceae and some of the Chromatiaceae and Rhodospirillaceae, unable to reduce sulfate, rely upon reduced sulfur for biosynthetic purposes.

Zinc biosorption by the purple non-sulfur bacterium Rhodobacter capsulatus.

PubMed

Magnin, Jean-Pierre; Gondrexon, Nicolas; Willison, John C

2014-12-01

This paper presents the first report providing information on the zinc (Zn) biosorption potentialities of the purple non-sulfur bacterium Rhodobacter capsulatus. The effects of various biological, physical, and chemical parameters on Zn biosorption were studied in both the wild-type strain B10 and a strain, RC220, lacking the endogenous plasmid. At an initial Zn concentration of 10 mg·L(-1), the Zn biosorption capacity at pH 7 for bacterial biomass grown in synthetic medium containing lactate as carbon source was 17 and 16 mg Zn·(g dry mass)(-1) for strains B10 and RC220, respectively. Equilibrium was achieved in a contact time of 30-120 min, depending on the initial Zn concentration. Zn sorption by live biomass was modelled, at equilibrium, according to the Redlich-Peterson and Langmuir isotherms, in the range of 1-600 mg Zn·L(-1). The wild-type strain showed a maximal Zn uptake capacity (Qm) of 164 ± 8 mg·(g dry mass)(-1) and an equilibrium constant (Kads) of 0.017 ± 0.00085 L·(mg Zn)(-1), compared with values of 73.9 mg·(g dry mass)(-1) and 0.361 L·mg(-1) for the strain lacking the endogenous plasmid. The Qm value observed for R. capsulatus B10 is one of the highest reported in the literature, suggesting that this strain may be useful for Zn bioremediation. The lower Qm value and higher equilibrium constant observed for strain RC220 suggest that the endogenous plasmid confers an enhanced biosorption capacity in this bacterium, although no genetic determinants for Zn resistance appear to be located on the plasmid, and possible explanations for this are discussed.

[Pigments of green sulfur bacteria isolated from reservoirs of Iavoriv sulfur deposit].

PubMed

Baran, I M; Hudz', S P; Hnatush, S O; Fedorovych, A M

2004-01-01

The enormous amount of hydrogen sulfide (up to 11 mg/ml) is present in the Yavoriv sulfur deposit reservoirs owing to sulfur reductive bacteria activity. As a consequence the ecological situation is badly affected and requires recovering. The biological H2S decomposition by photosynthetic sulfur bacteria, which use the hydrogen sulfide as electron donor during photosynthesis, can be one of the possible ways of this toxic substance destruction. The qualitative and quantitative analysis of photosynthetic pigments composition that derived from green photosynthesizing sulfur bacteria from reservoirs of Yavoriv sulfur deposit is carried out. It was fixed that Pelodictyon sp., Chlorobium sp. and isolated consortia "Pelochromatium sp." contain the bacteriochlorophyll c and d. All the isolated cultures contained bacteriochlorophyll a in trace amounts. The obtained photosynthetic pigments (bacteriochlorophylls, carotenoids) were recognized by their absorption spectra in the visible and far-red region and by their quantity. The difference was not essential. All investigated cultures of isolated bacteria contain some carotenoid the Chlorobium sp. and obtained consortia possesses isorenieratene. The absorption maxima of extracted pigments from young cultures of isolated green sulfur bacteria are more definitely displayed than those from old cultures. Investigations of phototrophic sulfur bacteria were carried out in Ukraine up to now. Ecological problem that occurred in the Yavoriv sulfur deposit as a result of the deposit exploitation caused a necessity of the investigation of photosynthetic sulfur bacteria and bacterial photosynthesis mechanism. The photosynthetic pigments nature identification will promote the fast and precise identification of the new forms of photosynthetic sulfur bacteria and will extend our knowledge about their role in the anoxygenic photosynthesis.

Enrichments for phototrophic bacteria and characterization by morphology and pigment analysis

NASA Technical Reports Server (NTRS)

Brune, D.

1985-01-01

The purpose of this investigation was to examine several sulfide containing environments for the presence of phototrophic bacteria and to obtain enriched cultures of some of the bacteria present. The field sites were Alum Rock State Park, the Palo Alto salt marsh, the bay area salt ponds, and Big Soda Lake (near Fallon, Nevada). Bacteria from these sites were characterized by microscopic examination, measurement of in vitro absorption spectra, and analysis of carotenoid pigments. Field observations at one of the bay area salt ponds, in which the salt concentration was saturating (about 30 percent NaCl) and the sediments along the shore of the pond covered with a gypsum crust, revealed a layer of purple photosynthetic bacteria under a green layer in the gypsum crust. Samples of this gypsum crust were taken to the laboratory to measure light transmission through the crust and to try to identify the purple photosynthetic bacteria present in this extremely saline environment.

16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs.

PubMed

Tsuji, K; Tsien, H C; Hanson, R S; DePalma, S R; Scholtz, R; LaRoche, S

1990-01-01

16S ribosomal RNAs (rRNA) of 12 methylotrophic bacteria have been almost completely sequenced to establish their phylogenetic relationships. Methylotrophs that are physiologically related are phylogenetically diverse and are scattered among the purple eubacteria (class Proteobacteria). Group I methylotrophs can be classified in the beta- and the gamma-subdivisions and group II methylotrophs in the alpha-subdivision of the purple eubacteria, respectively. Pink-pigmented facultative and non-pigmented obligate group II methylotrophs form two distinctly separate branches within the alpha-subdivision. The secondary structures of the 16S rRNA sequences of 'Methylocystis parvus' strain OBBP, 'Methylosinus trichosporium' strain OB3b, 'Methylosporovibrio methanica' strain 81Z and Hyphomicrobium sp. strain DM2 are similar, and these non-pigmented obligate group II methylotrophs form one tight cluster in the alpha-subdivision. The pink-pigmented facultative methylotrophs, Methylobacterium extorquens strain AM1, Methylobacterium sp. strain DM4 and Methylobacterium organophilum strain XX form another cluster within the alpha-subdivision. Although similar in phenotypic characteristics, Methylobacterium organophilum strain XX and Methylobacterium extorquens strain AM1 are clearly distinguishable by their 16S rRNA sequences. The group I methylotrophs, Methylophilus methylotrophus strain AS1 and methylotrophic species DM11, which do not utilize methane, are similar in 16S rRNA sequence to bacteria in the beta-subdivision. The methane-utilizing, obligate group I methanotrophs, Methylococcus capsulatus strain BATH and Methylomonas methanica, are placed in the gamma-subdivision. The results demonstrate that it is possible to distinguish and classify the methylotrophic bacteria using 16S rRNA sequence analysis.

Cytochromes and iron sulfur proteins in sulfur metabolism of phototrophic bacteria

NASA Technical Reports Server (NTRS)

Fischer, U.

1985-01-01

Dissimilatory sulfur metabolism in phototrophic sulfur bacteria provides the bacteria with electrons for photosynthetic electron transport chain and, with energy. Assimilatory sulfate reduction is necessary for the biosynthesis of sulfur-containing cell components. Sulfide, thiosulfate, and elemental sulfur are the sulfur compounds most commonly used by phototrophic bacteria as electron donors for anoxygenic photosynthesis. Cytochromes or other electron transfer proteins, like high-potential-iron-sulfur protein (HIPIP) function as electron acceptors or donors for most enzymatic steps during the oxidation pathways of sulfide or thiosulfate. Yet, heme- or siroheme-containing proteins themselves undergo enzymatic activities in sulfur metabolism. Sirohemes comprise a porphyrin-like prosthetic group of sulfate reductase. eenzymatic reactions involve electron transfer. Electron donors or acceptors are necessary for each reaction. Cytochromes and iron sulfur problems, are able to transfer electrons.

Discrepancy between experimental and theoretical excitation transfer rates in LH2 bacteriochlorophyll-protein complexes of purple bacteria.

PubMed

Borisov, A Y

2008-02-01

Discrepancy is revealed between the values of excitation transfer times measured experimentally, and those calculated, for the atomic structures of B800 --> B850 bacteriochlorophylls within the LH2 light-harvesting pigment-protein complex of the purple bacterium Rhodopseudomonas acidophila. The value 2.9-3.2 ps for the B800 --> B850 excitation transfer, calculated on the basis of atomic structure of LH2, is about 4-times longer than that measured for this bacterium (0.7 ps). This discrepancy appears common in at least two purple bacteria. Possible sources responsible for this discrepancy are discussed. It may either signify some drawback/s/ in our notions about the precise in vivo structure of LH2 complexes, for example, possible changes of LH2 structure during crystallization, or it may reflect our ignorance of some mechanisms involved in excitation migration.

Development of biomarkers and a diagnostic tool for investigation of coinfections by and interactions between potato purple top and potato witches’-broom phytoplasmas in tomato

USDA-ARS?s Scientific Manuscript database

Columbia Basin potato purple top (PPT) phytoplasma and Alaska potato witches’-broom (PWB) phytoplasma are two closely-related but mutually distinct pathogenic bacteria that infect potato and other vegetable crops. Inhabiting phloem sieve elements and being transmitted by phloem-feeding insect vecto...

Bioengineering and Coordination of Regulatory Networks and Intracellular Complexes to Maximize Hydrogen Production by Phototrophic Microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tabita, F. Robert

2013-07-30

In this study, the Principal Investigator, F.R. Tabita has teamed up with J. C. Liao from UCLA. This project's main goal is to manipulate regulatory networks in phototrophic bacteria to affect and maximize the production of large amounts of hydrogen gas under conditions where wild-type organisms are constrained by inherent regulatory mechanisms from allowing this to occur. Unrestrained production of hydrogen has been achieved and this will allow for the potential utilization of waste materials as a feed stock to support hydrogen production. By further understanding the means by which regulatory networks interact, this study will seek to maximize themore » ability of currently available “unrestrained” organisms to produce hydrogen. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Moreover, due to their great metabolic versatility, such organisms highly regulate these processes in the cell and since virtually all such capabilities are dispensable, excellent experimental systems to study aspects of molecular control and biochemistry/physiology are available.« less

Two-photon excitation spectroscopy of carotenoid-containing and carotenoid-depleted LH2 complexes from purple bacteria.

PubMed

Stepanenko, Ilya; Kompanetz, Viktor; Makhneva, Zoya; Chekalin, Sergey; Moskalenko, Andrei; Razjivin, Andrei

2009-08-27

We applied two-photon fluorescence excitation spectroscopy to LH2 complex from purple bacteria Allochromatium minutissimum and Rhodobacter sphaeroides . Bacteriochlorophyll fluorescence was measured under two-photon excitation of the samples within the 1200-1500 nm region. Spectra were obtained for both carotenoid-containing and -depleted complexes of each bacterium to allow their direct comparison. The depletion of carotenoids did not alter the two-photon excitation spectra of either bacteria. The spectra featured a wide excitation band around 1350 nm (2x675 nm, 14,800 cm(-1)) which strongly resembled two-photon fluorescence excitation spectra of similar complexes published by other authors. We consider obtained experimental data to be evidence of direct two-photon excitation of bacteriochlorophyll excitonic states in this spectral region.

Data set on the bioprecipitation of sulfate and trivalent arsenic by acidophilic non-traditional sulfur reducing bacteria.

PubMed

de Matos, Letícia Paiva; Costa, Patrícia Freitas; Moreira, Mariana; Gomes, Paula Cristine Silva; de Queiroz Silva, Silvana; Gurgel, Leandro Vinícius Alves; Teixeira, Mônica Cristina

2018-04-01

Data presented here are related to the original paper "Simultaneous removal of sulfate and arsenic using immobilized non-traditional sulfate reducing bacteria (SRB) mixed culture and alternative low-cost carbon sources" published by same authors (Matos et al., 2018) [1]. The data set here presented aims to facilitate this paper comprehension by giving readers some additional information. Data set includes a brief description of experimental conditions and the results obtained during both batch and semi-continuous reactors experiments. Data confirmed arsenic and sulfate were simultaneously removed under acidic pH by using a biological treatment based on the activity of a non-traditional sulfur reducing bacteria consortium. This microbial consortium was able to utilize glycerol, powdered chicken feathers as carbon donors, and proved to be resistant to arsenite up to 8.0 mg L - 1 . Data related to sulfate and arsenic removal efficiencies, residual arsenite and sulfate contents, pH and Eh measurements obtained under different experimental conditions were depicted in graphical format. Refers to https://doi.org/10.1016/j.cej.2017.11.035.

Quality of fresh-cut purple fleshed sweet potatoes after x-ray irradiation treatment and refrigerated storage

USDA-ARS?s Scientific Manuscript database

The effect of x-ray irradiation on the quality of fresh-cut, refrigerated purple-fleshed sweetpotato (PFSP) cubes was investigated. Packaged sweetpotato cubes were treated with 0, 250, 500, 750 or 1000 Gy x-ray irradiation and stored at 4 ± 1 ºC for 14 days. After 14 days, total aerobic bacteria cou...

Minerals and Microorganisms in Evaporite Environments

NASA Astrophysics Data System (ADS)

Morris, P. A.; Brigmon, R. L.

2010-12-01

Traditional analysis of evaporite environments have either focused on the geology or the halophilic organisms. It is relatively rare that the two have been combined and even rarer that both disciplines have been incorporated in comparing evaporite sites. The variation in evaporite environments does influence microbial ecology and fossilization processes as each site varies in pH, temperature, presence or absence springs, and spring chemistry. Understanding the evaporite environments is important for planetary scientists as they serve as analogs for evaluating extraterrestrial materials, including the potential for water and ultimately life. For example Mars lander, rover and orbital missions have identified the evaporite signatures of gypsum, carbonates and chlorides, all indicating that water existed at sometime in the planets geological history. Terrestrial evaporite sites all possess halophilic tolerant life. In some instances such as the Dead Sea, Israel, it is restricted to microbial life, but in other sites there are higher life forms. The microbes associated with these evaporite sites can produce biofilms as a method to develop their own microenvironments. Microorganisms can be observed colonizing specific ecological niches or gradients can be created by these environments. These gradients occur due the localized drying and weathering patterns that create different soil chemistry. The microorganisms in turn colonize specific areas more suitable to their specific metabolic needs. For example, under anaerobic conditions with sulfur and methane prevalent methanogenic and/or sulfur reducing microbial species may be observed. However, under similar chemistry environments with the exception of aerobic conditions sulfur oxidizer and/or methanotrophic microorganism may occur. Because of their conspicuous colored pigments purple sulfur bacteria are frequently observed in anoxic zones of lakes, sulfur springs, and stratified evaporite crusts. Some of these bacteria are of particular interest including Ectothiorhodospira spp. that deposit extracellular sulfur and are halophilic growing at high pH with NaCl concentrations approaching saturation. Fossilization and biofilm production appears to be relevant to the geochemistry of the systems. For example Dead Sea, Israel, microbes produce minimal biofilms, reside in the sediments, and the incidence of fossilization is low while hypersaline Storrs Lake, San Salvador, Bahamas microbes produce prodigious amounts of biofilms with many examples of fossilization. Some of the microbes appear to prefer solid substrates and may exhibit a preference, such as detrital or mineral, etc. In our studies we have found that some of the organisms, in relation to their substrate, can be tentatively characterized with laser confocal scanning microscopy. Terrestrial evaporite sites and understanding potential biomarkers and/or mineral signatures are important for identifying potential exoplanetary sites such as Mars that may harbor life.

Spectral diffusion and electron-phonon coupling of the B800 BChl a molecules in LH2 complexes from three different species of purple bacteria.

PubMed

Baier, J; Gabrielsen, M; Oellerich, S; Michel, H; van Heel, M; Cogdell, R J; Köhler, J

2009-11-04

We have investigated the spectral diffusion and the electron-phonon coupling of B800 bacteriochlorophyll a molecules in the peripheral light-harvesting complex LH2 for three different species of purple bacteria, Rhodobacter sphaeroides, Rhodospirillum molischianum, and Rhodopseudomonas acidophila. We come to the conclusion that B800 binding pockets for Rhodobacter sphaeroides and Rhodopseudomonas acidophila are rather similar with respect to the polarity of the protein environment but that the packaging of the alphabeta-polypeptides seems to be less tight in Rb. sphaeroides with respect to the other two species.

Efficiency of photochemical stages of photosynthesis in purple bacteria (a critical survey).

PubMed

Borisov, A Yu

2014-03-01

Based on currently available data, the energy transfer efficiency in the successive photophysical and photochemical stages has been analyzed for purple bacteria. This analysis covers the stages starting from migration of the light-induced electronic excitations from the bulk antenna pigments to the reaction centers up to irreversible stage of the electron transport along the transmembrane chain of cofactors-carriers. Some natural factors are revealed that significantly increase the rates of efficient processes in these stages. The influence on their efficiency by the "bottleneck" in the energy migration chain is established. The overall quantum yield of photosynthesis in these stages is determined.

Aerobic sulfur-oxidizing bacteria: Environmental selection and diversification

NASA Technical Reports Server (NTRS)

Caldwell, D.

1985-01-01

Sulfur-oxidizing bacteria oxidize reduced inorganic compounds to sulfuric acid. Lithotrophic sulfur oxidizer use the energy obtained from oxidation for microbial growth. Heterotrophic sulfur oxidizers obtain energy from the oxidation of organic compounds. In sulfur-oxidizing mixotrophs energy are derived either from the oxidation of inorganic or organic compounds. Sulfur-oxidizing bacteria are usually located within the sulfide/oxygen interfaces of springs, sediments, soil microenvironments, and the hypolimnion. Colonization of the interface is necessary since sulfide auto-oxidizes and because both oxygen and sulfide are needed for growth. The environmental stresses associated with the colonization of these interfaces resulted in the evolution of morphologically diverse and unique aerobic sulfur oxidizers.

Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

PubMed Central

Yamamoto, Hiroyuki; Hiraishi, Akira; Kato, Kenji; Chiura, Hiroshi X.; Maki, Yonosuke; Shimizu, Akira

1998-01-01

So-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in Japan. However, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. This study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16S rRNA genes amplified from the bulk DNAs of the mats. Common clones with 16S rDNA sequences with similarity levels of 94.8 to 99% were isolated from sulfur-turf mat samples from two geographically remote hot springs. Phylogenetic analysis showed that the phylotypes of the common clones formed a major cluster with members of the Aquifex-Hydrogenobacter complex, which represents the most deeply branching lineage of the domain bacteria. Furthermore, the bacteria of the sulfur-turf mat phylotypes formed a clade distinguishable from that of other members of the Aquifex-Hydrogenobacter complex at the order or subclass level. In situ hybridization with clone-specific probes for 16S rRNA revealed that the common phylotype of sulfur-turf mat bacteria is that of the predominant sausage-shaped bacteria. PMID:9572936

Marine bacteria from the Roseobacter clade produce sulfur volatiles via amino acid and dimethylsulfoniopropionate catabolism.

PubMed

Brock, Nelson L; Menke, Markus; Klapschinski, Tim A; Dickschat, Jeroen S

2014-07-07

Dimethylsulfoniopropionate (DMSP) is a versatile sulfur source for the production of sulfur-containing secondary metabolites by marine bacteria from the Roseobacter clade. (34)S-labelled DMSP and cysteine, and several DMSP derivatives with modified S-alkyl groups were synthesised and used in feeding experiments that gave insights into the biosynthesis of sulfur volatiles from these bacteria.

Properties and structure of a low-potential, penta-heme cytochrome c 552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum.

PubMed

Chen, Jing-Hua; Yu, Long-Jiang; Boussac, Alain; Wang-Otomo, Zheng-Yu; Kuang, Tingyun; Shen, Jian-Ren

2018-04-24

The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c', and one of two low-potential cytochrome c 552 (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c 552 (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.

Excitation energy transfer in photosynthetic protein-pigment complexes

NASA Astrophysics Data System (ADS)

Yeh, Shu-Hao

Quantum biology is a relatively new research area which investigates the rules that quantum mechanics plays in biology. One of the most intriguing systems in this field is the coherent excitation energy transport (EET) in photosynthesis. In this document I will discuss the theories that are suitable for describing the photosynthetic EET process and the corresponding numerical results on several photosynthetic protein-pigment complexes (PPCs). In some photosynthetic EET processes, because of the electronic coupling between the chromophores within the system is about the same order of magnitude as system-bath coupling (electron-phonon coupling), a non-perturbative method called hierarchy equation of motion (HEOM) is applied to study the EET dynamics. The first part of this thesis includes brief introduction and derivation to the HEOM approach. The second part of this thesis the HEOM method will be applied to investigate the EET process within the B850 ring of the light harvesting complex 2 (LH2) from purple bacteria, Rhodopseudomonas acidophila. The dynamics of the exciton population and coherence will be analyzed under different initial excitation configurations and temperatures. Finally, how HEOM can be implemented to simulate the two-dimensional electronic spectra of photosynthetic PPCs will be discussed. Two-dimensional electronic spectroscopy is a crucial experimental technique to probe EET dynamics in multi-chromophoric systems. The system we are interested in is the 7-chromophore Fenna-Matthews-Olson (FMO) complex from green sulfur bacteria, Prosthecochloris aestuarii. Recent crystallographic studies report the existence of an additional (eighth) chromophore in some of the FMO monomers. By applying HEOM we are able to calculate the two-dimensional electronic spectra of the 7-site and 8-site FMO complexes and investigate the functionality of the eighth chromophore.

Spectral heterogeneity and carotenoid-to-bacteriochlorophyll energy transfer in LH2 light-harvesting complexes from Allochromatium vinosum.

PubMed

Magdaong, Nikki M; LaFountain, Amy M; Hacking, Kirsty; Niedzwiedzki, Dariusz M; Gibson, George N; Cogdell, Richard J; Frank, Harry A

2016-02-01

Photosynthetic organisms produce a vast array of spectral forms of antenna pigment-protein complexes to harvest solar energy and also to adapt to growth under the variable environmental conditions of light intensity, temperature, and nutrient availability. This behavior is exemplified by Allochromatium (Alc.) vinosum, a photosynthetic purple sulfur bacterium that produces different types of LH2 light-harvesting complexes in response to variations in growth conditions. In the present work, three different spectral forms of LH2 from Alc. vinosum, B800-820, B800-840, and B800-850, were isolated, purified, and examined using steady-state absorption and fluorescence spectroscopy, and ultrafast time-resolved absorption spectroscopy. The pigment composition of the LH2 complexes was analyzed by high-performance liquid chromatography, and all were found to contain five carotenoids: lycopene, anhydrorhodovibrin, spirilloxanthin, rhodopin, and rhodovibrin. Spectral reconstructions of the absorption and fluorescence excitation spectra based on the pigment composition revealed significantly more spectral heterogeneity in these systems compared to LH2 complexes isolated from other species of purple bacteria. The data also revealed the individual carotenoid-to-bacteriochlorophyll energy transfer efficiencies which were correlated with the kinetic data from the ultrafast transient absorption spectroscopic experiments. This series of LH2 complexes allows a systematic exploration of the factors that determine the spectral properties of the bound pigments and control the rate and efficiency of carotenoid-to-bacteriochlorophyll energy transfer.

Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

NASA Technical Reports Server (NTRS)

Madigan, M. T.; Jung, D. O.; Woese, C. R.; Achenbach, L. A.

2000-01-01

A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15-18 degrees C with a growth temperature range of 0-25 degrees C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.

Scanning electron microscopy coupled with energy-dispersive X-ray spectrometry for quick detection of sulfur-oxidizing bacteria in environmental water samples

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Jiang, Fenghua; Gao, Wei; Li, Xiaoyun; Yu, Yanzhen; Yin, Xiaofei; Wang, Yong; Ding, Haibing

2017-01-01

Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry (EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time (within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.

Sulfate- and Sulfur-Reducing Bacteria as Terrestrial Analogs for Microbial Life on Jupiter's Satellite Io

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.; Six, N. Frank (Technical Monitor)

2001-01-01

Observations from the Voyager and Galileo spacecraft have revealed Jupiter's moon Io to be the most volcanically active body of our Solar System. The Galileo Near Infrared Imaging Spectrometer (NIMS) detected extensive deposits of sulfur compounds, elemental sulfur and SO2 frost on the surface of Io. There are extreme temperature variations on Io's surface, ranging from -130 C to over 2000 C at the Pillan Patera volcanic vent. The active volcanoes, fumaroles, calderas, and lava lakes and vast sulfur deposits on this frozen moon indicate that analogs of sulfur- and sulfate-reducing bacteria might inhabit Io. Hence Io may have great significance to Astrobiology. Earth's life forms that depend on sulfur respiration are members of two domains: Bacteria and Archaea. Two basic links of the biogeochemical sulfur cycle of Earth have been studied: 1) the sulfur oxidizing process (occurring at aerobic conditions) and 2) the process of sulfur-reduction to hydrogen sulfide (anaerobic conditions). Sulfate-reducing bacteria (StRB) and sulfur-reducing bacteria (SrRB) are responsible for anaerobic reducing processes. At the present time the systematics of StRB include over 112 species distributed into 35 genera of Bacteria and Archaea. Moderately thermophilic and mesophilic SrRB belong to the Bacteria. The hyperthermophilic SrRB predominately belong to the domain Archaea and are included in the genera: Pyrodictium, Thermoproteus, Pyrobaculum, Thermophilum, Desulfurococcus, and Thermodiscus. The StRB and SrRB use a wide spectrum of substrates as electron donors for lithotrophic and heterotrophic type nutrition. The electron acceptors for the StRB include: sulfate, thiosulfate, sulfite, sulfur, arsenate, dithionite, tetrathionate, sulfur monoxide, iron, nitrite, selenite, fumarate, oxygen, carbon dioxide, and chlorine-containing phenol compounds. The Sulfate- and Sulfur-reducing bacteria are widely distributed in anaerobic ecosystems, including extreme environments like hot springs, deepsea hydrothermal vents, soda and high salinity lakes, and cryo-environments. Furthermore, the StRB and SrRB have Astrobiological significance as these anaerobic extremophiles may represent the dominant relic life forms that inhabited our planet during the extensive volcanic activity in the Earth's early evolutionary period.

Swept Away: Resuspension of Bacterial Mats Regulates Benthic-Pelagic Exchange of Sulfur

NASA Astrophysics Data System (ADS)

Grant, Jonathan; Bathmann, Ulrich V.

1987-06-01

Filaments and extracellular material from colorless sulfur bacteria (Beggiatoa spp.) form extensive white sulfur mats on surface sediments of coastal, oceanic, and even deep-sea environments. These chemoautotrophic bacteria oxidize soluble reduced sulfur compounds and deposit elemental sulfur, enriching the sulfur content of surface sediment fivefold over that of deeper sediments. Laboratory flume experiments with Beggiatoa mats from an intertidal sandflat (Nova Scotia) demonstrated that even slight erosion of sediment causes a flux of 160 millimoles of sulfur per square meter per hour, two orders of magnitude greater than the flux produced by sulfur transformations involving either sulfate reduction or sulfide oxidation by benthic bacteria. These experiments indicate that resuspension of sulfur bacterial mats by waves and currents is a rapid mechanism by which sediment sulfur is recycled to the water column. Benthic communities thus lose an important storage intermediate for reduced sulfur as well as a high-quality bacterial food source for benthic grazers.

Reconstruction of the Paleoenvironment of the Early Cambrian Yurtus Black Shale in the Tarim Basin, Northwestern China, and Its Control on Organic Matter Accumulation

NASA Astrophysics Data System (ADS)

Li, J.; Ding, W.; Dong, L.

2017-12-01

The black shale in the early Cambrian Yurtus Formation (>521 Ma) in the Tarim basin, northwestern China, is characterized by its high TOC value (up to 16%) andgreat lateral continuity. It has been proven to be high-quality hydrocarbon source rocks. Abundant phytoplanktons and small shelly fossils have been reported from the lower Yurtus chert. However, recent biomarker discovery of aryl isoprenoid hydrocarbons suggests the existence of green sulfur bacteria, which indicates that the water column was stratified and the photic zone was prevailingly euxinic. These seemingly contradictory observations hamper our further understanding of the paleoenvironment in which the Yurtus shale was deposited and its control on the accumulation of organic matter. In this study, we systematically collected samples from the Yurtus Formation at the Kungaikuotan Section, and measured the organic carbon and nitrogen isotopic compositions and the content of trace element Barium (Ba). The strong negative excursions of nitrogen isotope ( -13‰) in the lower and upper parts of the Yurtus Formation are likely attributed to the biological activity of green and purple sulfur bacteria, which is consistent with our organic carbon isotope data as well as previous biomarker discovery. As green sulfur bacteria can only live in euxinic photic zone, it may indicate that the water column above this euxinic zone contains prolific organic matters which consume all the dissolved oxidants in surface ocean. It is well accepted that Ba flux can be used as an indicator for surface ocean primary productivity. Significant increase of barium content (from <100 to 2000 ppm) is observed at the same horizon as where the negative excursion of δ15Norg occurs, suggesting the substantive organic matter in the early Cambrian surface ocean mainly result from extremely high primary productivity. The abundant phytoplankton fossil record from this time period also supports this interpretation. In summary, high TOC in the Yurtus shale may derive from the extremely high primary productivity of phytoplanktons. Organic matter consumes all the dissolved oxidants in the water and generates the euxinic zone, which facilitates the accumulation and preservation of the surplus organic matter. This study also shed light on the ecology of the surface ocean before Cambrian Explosion.

Functional bacteria and process metabolism of the Denitrifying Sulfur conversion-associated Enhanced Biological Phosphorus Removal (DS-EBPR) system: An investigation by operating the system from deterioration to restoration.

PubMed

Guo, Gang; Wu, Di; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Wang, Haiguang; Chen, Guanghao

2016-05-15

A sulfur conversion-associated Enhanced Biological Phosphorus (P) Removal (EBPR) system is being developed to cater for the increasing needs to treat saline/brackish wastewater resulting from seawater intrusion into groundwater and sewers and frequent use of sulfate coagulants during drinking water treatment, as well as to meet the demand for eutrophication control in warm climate regions. However, the major functional bacteria and metabolism in this emerging biological nutrient removal system are still poorly understood. This study was thus designed to explore the functional microbes and metabolism in this new EBPR system by manipulating the deterioration, failure and restoration of a lab-scale system. This was achieved by changing the mixed liquor suspended solids (MLSS) concentration to monitor and evaluate the relationships among sulfur conversion (including sulfate reduction and sulfate production), P removal, variation in microbial community structures, and stoichiometric parameters. The results show that the stable Denitrifying Sulfur conversion-associated EBPR (DS-EBPR) system was enriched by sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB). These bacteria synergistically participated in this new EBPR process, thereby inducing an appropriate level of sulfur conversion crucial for achieving a stable DS-EBPR performance, i.e. maintaining sulfur conversion intensity at 15-40 mg S/L, corresponding to an optimal sludge concentration of 6.5 g/L. This range of sulfur conversion favors microbial community competition and various energy flows from internal polymers (i.e. polysulfide or elemental sulfur (poly-S(2-)/S(0)) and poly-β-hydroxyalkanoates (PHA)) for P removal. If this range was exceeded, the system might deteriorate or even fail due to enrichment of glycogen-accumulating organisms (GAOs). Four methods of restoring the failed system were investigated: increasing the sludge concentration, lowering the salinity or doubling the COD loading, non of which restored SRB and SOB activities for DS-EBPR; only the final novel approach of adding 25 ± 5 mg S/L of external sulfide into the reactor at the beginning of the anoxic phase could efficiently restore the DS-EBPR system from failure. The present study represents a step towards understanding the DS-EBPR metabolism and provides an effective remedial measure for recovering a deteriorating or failed DS-EBPR system. Copyright © 2016 Elsevier Ltd. All rights reserved.

Seasonal changes in the chemistry and biology of a meromictic lake (Big Soda Lake, Nevada, U.S.A.)

USGS Publications Warehouse

Cloern, J.E.; Cole, B.E.; Oremland, R.S.

1983-01-01

Big Soda Lake is an alkaline, saline lake with a permanent chemocline at 34.5 m and a mixolimnion that undergoes seasonal changes in temperature structure. During the period of thermal stratification, from summer through fall, the epilimnion has low concentrations of dissolved inorganic nutrients (N, Si) and CH4, and low biomass of phytoplankton (chlorophyll a ca. 1 mgm -3). Dissolved oxygen disappears near the compensation depth for algal photosynthesis (ca. 20 m). Surface water is transparent so that light is present in the anoxic hypolimnion, and a dense plate of purple sulfur photosynthetic bacteria (Ectothiorhodospira vacuolata) is present just below 20 m (Bchl a ca. 200 mgm-3). Concentrations of N H4+, Si, and CH4 are higher in the hypolimnion than in the epilimnion. As the mixolimnion becomes isothermal in winter, oxygen is mixed down to 28 m. Nutrients (NH4+, Si) and CH4 are released from the hypolimnion and mix to the surface, and a diatom bloom develops in the upper 20 m (chlorophyll a > 40 mgm-3). The deeper mixing of oxygen and enhanced light attenuation by phytoplankton uncouple the anoxic zone and photic zone, and the plate of photosynthetic bacteria disappears (Bchl a ca.10mgm-3). Hence, seasonal changes in temperature distribution and mixing create conditions such that the primary producer community is alternately dominated by phytoplankton and photosynthetic bacteria: the phytoplankton may be nutrient-limited during periods of stratification and the photosynthetic bacteria are light-limited during periods of mixing. ?? 1983 Dr W. Junk Publishers.

Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia).

PubMed

Namsaraev, Zorigto; Samylina, Olga; Sukhacheva, Marina; Borisenko, Gennadii; Sorokin, Dimitry Y; Tourova, Tatiana

2018-04-16

Bitter-1 is a shallow hypersaline soda lake in Kulunda Steppe (Altai region, Russia). During a study period between 2005 and 2016, the salinity in the littoral area of the lake fluctuated within the range from 85 to 400 g/L (in July of each year). Light-dependent nitrogen fixation occurred in this lake up to the salt-saturating conditions. The rates increased with a decrease in salinity, both under environmental conditions and in laboratory simulations. The salinities below 100 g/L were favorable for light-dependent nitrogen fixation, while the process was dramatically inhibited above 200 g/L salts. The analysis of nifH genes in environmental samples and in enrichment cultures of diazotrophic phototrophs suggested that anaerobic fermenting and sulfate-reducing bacteria could participate in the dark nitrogen fixation process up to soda-saturating conditions. However, we cannot exclude the possibility that haloalkaliphilic nonheterocystous cyanobacteria (Euhalothece sp. and Geitlerinema sp.) and anoxygenic purple sulfur bacteria (Ectothiorhodospira sp.) might also play a role in the process at light conditions. The heterocystous cyanobacterium Nodularia sp. develops at low salinity (below 80 g/L) that is not characteristic for Bitter-1 Lake and thus does not make a significant contribution to the nitrogen fixation in this lake.

[Diversity of culturable sulfur-oxidizing bacteria in deep-sea hydrothermal vent environments of the South Atlantic].

PubMed

Xu, Hongxiu; Jiang, Lijing; Li, Shaoneng; Zhong, Tianhua; Lai, Qiliang; Shao, Zongze

2016-01-04

To investigate the diversity of culturable sulfur-oxidizing bacteria in hydrothermal vent environments of the South Atlantic, and analyze their characteristics of sulfur oxidation. We enriched and isolated sulfur-oxidizing bacteria from hydrothermal vent samples collected from the South Atlantic. The microbial diversity in enrichment cultures was analyzed using the Denatural Gradient Gel Electrophoresis method. Sulfur-oxidizing characteristics of the isolates was further studied by using ion chromatography. A total of 48 isolates were obtained from the deep-sea hydrothermal vent samples, which belonged to 23 genera and mainly grouped into alpha-Proteobacteria (58.3%), Actinobacteria (22.9%) and gama-Proteobacteria (18.8%). Among them, the genus Thalassospira, Martelella and Microbacterium were dominant. About 60% of the isolates exibited sulfur-oxidizing ability and strain L6M1-5 had a higher sulfur oxidation rate by comparison analysis. The diversity of sulfur-oxidizing bacteria in hydrothermal environments of the South Atlantic was reported for the first time based on culture-dependent methods. The result will help understand the biogechemical process of sulfur compounds in the deep-sea hydrothermal environments.

Two transcription factors TaPpm1 and TaPpb1 co-regulate anthocyanin biosynthesis in purple pericarps of wheat

PubMed Central

Jiang, Wenhui; Liu, Tianxiang; Nan, Wenzhi; Jeewani, Diddugodage Chamila; Niu, Yanlu; Li, Chunlian; Shi, Xue; Wang, Cong; Wang, Jiahuan; Li, Yang; Wang, Zhonghua

2018-01-01

Abstract Purple pericarps of bread wheat (Triticum aestivum L.) are a useful source of dietary anthocyanins. Previous mapping results indicated that the purple pericarp trait is controlled by two complementary genes located on chromosomes 7D and 2A. However, the identity of the genes and the mechanisms by which they regulate the trait are unknown. In this study, two transcription factors were characterised as anthocyanin activators in purple pericarps: TaPpm1 (purple pericarp-MYB 1) and TaPpb1 (purple pericarp-bHLH 1). Three non-functional variants were detected in the coding sequence of TaPpm1 from non-purple seed lines, in which the function of TaPpm1 was destroyed either by insertion-induced frame shifts or truncated peptides. There were six 261-bp tandem repeats in the promoter region of TaPpb1 in the purple-grained varieties, while there was only one repeat unit present in the non-purple varieties. Furthermore, using yeast two-hybrid, dual luciferase, yeast one-hybrid, and transient assays, we were able to demonstrate that the interaction of TaPpm1 and TaPpb1 co-regulates the synthesis of anthocyanin. Overall, our results provide a better understanding of the molecular basis of anthocyanin synthesis in the wheat pericarp and indicate the existence of an integrated regulatory mechanism that controls production. PMID:29562292

Relationship between microbial community dynamics and process performance during thermophilic sludge bioleaching.

PubMed

Chen, Shen-Yi; Chou, Li-Chieh

2016-08-01

Heavy metals can be removed from the sludge using bioleaching technologies at thermophilic condition, thereby providing an option for biotreatment of wasted sludge generated from wastewater treatment. The purposes of this study were to establish a molecular biology technique, real-time PCR, for the detection and enumeration of the sulfur-oxidizing bacteria during the thermophilic sludge bioleaching. The 16S rRNA gene for real-time PCR quantification targeted the bioleaching bacteria: Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, and Acidithiobacillus caldus. The specificity and stringency for thermophilic sulfur-oxidizing bacteria were tested before the experiments of monitoring the bacterial community, bacterial number during the thermophilic sludge bioleaching and the future application on testing various environmental samples. The results showed that S. acidophilus was identified as the dominant sulfur-oxidizing bacteria, while A. caldus and S. thermosulfidooxidans occurred in relatively low numbers. The total number of the sulfur-oxidizing bacteria increased during the thermophilic bioleaching process. Meanwhile, the decrease of pH, production of sulfate, degradation of SS/VSS, and solubilization of heavy metal were found to correlate well with the population of thermophilic sulfur-oxidizing bacteria during the bioleaching process. The real-time PCR used in this study is a suitable method to monitor numbers of thermophilic sulfur-oxidizing bacteria during the bioleaching process.

Transport dynamics in membranes of photosynthetic purple bacteria

NASA Astrophysics Data System (ADS)

Caycedo, Felipe; Rodriguez, Ferney; Quiroga, Luis; Fassioli, Francesca; Johnson, Neil

2007-03-01

Photo-Syntethic Unit (PSU) of purple bacteria is conformed by three basic constituents: Light Harvesting Complex 2 (LH2) antenna complexes, where chromophores are distributed in a ring in close contact with caroteniods with a function of collecting light; LH1s, ring shaped structures of chromophores which harvest and funnel excitations to the Reaction Centre (RC), where phtosynthesis takes place. Studies concerning a single PSU have been capable of reproducing experimental transfer times, but incapable of explaining the fact that architecture LH2-LH1-RC of phototosynthetic membranes changes as light intensity conditions vary. The organization of antenna complexes in the membranes that support PSU seems to have its own functionality. A hopping model where excitations are transferred within a membrane is used, and populations of RC, LH1 and LH2 are investigated. Different statistics concerning arrival times of excitations that excite a single PSU are considered and compared with the global model where coordinates of a great portion of a membrane are included. The model permits in a classical basis to understand which parameters make photosynthesis in purple bateria efficient and reliable.

The LH2 complexes are assembled in the cells of purple sulfur bacterium Ectothiorhodospira haloalkaliphila with inhibition of carotenoid biosynthesis.

PubMed

Ashikhmin, Aleksandr; Makhneva, Zoya; Moskalenko, Andrey

2014-03-01

The effect of the inhibitor of carotenoid (Car) biosynthesis, diphenylamine (DPA), on the cells of the purple sulfur bacterium Ectothiorhodospira (Ect.) haloalkaliphila has been studied. There occurs an inhibition of the biosynthesis of colored Cars (≥99 %) at 71 μM DPA. Considering "empty" Car pockets (Moskalenko and Makhneva 2012) the content of Cars in the DPA-treated samples is first calculated more correctly. The total content of the colored Cars in the sample at 71 μM DPA does not exceed 1 % of the wild type. In the DPA-treated cells (membranes) a complete set of pigment-protein complexes is retained. The LH2 complex at 71 μM DPA is isolated, which is identical to the LH2 complex of the wild type in near IR absorption spectra. This suggests that the principles for assembling this LH2 complex in vivo in the absence of colored Cars remain the same. These results are in full agreement with the data obtained earlier for Allochromatium (Alc.) minutissimum (Moskalenko and Makhneva 2012). They are as follows: (1) DPA almost entirely inhibits the biosynthesis of the colored Cars in Ect. haloalkaliphila cells. (2) In the DPA-treated samples non-colored Cars are detected at 53.25 μM DPA (as traces) and at 71 μM DPA. (3) DPA may affect both phytoene synthase (at ≤71 μM DPA) and phytoene desaturase (at ≥53.25 μM DPA). (4) The assembly of LH2 complex does occur without any colored Cars.

Ultrasound improves antimicrobial effect of sodium dichloroisocyanurate to reduce Salmonella Typhimurium on purple cabbage.

PubMed

Duarte, Ana Lúcia Almeida; do Rosário, Denes Kaic Alves; Oliveira, Syllas Borburema Silva; de Souza, Hygor Lendell Silva; de Carvalho, Raquel Vieira; Carneiro, Joel Camilo Souza; Silva, Pollyanna Ibrahim; Bernardes, Patrícia Campos

2018-03-23

The consumer's interest in ready-to-eat, fast-ready, nutritious and fresh foods is a major challenge for the food industry. Thus, studies on new sanitization methods are relevant. The effect of Sodium Hypochlorite (SH), Benzalkonium Chloride (BC), and Sodium Dichloroisocyanurate (SD) isolated or combined with Ultrasound (US) in purple cabbage quality over 7 days of storage at 8 ± 1 °C was evaluated. The natural microbiota (mesophilic aerobic bacteria, lactic acid bacteria and coliforms), intentionally inoculated Salmonella Typhimurium, physicochemical quality (anthocyanins, pH, total titratable acidity, instrumental color and mass loss) and sensorial quality (multiple comparison test and visual sensory acceptance) were analyzed. The best treatments for natural microbiota reduction were BC and US + BC, which in general reduced between 1.9 and 3.2 log cfu/g. US improved (p < .05) the effect of SD reducing almost 4 log cycles in the population of S. Typhimurium adhered to cabbage. The treatments with benzalkonium chloride resulted in important physicochemical changes in cabbage. The treatments SD and US + SD did not alter the physicochemical and sensorial characteristics of purple cabbage. Therefore, ultrasound combined with sodium dichloroisocyanurate is a promising alternative for the reduction of microbiological contaminants of purple cabbage without physicochemical, sensory and anthocyanin content loss. Copyright © 2018 Elsevier B.V. All rights reserved.

Origin of mitochondria by intracellular enslavement of a photosynthetic purple bacterium

PubMed Central

Cavalier-Smith, Thomas

2006-01-01

Mitochondria originated by permanent enslavement of purple non-sulphur bacteria. These endosymbionts became organelles through the origin of complex protein-import machinery and insertion into their inner membranes of protein carriers for extracting energy for the host. A chicken-and-egg problem exists: selective advantages for evolving import machinery were absent until inner membrane carriers were present, but this very machinery is now required for carrier insertion. I argue here that this problem was probably circumvented by conversion of the symbiont protein-export machinery into protein-import machinery, in three phases. I suggest that the first carrier entered the periplasmic space via pre-existing β-barrel proteins in the bacterial outer membrane that later became Tom40, and inserted into the inner membrane probably helped by a pre-existing inner membrane protein, thereby immediately providing the protoeukaryote host with photosynthesate. This would have created a powerful selective advantage for evolving more efficient carrier import by inserting Tom70 receptors. Massive gene transfer to the nucleus inevitably occurred by mutation pressure. Finally, pressure from harmful, non-selected gene transfer to the nucleus probably caused evolution of the presequence mechanism, and photosynthesis was lost. PMID:16822756

Fermentative utilization of glycerol residue for the production of acetic acid

NASA Astrophysics Data System (ADS)

Irvan; Trisakti, B.; Hasibuan, R.; Joli, M.

2018-02-01

Glycerol residue, frequently known as pitch, is a waste produced from the downstream product of crude glycerine distillation. With the increasing need of pure glycerine in the world, the glycerol residue produced is also increasing. Glycerol residue is a solid waste at room temperature, highly alkaline (pH > 13), corrosive, and categorized as hazardous and poisonous waste. In this research, acetic acid was produced from glycerol residue through the anaerobic fermentation process by using purple non-sulphur photosynthetic bacteria. The purpose of this study was to find out the influence of concentration change of glycerol residue on time and to find out the possibility of glycerol residue to be utilized as acetic acid. In this research, at first 400 g of glycerol residue was diluted with 200 ml of distilled water to change the glycerine phase, from solid to liquid at room temperature, acidified by using hydrochloric acid until pH 2. The top layer formed was fatty acid and triglycerides that should be removed. Meanwhile, the bottom layer was diluted glycerol residue which was then neutralized with caustic soda. To produce acetic acid, glycerol residue with various concentrations, salt, and purple non-sulphur photosynthetic bacteria were put together into a 100 ml bottle which had been previously sterilized, then incubated for four weeks under the light of 40-watt bulb. The result showed that on the 28th day of fermentation, the produced acetic acid were 0.28, 1.85, and 0.2% (w/w) by using glycerine with the concentration of 0.5, 1.0, and 1.5% (w/w), respectively.

Excitons in intact cells of photosynthetic bacteria.

PubMed

Freiberg, Arvi; Pajusalu, Mihkel; Rätsep, Margus

2013-09-26

Live cells and regular crystals seem fundamentally incompatible. Still, effects characteristic to ideal crystals, such as coherent sharing of excitation, have been recently used in many studies to explain the behavior of several photosynthetic complexes, especially the inner workings of the light-harvesting apparatus of the oldest known photosynthetic organisms, the purple bacteria. To this date, there has been no concrete evidence that the same effects are instrumental in real living cells, leaving a possibility that this is an artifact of unnatural study conditions, not a real effect relevant to the biological operation of bacteria. Hereby, we demonstrate survival of collective coherent excitations (excitons) in intact cells of photosynthetic purple bacteria. This is done by using excitation anisotropy spectroscopy for tracking the temperature-dependent evolution of exciton bands in light-harvesting systems of increasing structural complexity. The temperature was gradually raised from 4.5 K to ambient temperature, and the complexity of the systems ranged from detergent-isolated complexes to complete bacterial cells. The results provide conclusive evidence that excitons are indeed one of the key elements contributing to the energetic and dynamic properties of photosynthetic organisms.

[Roseibacula alcaliphilum gen. nov. sp. nov., a new alkaliphilic aerobic anoxygenic phototrophic bacterium from a meromictic soda Lake Doroninskoe (East Siberia, Russia)].

PubMed

Nuianzina-Boldareva, E N; Gorlenko, V M

2014-01-01

A bacterial strain De was isolated from the surface water layer of the meromictic soda lake Doroninskoe. When grown in the dark, it formed-pink colonies on agar media. The cells were nonmotile, contained bacteriochlorophyll a and carotenoids. Stationary-phase cells contained intracellular vesicular membranes similar to the membranes of the photosynthetic apparatus of some ndnsulfur purple bacteria. Aerobic growth did not occur. Sucrose, citrate, mannitol, sorbitol, case in hydrolysate,and yeast extract were the preferable substrates for aerobic growth, Xylose, lactose, aspartate, benzoate, malate, malonate, succinate, tartrate, formate, fumarate, glycerol, methanol, and ethanol were not utilized; Growth occurred at up to 50.g/L NaCl (optimum at 5 g/L) and pH 9.8. According to the 16S rRNA gene sequencing, similarity between the isolate and the known alkaliphilic genera of nonsulfur purple bacteria (Rhodobaca) and of aerobic anoxygenic phototrophic bacteria (Roseinatronobacter) was 96%, which was sufficient for description ofa new genus of aerobic anoxygenic phototrophic bacteria. The name Roseibacula alcaliphiluin gen. nov., sp. nov. was, proposed for the isolate.

Role of Rhodobacter sp. Strain PS9, a Purple Non-Sulfur Photosynthetic Bacterium Isolated from an Anaerobic Swine Waste Lagoon, in Odor Remediation

PubMed Central

Do, Young S.; Schmidt, Thomas M.; Zahn, James A.; Boyd, Eric S.; de la Mora, Arlene; DiSpirito, Alan A.

2003-01-01

Temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period. The major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons. By using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of Rhodobacter, designated Rhodobacter sp. strain PS9. Rhodobacter sp. strain PS9 is capable of photoorganotrophic growth on a variety of organic compounds, including all of the characteristic volatile organic compounds (VOC) responsible for the odor associated with swine production facilities (J. A. Zahn, A. A. DiSpirito, Y. S. Do, B. E. Brooks, E. E. Copper, and J. L. Hatfield, J. Environ. Qual. 30:624-634, 2001). The seasonal variations in airborne VOC emitted from waste lagoons showed that there was a 80 to 93% decrease in the concentration of VOC during a photosynthetic bloom. During the height of a bloom, the Rhodobacter sp. strain PS9 population accounted for 10% of the total community and up to 27% of the eubacterial community based on 16S ribosomal DNA signals. Additional observations based on seasonal variations in meteorological, biological, and chemical parameters suggested that the photosynthetic blooms of Rhodobacter sp. strain PS9 were correlated with lagoon water temperature and with the concentrations of sulfate and phosphate. In addition, the photosynthetic blooms of Rhodobacter sp. strain PS9 were inversely correlated with the concentrations of protein and fluoride. PMID:12620863

Extraction of manganese from electrolytic manganese residue by bioleaching.

PubMed

Xin, Baoping; Chen, Bing; Duan, Ning; Zhou, Changbo

2011-01-01

Extraction of manganese from electrolytic manganese residues using bioleaching was investigated in this paper. The maximum extraction efficiency of Mn was 93% by sulfur-oxidizing bacteria at 4.0 g/l sulfur after bioleaching of 9days, while the maximum extraction efficiency of Mn was 81% by pyrite-leaching bacteria at 4.0 g/l pyrite. The series bioleaching first by sulfur-oxidizing bacteria and followed by pyrite-leaching bacteria evidently promoted the extraction of manganese, witnessing the maximum extraction efficiency of 98.1%. In the case of sulfur-oxidizing bacteria, the strong dissolution of bio-generated sulfuric acid resulted in extraction of soluble Mn2+, while both the Fe2+ catalyzed reduction of Mn4+ and weak acidic dissolution of Mn2+ accounted for the extraction of manganese with pyrite-leaching bacteria. The chemical simulation of bioleaching process further confirmed that the acid dissolution of Mn2+ and Fe2+ catalyzed reduction of Mn4+ were the bioleaching mechanisms involved for Mn extraction from electrolytic manganese residues. Copyright © 2010 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

James C. Liao

This project is a collaboration with F. R. Tabita of Ohio State. Our major goal is to understand the factors and regulatory mechanisms that influence hydrogen production. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Our part of the project was to develop a modeling technique to investigate the metabolic network in connection to hydrogen production and regulation. Organisms must balance the pathways that generate and consume reducing powermore » in order to maintain redox homeostasis to achieve growth. Maintaining this homeostasis in the nonsulfur purple photosynthetic bacteria is a complex feat with many avenues that can lead to balance, as these organisms possess versatile metabolic capabilities including anoxygenic photosynthesis, aerobic or anaerobic respiration, and fermentation. Growth is achieved by using H{sub 2} as an electron donor and CO{sub 2} as a carbon source during photoautotrophic and chemoautotrophic growth, where CO{sub 2} is fixed via the Calvin-Benson-Bassham (CBB) cycle. Photoheterotrophic growth can also occur when alternative organic carbon compounds are utilized as both the carbon source and electron donor. Regardless of the growth mode, excess reducing equivalents generated as a result of oxidative processes, must be transferred to terminal electron acceptors, thus insuring that redox homeostasis is maintained in the cell. Possible terminal acceptors include O{sub 2}, CO{sub 2}, organic carbon, or various oxyanions. Cells possess regulatory mechanisms to balance the activity of the pathways which supply energy, such as photosynthesis, and those that consume energy, such as CO{sub 2} assimilation or N{sub 2} fixation. The major route for CO{sub 2} assimilation is the CBB reductive pentose phosphate pathway, whose key enzyme is ribulose 1,5-biphosphate carboxylase/oxygenase (RubisCO). In addition to providing virtually all cellular carbon during autotrophic metabolism, RubisCO-mediated CO{sub 2} assimilation is also very important for nonsulfur purple photosynthetic bacteria under photoheterotrophic growth conditions since CO{sub 2} becomes the major electron sink under these conditions. In this work, Ensemble Modeling (EM) was developed to examine the behavior of CBB-compromised RubisCO knockout mutant strains of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Mathematical models of metabolism can be a great aid in studying the effects of large perturbations to the system, such as the inactivation of RubisCO. Due to the complex and highly-interconnected nature of these networks, it is not a trivial process to understand what the effect of perturbations to the metabolic network will be, or vice versa, what enzymatic perturbations are necessary to yield a desired effect. Flux distribution is controlled by multiple enzymes in the network, often indirectly linked to the pathways of interest. Further, depending on the state of the cell and the environmental conditions, the effect of a perturbation may center around how it effects the carbon flow in the network, the balancing of cofactors, or both. Thus, it is desirable to develop mathematical models to describe, understand, and predict network behavior. Through the development of such models, one may gain the ability to generate a set of testable hypotheses for system behavior.« less

Bacteria and Acidic Drainage from Coal Refuse: Inhibition by Sodium Lauryl Sulfate and Sodium Benzoate

PubMed Central

Dugan, Patrick R.; Apel, William A.

1983-01-01

The application of an aqueous solution of sodium lauryl sulfate and sodium benzoate to the surface of high-sulfur coal refuse resulted in the inhibition of iron-and sulfur-oxidizing chemoautotrophic bacteria and in the decrease of acidic drainage from the refuse, suggesting that acid drainage can be abated in the field by inhibiting iron- and sulfur-oxidizing bacteria. PMID:16346347

Evidence for the bacterial origin of genes encoding fermentation enzymes of the amitochondriate protozoan parasite Entamoeba histolytica.

PubMed

Rosenthal, B; Mai, Z; Caplivski, D; Ghosh, S; de la Vega, H; Graf, T; Samuelson, J

1997-06-01

Entamoeba histolytica is an amitochondriate protozoan parasite with numerous bacterium-like fermentation enzymes including the pyruvate:ferredoxin oxidoreductase (POR), ferredoxin (FD), and alcohol dehydrogenase E (ADHE). The goal of this study was to determine whether the genes encoding these cytosolic E. histolytica fermentation enzymes might derive from a bacterium by horizontal transfer, as has previously been suggested for E. histolytica genes encoding heat shock protein 60, nicotinamide nucleotide transhydrogenase, and superoxide dismutase. In this study, the E. histolytica por gene and the adhE gene of a second amitochondriate protozoan parasite, Giardia lamblia, were sequenced, and their phylogenetic positions were estimated in relation to POR, ADHE, and FD cloned from eukaryotic and eubacterial organisms. The E. histolytica por gene encodes a 1,620-amino-acid peptide that contained conserved iron-sulfur- and thiamine pyrophosphate-binding sites. The predicted E. histolytica POR showed fewer positional identities to the POR of G. lamblia (34%) than to the POR of the enterobacterium Klebsiella pneumoniae (49%), the cyanobacterium Anabaena sp. (44%), and the protozoan Trichomonas vaginalis (46%), which targets its POR to anaerobic organelles called hydrogenosomes. Maximum-likelihood, neighbor-joining, and parsimony analyses also suggested as less likely E. histolytica POR sharing more recent common ancestry with G. lamblia POR than with POR of bacteria and the T. vaginalis hydrogenosome. The G. lamblia adhE encodes an 888-amino-acid fusion peptide with an aldehyde dehydrogenase at its amino half and an iron-dependent (class 3) ADH at its carboxy half. The predicted G. lamblia ADHE showed extensive positional identities to ADHE of Escherichia coli (49%), Clostridium acetobutylicum (44%), and E. histolytica (43%) and lesser identities to the class 3 ADH of eubacteria and yeast (19 to 36%). Phylogenetic analyses inferred a closer relationship of the E. histolytica ADHE to bacterial ADHE than to the G. lamblia ADHE. The 6-kDa FD of E. histolytica and G. lamblia were most similar to those of the archaebacterium Methanosarcina barkeri and the delta-purple bacterium Desulfovibrio desulfuricans, respectively, while the 12-kDa FD of the T. vaginalis hydrogenosome was most similar to the 12-kDa FD of gamma-purple bacterium Pseudomonas putida. E. histolytica genes (and probably G. lamblia genes) encoding fermentation enzymes therefore likely derive from bacteria by horizontal transfer, although it is not clear from which bacteria these amebic genes derive. These are the first nonorganellar fermentation enzymes of eukaryotes implicated to have derived from bacteria.

Phylogenetic relationship between symbionts of tubeworm Lamellibrachia satsuma and the sediment microbial community in Kagoshima Bay

NASA Astrophysics Data System (ADS)

Patra, Ajit Kumar; Cho, Hyun Hee; Kwon, Yong Min; Kwon, Kae Kyoung; Sato, Takako; Kato, Chiaki; Kang, Sung Gyun; Kim, Sang-Jin

2016-09-01

Vestimentiferan tubeworms acquire their symbionts through horizontal transmission from the surrounding environment. In the present study, we constructed a 16S rRNA gene clone library to investigate the phylogenetic relationship between diverse microbes in the sediment and symbiotic bacteria in the trophosome of the tubeworm, Lamellibrachia satsuma, from Kagoshima Bay, Japan. Two symbiotic bacterial phylotypes belonging to the classes γ- and ɛ-Proteobacteria were found from this tubeworm trophosome. They were very closely related to the symbionts of several other marine invertebrates. The most predominant bacteria in the sediment were ɛ-Proteobacteria. A broad diversity of bacteria belonged to non-proteobacterial phyla such as Planctomycetes, Acidobacteria, and Chloroflexi was observed. The presence of sulfur oxidizers (i.e., ɛ-Proteobacteria and γ-Proteobacteria) and sulfur reducers (i.e., δ-Proteobacteria) may play a significant role in the sulfur cycle in these habitats and provide multiple sources of nutrition to the cold-seep communities. Closely related clones of ɛ-Proteobacteria symbiont in the species level and of γ-Proteobacteria symbiont in the genus level were found in the surrounding sediment. The similarity of symbiont clones of L. satsuma with other symbionts and free-living bacteria suggests the possibility of opportunistic symbiosis in ɛ-Proteobacteria and the co-evolution of γ-Proteobacteria having occurred after symbiosis with the tubeworms.

34S/32S fractionation in sulfur cycles catalyzed by anaerobic bacteria

NASA Technical Reports Server (NTRS)

Fry, B.; Gest, H.; Hayes, J. M.

1988-01-01

Stable isotopic distributions in the sulfur cycle were studied with pure and mixed cultures of the anaerobic bacteria, Chlorobium vibrioforme and Desulfovibrio vulgaris. D. vulgaris and C. vibrioforme can catalyze three reactions constituting a complete anaerobic sulfur cycle: reduction of sulfate to sulfide (D. vulgaris), oxidation of sulfide to elemental sulfur (C. vibrioforme), and oxidation of sulfur to sulfate (C. vibrioforme). In all experiments, the first and last reactions favored concentration of the light 32S isotope in products (isotopic fractionation factor epsilon = -7.2 and -1.7%, respectively), whereas oxidation of sulfide favored concentration of the heavy 34S isotope in products (epsilon = +1.7%). Experimental results and model calculations suggest that elemental sulfur enriched in 34S versus sulfide may be a biogeochemical marker for the presence of sulfide-oxidizing bacteria in modern and ancient environments.

Sulfur Dioxide Plume During the Continuing Eruption of Mt. Etna, Italy

NASA Image and Video Library

2001-08-03

The current eruption of Mt. Etna started on July 17, and has continued to the present. This ASTER image was acquired on Sunday, July 29 and shows the sulfur dioxide plume (in purple) originating form the summit, drifting over the city of Catania, and continuing over the Ionian Sea. ASTER's unique combination of multiple thermal infrared channels and high spatial resolution allows the determination of the thickness and position of the SO2 plume. The image covers an area of 24 x 30 km. The image is centered at 37.7 degrees north latitude, 15 degrees east longitude. http://photojournal.jpl.nasa.gov/catalog/PIA02678

Quantification of two forms of green sulfur bacteria in their natural habitat using bacteriochlorophyll fluorescence spectra

NASA Astrophysics Data System (ADS)

Kharcheva, Anastasia V.; Zhiltsova, Anna A.; Lunina, Olga N.; Savvichev, Alexander S.; Patsaeva, Svetlana V.

2016-04-01

Detection of phototropic organisms in their natural habitat using optical instruments operating under water is urgently needed for many tasks of ecological monitoring. While fluorescence methods are widely applied nowadays to detect and characterize phytoplankton communities, the techniques for detection and recognition of anoxygenic phototrophs are considered challenging. Differentiation of the forms of anoxygenic green sulfur bacteria in natural water using spectral techniques remains problematic. Green sulfur bacteria could be found in two forms, green-colored (containing BChl d in pigment compound) and brown-colored (containing BChl e), have the special ecological niche in such reservoirs. Separate determination of these microorganisms by spectral methods is complicated because of similarity of spectral characteristics of their pigments. We describe the novel technique of quantification of two forms of green sulfur bacteria directly in water using bacteriochlorophyll fluorescence without pigment extraction. This technique is noninvasive and could be applied in remote mode in the water bodies with restricted water circulation to determine simultaneously concentrations of two forms of green sulfur bacteria in their natural habitat.

Research in photobiology and photochemistry

NASA Technical Reports Server (NTRS)

Gaffron, H.

1973-01-01

Publications are listed covering NASA research from 1966 to 1973. Several major works covering chloroplast reactions, aerobic green algae and hydrogenease, production of molecular hydrogen, and hydrogen and nitrogen metabolism in purple bacteria are summarized.

The role of "blebbing" in overcoming the hydrophobic barrier during biooxidation of elemental sulfur by Thiobacillus thiooxidans

USGS Publications Warehouse

Knickerbocker, C.; Nordstrom, D. Kirk; Southam, G.

2000-01-01

Brimstone Basin, in southeastern Yellowstone National Park, Wyoming is an ancient hydrothermal area containing solfataric alteration. Drainage waters flowing from Brimstone Basin had pH values as low as 1.23 and contained up to 1.7×106 MPN/ml acidophilic sulfur-oxidizing bacteria. Thiobacillus thiooxidans was the dominant sulfur-oxidizing bacterium recovered from an enrichment culture and was used in a structural examination of bacterial sulfur oxidation. Growth in these sulfur cultures occurred in two phases with cells in association with the macroscopic sulfur grains and in suspension above these grains. Colonization of sulfur grains by individual cells and microcolonies was facilitated by organic material that appeared to be responsible for bacterial adhesion. Transmission electron microscopy of negatively stained (2% [wt./vol.] uranyl acetate), sulfur-grown T. thiooxidans revealed extensive membrane blebbing (sloughing of outer membrane vesicles) and the presence of approximately 100 nm sized sulfur particles adsorbed to membrane material surrounding individual bacteria. Sulfite-grown bacteria did not possess membrane blebs. The amphipathic nature of these outer membrane vesicles appear to be responsible for overcoming the hydrophobic barrier necessary for the growth of T. thiooxidans on elemental sulfur.

Influence of organics and silica on Fe(II) oxidation rates and cell-mineral aggregate formation by the green-sulfur Fe(II)-oxidizing bacterium Chlorobium ferrooxidans KoFox - Implications for Fe(II) oxidation in ancient oceans

NASA Astrophysics Data System (ADS)

Gauger, Tina; Byrne, James M.; Konhauser, Kurt O.; Obst, Martin; Crowe, Sean; Kappler, Andreas

2016-06-01

Most studies on microbial phototrophic Fe(II) oxidation (photoferrotrophy) have focused on purple bacteria, but recent evidence points to the importance of green-sulfur bacteria (GSB). Their recovery from modern ferruginous environments suggests that these photoferrotrophs can offer insights into how their ancient counterparts grew in Archean oceans at the time of banded iron formation (BIF) deposition. It is unknown, however, how Fe(II) oxidation rates, cell-mineral aggregate formation, and Fe-mineralogy vary under environmental conditions reminiscent of the geological past. To address this, we studied the Fe(II)-oxidizer Chlorobium ferrooxidans KoFox, a GSB living in co-culture with the heterotrophic Geospirillum strain KoFum. We investigated the mineralogy of Fe(III) metabolic products at low/high light intensity, and in the presence of dissolved silica and/or fumarate. Silica and fumarate influenced the crystallinity and particle size of the produced Fe(III) minerals. The presence of silica also enhanced Fe(II) oxidation rates, especially at high light intensities, potentially by lowering Fe(II)-toxicity to the cells. Electron microscopic imaging showed no encrustation of either KoFox or KoFum cells with Fe(III)-minerals, though weak associations were observed suggesting co-sedimentation of Fe(III) with at least some biomass via these aggregates, which could support diagenetic Fe(III)-reduction. Given that GSB are presumably one of the most ancient photosynthetic organisms, and pre-date cyanobacteria, our findings, on the one hand, strengthen arguments for photoferrotrophic activity as a likely mechanism for BIF deposition on a predominantly anoxic early Earth, but, on the other hand, also suggest that preservation of remnants of Fe(II)-oxidizing GSB as microfossils in the rock record is unlikely.

Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria.

PubMed

Iino, Takao; Mori, Koji; Uchino, Yoshihito; Nakagawa, Tatsunori; Harayama, Shigeaki; Suzuki, Ken-Ichiro

2010-06-01

A moderately thermophilic chemoheterotrophic bacterium, strain Mat9-16(T), was isolated from microbial mats developed in hot spring water streams from Yumata, Nagano, Japan. Cells of strain Mat9-16(T) were strictly anaerobic, Gram-stain-negative, non-sporulating, non-motile and short to long rods (2.0-15.5 mum in length). Strain Mat9-16(T) grew fermentatively with optimum growth at 45 degrees C, pH 7.0-7.5 and 1 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene revealed that strain Mat9-16(T) was affiliated with an uncultivated lineage, and the nearest cultivated neighbours were green sulfur bacteria belonging to the class Chlorobea with 77-83 % sequence similarity. However, strain Mat9-16(T) could not grow phototrophically and did not possess light-harvesting structures, morphologically and genetically, such as the chlorosomes of green sulfur bacteria. On the basis of phenotypic features and phylogenetic position, a novel genus and species are proposed for strain Mat9-16(T), to be named Ignavibacterium album gen. nov., sp. nov. (=NBRC 101810(T) =DSM 19864(T)). We also propose to place the cultivated bacterial lineage accommodating the sole representative Mat9-16(T) in a novel class, Ignavibacteria classis nov. In addition, we present a formal description of the phylum-level taxon 'Chlorobi' as Chlorobi phyl. nov.

Investigation of energy gene expressions and community structures of free and attached acidophilic bacteria in chalcopyrite bioleaching.

PubMed

Zhu, Jianyu; Jiao, Weifeng; Li, Qian; Liu, Xueduan; Qin, Wenqing; Qiu, Guanzhou; Hu, Yuehua; Chai, Liyuan

2012-12-01

In order to better understand the bioleaching mechanism, expression of genes involved in energy conservation and community structure of free and attached acidophilic bacteria in chalcopyrite bioleaching were investigated. Using quantitative real-time PCR, we studied the expression of genes involved in energy conservation in free and attached Acidithiobacillus ferrooxidans during bioleaching of chalcopyrite. Sulfur oxidation genes of attached A. ferrooxidans were up-regulated while ferrous iron oxidation genes were down-regulated compared with free A. ferrooxidans in the solution. The up-regulation may be induced by elemental sulfur on the mineral surface. This conclusion was supported by the results of HPLC analysis. Sulfur-oxidizing Acidithiobacillus thiooxidans and ferrous-oxidizing Leptospirillum ferrooxidans were the members of the mixed culture in chalcopyrite bioleaching. Study of the community structure of free and attached bacteria showed that A. thiooxidans dominated the attached bacteria while L. ferrooxidans dominated the free bacteria. With respect to available energy sources during bioleaching of chalcopyrite, sulfur-oxidizers tend to be on the mineral surfaces whereas ferrous iron-oxidizers tend to be suspended in the aqueous phase. Taken together, these results indicate that the main role of attached acidophilic bacteria was to oxidize elemental sulfur and dissolution of chalcopyrite involved chiefly an indirect bioleaching mechanism.

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

PubMed

Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

2014-11-01

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

THE ANTIBACTERIAL PROPERTIES OF SULFUR

PubMed Central

Weld, Julia T.; Gunther, Anne

1947-01-01

1. Saturated solutions of sulfur in alcohol (alcohol-sulfur) when diluted with broth are inhibitory to the growth of various Gram-positive bacteria and to C. hominis. By an arbitrary method of unitage with S. aureus as the test organism, our alcohol-sulfur contains 1,600 to 2,000 units per cc. and one unit contains between 0.24 and 0.34 gamma sulfur. The activity of a preparation is in general directly proportional to its sulfur content. 2. Solutions of sulfur in carbowax (carbowax-sulfur) when diluted with broth are likewise inhibitory to the growth of various Gram-positive bacteria and to C. hominis. When S. aureus is used as test organism, 1 unit contains between 0.1 and 0.2 gamma sulfur. The activity of these preparations is also in general directly proportional to their sulfur content. 3. Carbowax-sulfur when incorporated in agar in 1–500 to 1–2,000 dilution inhibits the growth of various Gram-positive aerobic and anaerobic bacteria, C. hominis, and certain dermatophytes. 4. Our experiments appear to show that both alcohol-sulfur and carbowax-sulfur owe their inhibitory properties to the sulfur particles that are dispersed throughout the medium when these sulfur preparations are diluted with broth. The inhibitory effect of these particles may or may not be due to a combination of the sulfur particles with substances in the medium in which they are suspended. 5. Evidence suggests that the activity of both alcohol-sulfur and carbowax-sulfur is due to sulfur in the same form. The inhibitory effect is characterized by prolonged bacteriostasis with similar activity over a wide range of dilutions. There is no evidence of true bactericidal action even with the highest concentrations used. PMID:19871634

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wasielewski, M.R.; Gast, P.; Norris, J.R.

Photoexcitation of the reaction center protein from purple photosynthetic bacteria results in rapid (< 5 ps) formation of a radical pair, P/sup F/ composed of an oxidized bacteriochlorophyll a dimer, P/sup +/ and a reduced bacteriopheophytin a, I/sup -/. The recent crystallization of the reaction center protein from R. viridis enables us to use magnetic resonance to obtain structural information about the reaction center relatively rapidly. We have grown large numbers of R. viridis reaction center crystals and have determined the orientation of the triplet axis system of the primary donor to within + 1 degree as well as amore » number of magnetically non-equivalent donor sites in the crystal.« less

Biomediated Precipitation of Calcium Carbonate in a Slightly Acidic Hot Spring

NASA Astrophysics Data System (ADS)

Jiang, L.

2015-12-01

A slightly acidic hot spring named "Female Tower" (T=73.5 °C, pH=6.64) is located in the Jifei Geothermal Field, Yunnan Province, Southwest China. The precipitates in the hot spring are composed of large amounts of calcite, aragonite, and sulfur. Scanning electron microscopy (SEM) analyses revealed that the microbial mats were formed of various coccoid, rod-shaped, and filamentous microbes. Transmission electron microscopy (TEM) showed that the intracellular sulfur granules were commonly associated with these microbes. A culture-independent molecular phylogenetic analysis demonstrated that the majority of the bacteria in the spring were sulfur-oxidizing bacteria. In the spring water, H2S concentration was up to 60 ppm, while SO42- concentration was only about 10 ppm. We speculated that H2S might be utilized by sulfur-oxidizing bacteria in this hot spring water, leading to the intracellular formation of sulfur granules. In the meantime, this reaction increased the pH in the micron-scale microdomains, which fostered the precipitation of calcium carbonate in the microbial mats. The results of this study indicated that the sulfur-oxidizing bacteria could play an important role in calcium carbonate precipitation in slightly acidic hot spring environments.

Purple Phototrophic Bacterium Enhances Stevioside Yield by Stevia rebaudiana Bertoni via Foliar Spray and Rhizosphere Irrigation

PubMed Central

Wu, Jing; Wang, Yiming; Lin, Xiangui

2013-01-01

This study was conducted to compare the effects of foliar spray and rhizosphere irrigation with purple phototrophic bacteria (PPB) on growth and stevioside (ST) yield of Stevia. rebaudiana. The S. rebaudiana plants were treated by foliar spray, rhizosphere irrigation, and spray plus irrigation with PPB for 10 days, respectively. All treatments enhanced growth of S. rebaudiana, and the foliar method was more efficient than irrigation. Spraying combined with irrigation increased the ST yield plant -1 by 69.2% as compared to the control. The soil dehydrogenase activity, S. rebaudiana shoot biomass, chlorophyll content in new leaves, and soluble sugar in old leaves were affected significantly by S+I treatment, too. The PPB probably works in the rhizosphere by activating the metabolic activity of soil bacteria, and on leaves by excreting phytohormones or enhancing the activity of phyllosphere microorganisms. PMID:23825677

Isolation, purification, and characterization of AgUCGalT1, a galactosyltransferase involved in anthocyanin galactosylation in purple celery (Apium graveolens L.).

PubMed

Feng, Kai; Xu, Zhi-Sheng; Liu, Jie-Xia; Li, Jing-Wen; Wang, Feng; Xiong, Ai-Sheng

2018-06-01

This study showed that a galactosyltransferase, AgUCGalT1, is involved in anthocyanin galactosylation in purple celery. Celery is a well-known vegetable because of its rich nutrients, low calories, and medicinal values. Its petioles and leaf blades are the main organs acting as nutrient sources. UDP-galactose: cyanidin 3-O-galactosyltransferase can transfer the galactosyl moiety from UDP-galactose to the 3-O-position of cyanidin through glycosylation. This process enhances the stability and water solubility of anthocyanins. In the present study, LC-MS data indicated that abundant cyanidin-based anthocyanins accumulated in the petioles of purple celery ('Nanxuan liuhe purple celery'). A gene encoding UDP-galactose: cyanidin 3-O-galactosyltransferase, namely AgUCGalT1, was isolated from purple celery and expressed in Escherichia coli BL21 (DE3). Sequence alignments revealed that the AgUCGalT1 protein contained a highly conserved putative secondary plant glycosyltransferase (PSPG) motif. The glycosylation product catalyzed by AgUCGalT1 was detected using UPLC equipment. The recombinant AgUCGalT1 had an optimal enzyme activity at 35 °C and pH 8.0, and showed highest enzyme activity toward cyanidin among the enzyme activities involving other substances, namely, peonidin, quercetin, and kaempferol. The expression levels of AgUCGalT1 were positively correlated with the total anthocyanin contents in purple and non-purple celery varieties. Crude enzymes extracted from purple celery exhibited glycosylation ability, whereas crude enzymes obtained from non-purple celery did not have this ability. This work provided evidence as a basis for investigations on the function of AgUCGalT1 in anthocyanin glycosylation in purple celery.

Non-invasive investigation on a VI century purple codex from Brescia, Italy.

PubMed

Aceto, Maurizio; Idone, Ambra; Agostino, Angelo; Fenoglio, Gaia; Gulmini, Monica; Baraldi, Pietro; Crivello, Fabrizio

2014-01-03

Purple codices are among the most relevant and prestigious book productions of Late Antique and Medieval age. They usually contained texts from Holy Writings written with golden or silver inks on parchment dyed in a purple hue. According to the tradition, the colour of parchment was obtained by the well renowned Tyrian purple dye. From the material point of view, however, very little is known about the compounds actually used in the manufacture of these manuscripts. Presently, the information available is limited to the ancient art treatises, with very few diagnostic evidences supporting them and, moreover, none confirming the presence of Tyrian purple. It is more than apparent, then, the need to have at disposal larger and more complete information at the concern, in order to verify what came to us from the literary tradition only. In this study, preliminary results are presented from non-invasive investigation on a VI century purple codex, the so-called CodexBrixianus, held in the Biblioteca Civica Queriniana at Brescia (Italy). Analyses were carried out with XRF spectrometry, UV-visible diffuse reflectance spectrophotometry, molecular spectrofluorimetry and optical microscopy. The results suggest the hypothesis that Tyrian purple had been used as a minor component mixed with other less precious dyes such as folium or orchil. Copyright © 2013 Elsevier B.V. All rights reserved.

Non-invasive investigation on a VI century purple codex from Brescia, Italy

NASA Astrophysics Data System (ADS)

Aceto, Maurizio; Idone, Ambra; Agostino, Angelo; Fenoglio, Gaia; Gulmini, Monica; Baraldi, Pietro; Crivello, Fabrizio

2014-01-01

Purple codices are among the most relevant and prestigious book productions of Late Antique and Medieval age. They usually contained texts from Holy Writings written with golden or silver inks on parchment dyed in a purple hue. According to the tradition, the colour of parchment was obtained by the well renowned Tyrian purple dye. From the material point of view, however, very little is known about the compounds actually used in the manufacture of these manuscripts. Presently, the information available is limited to the ancient art treatises, with very few diagnostic evidences supporting them and, moreover, none confirming the presence of Tyrian purple. It is more than apparent, then, the need to have at disposal larger and more complete information at the concern, in order to verify what came to us from the literary tradition only. In this study, preliminary results are presented from non-invasive investigation on a VI century purple codex, the so-called CodexBrixianus, held in the Biblioteca Civica Queriniana at Brescia (Italy). Analyses were carried out with XRF spectrometry, UV-visible diffuse reflectance spectrophotometry, molecular spectrofluorimetry and optical microscopy. The results suggest the hypothesis that Tyrian purple had been used as a minor component mixed with other less precious dyes such as folium or orchil.

Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes.

PubMed

Poser, Alexander; Lohmayer, Regina; Vogt, Carsten; Knoeller, Kay; Planer-Friedrich, Britta; Sorokin, Dimitry; Richnow, Hans-H; Finster, Kai

2013-11-01

Microbial disproportionation of elemental sulfur to sulfide and sulfate is a poorly characterized part of the anoxic sulfur cycle. So far, only a few bacterial strains have been described that can couple this reaction to cell growth. Continuous removal of the produced sulfide, for instance by oxidation and/or precipitation with metal ions such as iron, is essential to keep the reaction exergonic. Hitherto, the process has exclusively been reported for neutrophilic anaerobic bacteria. Here, we report for the first time disproportionation of elemental sulfur by three pure cultures of haloalkaliphilic bacteria isolated from soda lakes: the Deltaproteobacteria Desulfurivibrio alkaliphilus and Desulfurivibrio sp. AMeS2, and a member of the Clostridia, Dethiobacter alkaliphilus. All cultures grew in saline media at pH 10 by sulfur disproportionation in the absence of metals as sulfide scavengers. Our data indicate that polysulfides are the dominant sulfur species under highly alkaline conditions and that they might be disproportionated. Furthermore, we report the first organism (Dt. alkaliphilus) from the class Clostridia that is able to grow by sulfur disproportionation.

SpTransformer proteins from the purple sea urchin opsonize bacteria, augment phagocytosis, and retard bacterial growth

PubMed Central

Chou, Hung-Yen; Lun, Cheng Man

2018-01-01

The purple sea urchin, Strongylocentrotus purpuratus, has a complex and robust immune system that is mediated by a number of multi-gene families including the SpTransformer (SpTrf) gene family (formerly Sp185/333). In response to immune challenge from bacteria and various pathogen-associated molecular patterns, the SpTrf genes are up-regulated in sea urchin phagocytes and express a diverse array of SpTrf proteins. We show here that SpTrf proteins from coelomocytes and isolated by nickel affinity (cNi-SpTrf) bind to Gram-positive and Gram-negative bacteria and to Baker’s yeast, Saccharomyces cerevisiae, with saturable kinetics and specificity. cNi-SpTrf opsonization of the marine bacteria, Vibrio diazotrophicus, augments phagocytosis, however, opsonization by the recombinant protein, rSpTrf-E1, does not. Binding by cNi-SpTrf proteins retards growth rates significantly for several species of bacteria. SpTrf proteins, previously thought to be strictly membrane-associated, are secreted from phagocytes in short term cultures and bind V. diazotrophicus that are located both outside of and within phagocytes. Our results demonstrate anti-microbial activities of native SpTrf proteins and suggest variable functions among different SpTrf isoforms. Multiple isoforms may act synergistically to detect a wide array of pathogens and provide flexible and efficient host immunity. PMID:29738524

In Situ Detection, Isolation, and Physiological Properties of a Thin Filamentous Microorganism Abundant in Methanogenic Granular Sludges: a Novel Isolate Affiliated with a Clone Cluster, the Green Non-Sulfur Bacteria, Subdivision I

PubMed Central

Sekiguchi, Yuji; Takahashi, Hiroki; Kamagata, Yoichi; Ohashi, Akiyoshi; Harada, Hideki

2001-01-01

We previously showed that very thin filamentous bacteria affiliated with the division green non-sulfur bacteria were abundant in the outermost layer of thermophilic methanogenic sludge granules fed with sucrose and several low-molecular-weight fatty acids (Y. Sekiguchi, Y. Kamagata, K. Nakamura, A. Ohashi, H. Harada, Appl. Environ. Microbiol. 65:1280–1288, 1999). Further 16S ribosomal DNA (rDNA) cloning-based analysis revealed that the microbes were classified within a unique clade, green non-sulfur bacteria (GNSB) subdivision I, which contains a number of 16S rDNA clone sequences from various environmental samples but no cultured representatives. To investigate their function in the community and physiological traits, we attempted to isolate the yet-to-be-cultured microbes from the original granular sludge. The first attempt at isolation from the granules was, however, not successful. In the other thermophilic reactor that had been treating fried soybean curd-manufacturing wastewater, we found filamentous microorganisms to outgrow, resulting in the formation of projection-like structures on the surface of granules, making the granules look like sea urchins. 16S rDNA-cloning analysis combined with fluorescent in situ hybridization revealed that the projections were comprised of the uncultured filamentous cells affiliated with the GNSB subdivision I and Methanothermobacter-like cells and the very ends of the projections were comprised solely of the filamentous cells. By using the tip of the projection as the inoculum for primary enrichment, a thermophilic, strictly anaerobic, filamentous bacterium, designated strain UNI-1, was successfully isolated with a medium supplemented with sucrose and yeast extract. The strain was a very slow growing bacterium which is capable of utilizing only a limited range of carbohydrates in the presence of yeast extract and produced hydrogen from these substrates. The growth was found to be significantly stimulated when the strain was cocultured with a hydrogen-utilizing methanogen, Methanothermobacter thermautotrophicus, suggesting that the strain is a sugar-fermenting bacterium, the growth of which is dependent on hydrogen consumers in the granules. PMID:11722931

Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma).

PubMed

Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

2004-02-01

Bacterial diversity in caves is still rarely investigated using culture-independent techniques. In the present study, bacterial communities on Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma) were analyzed, using 16S rDNA-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. Results revealed complex bacterial communities consisting of a high number of novel 16S rDNA sequence types and indicated a high biodiversity of lithotrophic and heterotrophic bacteria. Identified bacteria were related to already cultured bacteria (39 clones) and to environmental 16S rDNA clones (46 clones). The nearest phylogenetic relatives were members of the Proteobacteria (41.1%), of the Acidobacterium division (16.5%), Actinobacteria (20%), Firmicutes (10.6%), of the Cytophaga/Flexibacter/Bacteroides division (5.9%), Nitrospira group (3.5%), green non-sulfur bacteria (1.2%), and candidate WS3 division (1.2%). Thirteen of these clones were most closely related to those obtained from the previous studies on Tito Bustillo Cave. The comparison of the present data with the data obtained previously from Altamira and Tito Bustillo Caves revealed similarities in the bacterial community components, especially in the high abundance of the Acidobacteria and Rhizobiaceae, and in the presence of bacteria related to ammonia and sulfur oxidizers.

SULFUR COMPOUNDS IN MORPHOGENESIS.

DTIC Science & Technology

CHICKENS, GROWTH(PHYSIOLOGY), MITOSIS, BACTERIA, ALGAE, LIPOIC ACID , THIOLS, BELGIUM...ORGANIC SULFUR COMPOUNDS, METABOLISM), (*MORPHOLOGY(BIOLOGY), ORGANIC SULFUR COMPOUNDS), (*NUCLEIC ACIDS , BIOSYNTHESIS), EGGS, EMBRYOS, AMPHIBIANS

A study on the selection of indigenous leaching-bacteria for effective bioleaching

NASA Astrophysics Data System (ADS)

Oh, S. J.; Cho, K. H.; Kim, B. J.; Choi, N. C.; Park, C. Y.

2012-04-01

Bioleaching technology, which is based on the ability of microorganisms to transform solid compounds into soluble and extractable valuable elements that can be recovered, has been rapidly developed in recent decades for its advantages, which include mild reaction condition, low energy consumption, simple process, low environmental impact and being suitable for low grade mine tailings and residues. The bacteria activities (survival, adaptation of toxically environments etc.) in the bioleaching technology play a key role in the solubilization of metals. The purpose of this study was to selection of optimal leaching-bacteria through changed pH and redox potential on bio-oxidation in batch experiments for successful bioleaching technology. Twenty three indigenous bacteria used throughout this study, leaching-bacteria were obtained from various geochemical conditions; bacteria inhabitation type (acid mine drainage, mine wastes leachate and sulfur hot springs) and base-metal type (sulfur, sulfide, iron and coal). Bio-oxidation experiment result was showed that 9 cycles (1 cycle - 28days) after the leaching-bacteria were inoculated to a leaching medium, pH was observed decreasing and redox potential increased. In the bacteria inhabitation type, bio-oxidation of sulfur hot springs bacteria was greater than other types (acid mine drainage and mine wastes leachate). In addition, bio-oxidation on base-metal type was appeared sulfur was greater than other types (sulfide, iron and coal). This study informs basic knowledge when bacteria apply to eco-/economic resources utilization studies including the biomining and the recycling of mine waste system.

Apparatus and method for the desulfurization of petroleum by bacteria

DOEpatents

Lizama, H.M.; Scott, T.C.; Scott, C.D.

1995-10-17

A method is described for treating petroleum with anaerobic microorganisms acting as biocatalysts that can remove sulfur atoms from hydrocarbon molecules, under anaerobic conditions, and then convert the sulfur atoms to hydrogen sulfide. The microorganisms utilized are from the family known as the ``Sulfate Reducing Bacteria``. These bacteria generate metabolic energy from the oxidation of organic compounds, but use oxidized forms of sulfur as an electron acceptor. Because the biocatalyst is present in the form of bacteria in an aqueous suspension, whereas the reacting substrate consists of hydrocarbon molecules in an organic phase, the actual desulfurization reaction takes place at the aqueous-organic interphase. To ensure adequate interfacial contacting and mass transfer, a biphasic electrostatic bioreactor system is utilized. The bioreactor is utilized to disperse and recoalesce a biocatalyst contained in the aqueous liquid phase into the organic liquid phase containing the sulfur. High-intensity electrical fields rupture the aqueous drops into a plurality of microdroplets and induce continuous coalescence and redispersion as the microdroplets travel through the organic phase, thus increasing surface area. As the aqueous microdroplets progress through the organic phase, the biocatalyst then reacts with the sulfur to produce hydrogen sulfide which is then removed from the bioreactor. The organic liquid, now free of the sulfur, is ready for immediate use or further processing. 5 figs.

Apparatus and method for the desulfurization of petroleum by bacteria

DOEpatents

Lizama, Hector M.; Scott, Timothy C.; Scott, Charles D.

1995-01-01

A method for treating petroleum with anaerobic microorganisms acting as biocatalysts that can remove sulfur atoms from hydrocarbon molecules, under anaerobic conditions, and then convert the sulfur atoms to hydrogen sulfide. The microorganisms utilized are from the family known as the "Sulfate Reducing Bacteria." These bacteria generate metabolic energy from the oxidation of organic compounds, but use oxidized forms of sulfur as an electron acceptor. Because the biocatalyst is present in the form of bacteria in an aqueous suspension, whereas the reacting substrate consists of hydrocarbon molecules in an organic phase, the actual desulfurization reaction takes place at the aqueous-organic interphase. To ensure adequate interfacial contacting and mass transfer, a biphasic electrostatic bioreactor system is utilized. The bioreactor is utilized to disperse and recoalesce a biocatalyst contained in the aqueous liquid phase into the organic liquid phase containing the sulfur. High-intensity electrical fields rupture the aqueous drops into a plurality of microdroplets and induce continuous coalescence and redispersion as the microdroplets travel through the organic phase, thus increasing surface area. As the aqueous microdroplets progress through the organic phase, the biocatalyst then reacts with the sulfur to produce hydrogen sulfide which is then removed from the bioreactor. The organic liquid, now free of the sulfur, is ready for immediate use or further processing.

Light-controlled motility in prokaryotes and the problem of directional light perception

PubMed Central

Wilde, Annegret

2017-01-01

Abstract The natural light environment is important to many prokaryotes. Most obviously, phototrophic prokaryotes need to acclimate their photosynthetic apparatus to the prevailing light conditions, and such acclimation is frequently complemented by motility to enable cells to relocate in search of more favorable illumination conditions. Non-phototrophic prokaryotes may also seek to avoid light at damaging intensities and wavelengths, and many prokaryotes with diverse lifestyles could potentially exploit light signals as a rich source of information about their surroundings and a cue for acclimation and behavior. Here we discuss our current understanding of the ways in which bacteria can perceive the intensity, wavelength and direction of illumination, and the signal transduction networks that link light perception to the control of motile behavior. We discuss the problems of light perception at the prokaryotic scale, and the challenge of directional light perception in small bacterial cells. We explain the peculiarities and the common features of light-controlled motility systems in prokaryotes as diverse as cyanobacteria, purple photosynthetic bacteria, chemoheterotrophic bacteria and haloarchaea. PMID:29077840

Light-controlled motility in prokaryotes and the problem of directional light perception.

PubMed

Wilde, Annegret; Mullineaux, Conrad W

2017-11-01

The natural light environment is important to many prokaryotes. Most obviously, phototrophic prokaryotes need to acclimate their photosynthetic apparatus to the prevailing light conditions, and such acclimation is frequently complemented by motility to enable cells to relocate in search of more favorable illumination conditions. Non-phototrophic prokaryotes may also seek to avoid light at damaging intensities and wavelengths, and many prokaryotes with diverse lifestyles could potentially exploit light signals as a rich source of information about their surroundings and a cue for acclimation and behavior. Here we discuss our current understanding of the ways in which bacteria can perceive the intensity, wavelength and direction of illumination, and the signal transduction networks that link light perception to the control of motile behavior. We discuss the problems of light perception at the prokaryotic scale, and the challenge of directional light perception in small bacterial cells. We explain the peculiarities and the common features of light-controlled motility systems in prokaryotes as diverse as cyanobacteria, purple photosynthetic bacteria, chemoheterotrophic bacteria and haloarchaea. © FEMS 2017.

Thiol biochemistry of prokaryotes

NASA Technical Reports Server (NTRS)

Fahey, Robert C.

1986-01-01

The present studies have shown that GSH metabolism arose in the purple bacteria and cyanobacteria where it functions to protect against oxygen toxicity. Evidence was obtained indicating that GSH metabolism was incorporated into eucaryotes via the endosymbiosis giving rise to mitochrondria and chloroplasts. Aerobic bacteria lacking GSH utilize other thiols for apparently similar functions, the thiol being coenzyme A in Gram positive bacteria and chi-glutamylcysteine in the halobacteria. The thiol biochemistry of prokaryotes is thus seen to be much more highly diversified than that of eucaryotes and much remains to be learned about this subject.

Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

USGS Publications Warehouse

Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

2016-01-01

The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS.

PubMed

Tengölics, Roland; Mészáros, Lívia; Győri, E; Doffkay, Zsolt; Kovács, Kornél L; Rákhely, Gábor

2014-10-01

Thiocapsa. roseopersicina BBS has four active [NiFe] hydrogenases, providing an excellent opportunity to examine their metabolic linkages to the cellular redox processes. Hyn is a periplasmic membrane-associated hydrogenase harboring two additional electron transfer subunits: Isp1 is a transmembrane protein, while Isp2 is located on the cytoplasmic side of the membrane. In this work, the connection of HynSL to various electron transport pathways is studied. During photoautotrophic growth, electrons, generated from the oxidation of thiosulfate and sulfur, are donated to the photosynthetic electron transport chain via cytochromes. Electrons formed from thiosulfate and sulfur oxidation might also be also used for Hyn-dependent hydrogen evolution which was shown to be light and proton motive force driven. Hyn-linked hydrogen uptake can be promoted by both sulfur and nitrate. The electron flow from/to HynSL requires the presence of Isp2 in both directions. Hydrogenase-linked sulfur reduction could be inhibited by a QB site competitive inhibitor, terbutryne, suggesting a redox coupling between the Hyn hydrogenase and the photosynthetic electron transport chain. Based on these findings, redox linkages of Hyn hydrogenase are modeled. Copyright © 2014 Elsevier B.V. All rights reserved.

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vavourakis, Charlotte D.; Ghai, Rohit; Rodriguez-Valera, Francisco

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that themore » top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermace ae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.« less

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

PubMed Central

Vavourakis, Charlotte D.; Ghai, Rohit; Rodriguez-Valera, Francisco; Sorokin, Dimitry Y.; Tringe, Susannah G.; Hugenholtz, Philip; Muyzer, Gerard

2016-01-01

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first “metagenomic snapshots” of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a “salt-in” strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds. PMID:26941731

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

DOE PAGES

Vavourakis, Charlotte D.; Ghai, Rohit; Rodriguez-Valera, Francisco; ...

2016-02-25

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that themore » top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermace ae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.« less

A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

PubMed Central

Weissgerber, Thomas; Sylvester, Marc; Kröninger, Lena

2014-01-01

In the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified A. vinosum proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515). PMID:24487535

Regulators of nonsulfur purple phototrophic bacteria and the interactive control of CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation.

PubMed

Dubbs, James M; Tabita, F Robert

2004-06-01

For the metabolically diverse nonsulfur purple phototrophic bacteria, maintaining redox homeostasis requires balancing the activities of energy supplying and energy-utilizing pathways, often in the face of drastic changes in environmental conditions. These organisms, members of the class Alphaproteobacteria, primarily use CO2 as an electron sink to achieve redox homeostasis. After noting the consequences of inactivating the capacity for CO2 reduction through the Calvin-Benson-Bassham (CBB) pathway, it was shown that the molecular control of many additional important biological processes catalyzed by nonsulfur purple bacteria is linked to expression of the CBB genes. Several regulator proteins are involved, with the two component Reg/Prr regulatory system playing a major role in maintaining redox poise in these organisms. Reg/Prr was shown to be a global regulator involved in the coordinate control of a number of metabolic processes including CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy-generation pathways. Accumulating evidence suggests that the Reg/Prr system senses the oxidation/reduction state of the cell by monitoring a signal associated with electron transport. The response regulator RegA/PrrA activates or represses gene expression through direct interaction with target gene promoters where it often works in concert with other regulators that can be either global or specific. For the key CO2 reduction pathway, which clearly triggers whether other redox balancing mechanisms are employed, the ability to activate or inactivate the specific regulator CbbR is of paramount importance. From these studies, it is apparent that a detailed understanding of how diverse regulatory elements integrate and control metabolism will eventually be achieved.

A techno-economic analysis of polyhydroxyalkanoate and hydrogen production from syngas fermentation of gasified biomass.

PubMed

Choi, DongWon; Chipman, David C; Bents, Scott C; Brown, Robert C

2010-02-01

A techno-economic analysis was conducted to investigate the feasibility of a gasification-based hybrid biorefinery producing both hydrogen gas and polyhydroxyalkanoates (PHA), biodegradable polymer materials that can be an attractive substitute for conventional petrochemical plastics. The biorefinery considered used switchgrass as a feedstock and converted that raw material through thermochemical methods into syngas, a gaseous mixture composed mainly of hydrogen and carbon monoxide. The syngas was then fermented using Rhodospirillum rubrum, a purple non-sulfur bacterium, to produce PHA and to enrich hydrogen in the syngas. Total daily production of the biorefinery was assumed to be 12 Mg of PHA and 50 Mg of hydrogen gas. Grassroots capital for the biorefinery was estimated to be $55 million, with annual operating costs at $6.7 million. With a market value of $2.00/kg assumed for the hydrogen, the cost of producing PHA was determined to be $1.65/kg.

Transcriptome sequencing of purple petal spot region in tree peony reveals differentially expressed anthocyanin structural genes.

PubMed

Zhang, Yanzhao; Cheng, Yanwei; Ya, Huiyuan; Xu, Shuzhen; Han, Jianming

2015-01-01

The pigmented cells in defined region of a petal constitute the petal spots. Petal spots attract pollinators and are found in many angiosperm families. Several cultivars of tree peony contain a single red or purple spot at the base of petal that makes the flower more attractive for the ornamental market. So far, the understanding of the molecular mechanism of spot formation is inadequate. In this study, we sequenced the transcriptome of the purple spot and the white non-spot of tree peony flower. We assembled and annotated 67,892 unigenes. Comparative analyses of the two transcriptomes showed 1,573 differentially expressed genes, among which 933 were up-regulated, and 640 were down-regulated in the purple spot. Subsequently, we examined four anthocyanin structural genes, including PsCHS, PsF3'H, PsDFR, and PsANS, which expressed at a significantly higher level in the purple spot than in the white non-spot. We further validated the digital expression data using quantitative real-time PCR. Our result uncovered transcriptome variance between the spot and non-spot of tree peony flower, and revealed that the co-expression of four anthocyanin structural genes was responsible for spot pigment in tree peony. The data will further help to unravel the genetic mechanism of peony flower spot formation.

Genes essential for phototrophic growth by a purple alphaproteobacterium: Genes for phototrophic growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Jianming; Yin, Liang; Lessner, Faith H.

Anoxygenic purple phototrophic bacteria have served as important models for studies of photophosphorylation. The pigment-protein complexes responsible for converting light energy to ATP are relatively simple and these bacteria can grow heterotrophically under aerobic conditions, thus allowing for the study of mutants defective in photophosphorylation. In the past, genes responsible for anoxygenic phototrophic growth have been identified in a number of different bacterial species. Here we systematically studied the genetic basis for this metabolism by using Tn-seq to identify genes essential for the anaerobic growth of the purple bacterium Rhodopseudomonas palustris on acetate in light. We identified 171 genes requiredmore » for growth in this condition, 35 of which are annotated as photosynthesis genes. Among these are a few new genes not previously shown to be essential for phototrophic growth. We verified the essentiality of many of the genes we identified by analyzing the phenotypes of mutants we generated by Tn mutagenesis that had altered pigmentation. We used directed mutagenesis to verify that the R. palustris NADH:quinone oxidoreductase complex IE is essential for phototrophic growth. As a complement to the genetic data, we carried out proteomics experiments in which we found that 429 proteins were present in significantly higher amounts in cells grown anaerobically in light compared to aerobically. Among these were proteins encoded by subset of the phototrophic growth-essential genes.« less

Effect of Thiobacillus, sulfur, and vermicompost on the water-soluble phosphorus of hard rock phosphate.

PubMed

Aria, Marzieh Mohammady; Lakzian, Amir; Haghnia, Gholam Hosain; Berenji, Ali Reza; Besharati, Hosein; Fotovat, Amir

2010-01-01

Sulfur, organic matter, and inoculation with sulfur-oxidizing bacteria are considered as amendments to increase the availability of phosphorus from rock phosphate. The present study was conducted to evaluate the best combination of sulfur, vermicompost, and Thiobacillus thiooxidans inoculation with rock phosphate from Yazd province for direct application to agricultural lands in Iran. For such study, an experiment was carried out in a completely randomized design with factorial arrangement: Elemental sulfur originated from Sarakhs mine at three rates, 0% (S1), 10% (S2), 20% (S3), vermicompost at two rates, 0% (V1), 15% (V2), and inoculation without (B1) and with (B2) T. thiooxidans, in three replications. The results showed that water-soluble phosphorus (WSP) content was significantly higher in inoculated treatments compared to non-inoculated treatments. Sulfur had a significant effect on WSP. The highest solubility rate of rock phosphate was obtained in 20% of sulfur (S3) treatments and it was 2.4 times more than S1 treatments. Vermicompost also had a significant and positive effect on WSP of rock phosphate dissolution. The results also revealed that the highest concentration of WSP, sulfate and the lowest pH were obtained in treatments with 20% sulfur, 15% vermicompost inoculated with T. thiooxidans (B2S3V2).

Contribution of low-temperature single-molecule techniques to structural issues of pigment–protein complexes from photosynthetic purple bacteria

PubMed Central

Löhner, Alexander; Cogdell, Richard

2018-01-01

As the electronic energies of the chromophores in a pigment–protein complex are imposed by the geometrical structure of the protein, this allows the spectral information obtained to be compared with predictions derived from structural models. Thereby, the single-molecule approach is particularly suited for the elucidation of specific, distinctive spectral features that are key for a particular model structure, and that would not be observable in ensemble-averaged spectra due to the heterogeneity of the biological objects. In this concise review, we illustrate with the example of the light-harvesting complexes from photosynthetic purple bacteria how results from low-temperature single-molecule spectroscopy can be used to discriminate between different structural models. Thereby the low-temperature approach provides two advantages: (i) owing to the negligible photobleaching, very long observation times become possible, and more importantly, (ii) at cryogenic temperatures, vibrational degrees of freedom are frozen out, leading to sharper spectral features and in turn to better resolved spectra. PMID:29321265

[Quantum differences of ortho/para H2O2 spin-isomers as a factor of the femtosecond charge separation kinetics modulation in reaction centers of purple bacteria].

PubMed

Pishchal'nikov, R Iu; Pershin, S M; Bunkin, A F

2012-01-01

We have proposed the mechanism of coherent modulations of the P* state in the transient absorption spectra of the reaction center isolated from purple bacteria. Two water molecules, located between special pair, Ba, Bb chlorophylls and histidine L173 and M202, are supposed to be ortho-H2O and para-H2O isomers with different magnetic properties. The distinctive modulation frequencies were labeling as rotational resonances of ortho-H2O. According to our assumption, the interaction of rotational modes of water isomers with the charge-transfer states is a reason of coherent modulations of kinetics. We have modified a Hamiltonian system in order to take into account the rotational modes of ortho-H2O. Evolution of the density matrix was calculated in Liouville space. The Redfield relaxation theory for molecular aggregates was used to model kinetics up to 3 ps.

Photosynthetic Photovoltaic Cells

DTIC Science & Technology

2007-06-21

OFF (T). B. SPR detection of the binding of Ni2+, RC, and cytochrome to NTA surface. The arrows indicate the periods of time ON (t) and OFF (1) when...photosynthesis. Structure and spectroscopy of reaction centers of purple bacteria . Physics Reports-Review Section of Physics Letters, 1997. 287(1-2): p. 2-247. 7...photosynthetic bacteria reaction centers. Journal of Photochemistry and Photobiology a-Chemistry, 1997. 111(1-3): p. 111-138. 27. Beratan, D.N., J.N. Betts, and

Characterization and application of lactic acid bacteria for tropical silage preparation.

PubMed

Pholsen, Suradej; Khota, Waroon; Pang, Huili; Higgs, David; Cai, Yimin

2016-10-01

Strains TH 14, TH 21 and TH 64 were isolated from tropical silages, namely corn stover, sugar cane top and rice straw, respectively, prepared in Thailand. These strains were selected by low pH growth range and high lactic acid-producing ability, similar to some commercial inoculants. Based on the analysis of 16S ribosomal RNA gene sequence and DNA-DNA relatedness, strain TH 14 was identified as Lactobacillus casei, and strains TH 21 and TH 64 were identified as L. plantarum. Strains TH 14, TH 21, TH 64 and two commercial inoculants, CH (L. plantarum) and SN (L. rhamnosus), were used as additives to fresh and wilted purple Guinea and sorghum silages prepared using a small-scale fermentation method. The number of epiphytic lactic acid bacteria (LAB) in the forages before ensilage was relatively low but the numbers of coliform and aerobic bacteria were higher. Sorghum silages at 30 days of fermentation were all well preserved with low pH (3.56) and high lactic acid production (72.86 g/kg dry matter). Purple Guinea silage inoculated with LAB exhibited reduced count levels of aerobic and coliform bacteria, lower pH, butyric acid and ammonia nitrogen and increased lactic acid concentration, compared with the control. Strain TH 14 more effectively improved lactic acid production compared with inoculants and other strains. © 2016 Japanese Society of Animal Science. © 2016 Japanese Society of Animal Science.

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea.

PubMed

Wu, Yuzhi; Qiu, Jian-Wen; Qian, Pei-Yuan; Wang, Yong

2018-05-01

In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.

Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction.

PubMed

Sekowska, A; Kung, H F; Danchin, A

2000-04-01

Living organisms are composed of macromolecules made of hydrogen, carbon, nitrogen, oxygen, phosphorus and sulfur. Much work has been devoted to the metabolism of the first five elements, but much remains to be understood about sulfur metabolism. We review here the situation in Escherichia coli and related bacteria, where more than one hundred genes involved in sulfur metabolism have already been discovered in this organism. Examination of the genome suggests that many more will be found, especially genes involved in regulation, scavenging of sulfur containing molecules and synthesis of coenzymes or prosthetic groups. Furthermore, the involvement of methionine as the universal start of proteins as well as that of its derivative S-adenosylmethionine in a vast variety of cell processes argue in favour of a major importance of sulfur metabolism in all organisms.

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column.

PubMed

Bertagnolli, Anthony D; Padilla, Cory C; Glass, Jennifer B; Thamdrup, Bo; Stewart, Frank J

2017-11-01

Marinimicrobia bacteria are widespread in subeuphotic areas of the oceans and particularly abundant in oxygen minimum zones (OMZs). Information on Marinimicrobia metabolism is sparse, making the biogeochemical influence of this group challenging to predict. Here, metagenome-assembled genomes representing Marinimicrobia subgroups PN262000N21 and ARCTIC96B-7 were retrieved to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in ARCTIC96B-7. Genes for aerobic carbon monoxide (CO) oxidation, polysulfide metabolism and hydrogen utilization were identified only in PN262000N21, while genes for partial denitrification occurred in both genomes. Transcripts mapping to these genomes increased from <0.3% of total mRNA from the oxic zone to a max of 22% under anoxia. ARCTIC96B-7 transcript representation decreased an order of magnitude from non-sulfidic to sulfidic depths. In contrast, PN262000N21 representation was relatively constant throughout the OMZ, although transcripts encoding sulfur-utilizing proteins, including sulfur transferases, were enriched at sulfidic depths. PN262000N21 transcripts encoding a protein with fibronectin domains similar to those in cellulosome-producing bacteria were also abundant, suggesting a potential for high molecular weight carbon cycling. These data provide omic-level descriptions of metabolic potential and activity in OMZ-associated Marinimicrobia, suggesting differentiation between subgroups with roles in carbon and dissimilatory inorganic nitrogen and sulfur cycling. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Metabolism in the Uncultivated Giant Sulfide-Oxidizing Bacterium Thiomargarita Namibiensis Assayed Using a Redox-Sensitive Dye

NASA Astrophysics Data System (ADS)

Bailey, J.; Flood, B.; Ricci, E.

2014-12-01

The colorless sulfur bacteria are non-photosynthetic chemolithotrophs that live at interfaces between nitrate, or oxygen, and hydrogen sulfide. In sulfidic settings such as cold seeps and oxygen minimum zones, these bacteria are thought to constitute a critical node in the geochemical cycling of carbon, sulfur, nitrogen, and phosphorous. Many of these bacteria remain uncultivated and their metabolisms and physiologies are incompletely understood. Thiomargarita namibiensis is the largest of these sulfur bacteria, with individual cells reaching millimetric diameters. Despite the current inability to maintain a Thiomargarita culture in the lab, their large size allows for individual cells to be followed in time course experiments. Here we report on the novel use of a tetrazolium-based dye that measures the flux of NADH production from catabolic pathways via a colorimetric response. Staining with this dye allows for metabolism to be detected, even in the absence of observable cell division. When coupled to microscopy, this approach also allows for metabolism in Thiomargaritato be differentiated from that of epibionts or contaminants in xenic samples. The results of our tetrazolium dye-based assay suggests that Thiomargarita is the most metabolically versatile under anoxic conditions where it appears capable of using acetate, succinate, formate, thiosulfate, citrate, thiotaurine, hydrogen sulfide, and perhaps hydrogen as electron donors. Under hypoxic conditions, staining results suggest the utilization of acetate, citrate, and hydrogen sulfide. Cells incubated under oxic conditions showed the weakest tetrazolium staining response, and then only to hydrogen sulfide and questionably succinate. These initial results using a redox sensitive dye suggest that Thiomargarita is most metabolically versatile under anaerobic and hypoxic conditions. The results of this assay can be further evaluated using molecular approaches such as transcriptomics, as well as provide cultivation strategies.

A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria.

PubMed

Bóna-Lovász, Judit; Bóna, Aron; Ederer, Michael; Sawodny, Oliver; Ghosh, Robin

2013-10-11

A simple, rapid, and inexpensive extraction method for carotenoids and other non-polar compounds present in phototrophic bacteria has been developed. The method, which has been extensively tested on the phototrophic purple non-sulphur bacterium Rhodospirillum rubrum, is suitable for extracting large numbers of samples, which is common in systems biology studies, and yields material suitable for subsequent analysis using HPLC and mass spectroscopy. The procedure is particularly suitable for carotenoids and other terpenoids, including quinones, bacteriochlorophyll a and bacteriopheophytin a, and is also useful for the analysis of polar phospholipids. The extraction procedure requires only a single step extraction with a hexane/methanol/water mixture, followed by HPLC using a Spherisorb C18 column, with a mobile phase consisting of acetone-water and a non-linear gradient of 50%-100% acetone. The method was employed for examining the carotenoid composition observed during microaerophilic growth of R. rubrum strains, and was able to determine 18 carotenoids, 4 isoprenoid-quinones, bacteriochlorophyll a and bacteriopheophytin a as well as four different phosphatidylglycerol species of different acyl chain compositions. The analytical procedure was used to examine the dynamics of carotenoid biosynthesis in the major and minor pathways operating simultaneously in a carotenoid biosynthesis mutant of R. rubrum.

Isolation and characterization of a sulfur-oxidizing chemolithotroph growing on crude oil under anaerobic conditions.

PubMed

Kodama, Yumiko; Watanabe, Kazuya

2003-01-01

Molecular approaches have shown that a group of bacteria (called cluster 1 bacteria) affiliated with the epsilon subclass of the class Proteobacteria constituted major populations in underground crude-oil storage cavities. In order to unveil their physiology and ecological niche, this study isolated bacterial strains (exemplified by strain YK-1) affiliated with the cluster 1 bacteria from an oil storage cavity at Kuji in Iwate, Japan. 16S rRNA gene sequence analysis indicated that its closest relative was Thiomicrospira denitrificans (90% identity). Growth experiments under anaerobic conditions showed that strain YK-1 was a sulfur-oxidizing obligate chemolithotroph utilizing sulfide, elemental sulfur, thiosulfate, and hydrogen as electron donors and nitrate as an electron acceptor. Oxygen also supported its growth only under microaerobic conditions. Strain YK-1 could not grow on nitrite, and nitrite was the final product of nitrate reduction. Neither sugars, organic acids (including acetate), nor hydrocarbons could serve as carbon and energy sources. A typical stoichiometry of its energy metabolism followed an equation: S(2-) + 4NO(3)(-) --> SO(4)(2-) + 4NO(2)(-) (Delta G(0) = -534 kJ mol(-1)). In a difference from other anaerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 1% NaCl was negligible. When YK-1 was grown anaerobically in a sulfur-depleted inorganic medium overlaid with crude oil, sulfate was produced, corresponding to its growth. On the contrary, YK-1 could not utilize crude oil as a carbon source. These results suggest that the cluster 1 bacteria yielded energy for growth in oil storage cavities by oxidizing petroleum sulfur compounds. Based on its physiology, ecological interactions with other members of the groundwater community are discussed.

Effect of inoculum and sulfide type on simultaneous hydrogen sulfide removal from biogas and nitrogen removal from swine slurry and microbial mechanism.

PubMed

Wang, Lan; Wei, Benping; Chen, Ziai; Deng, Liangwei; Song, Li; Wang, Shuang; Zheng, Dan; Liu, Yi; Pu, Xiaodong; Zhang, Yunhong

2015-12-01

Four reactors were initiated to study the effect of inoculum and sulfide type on the simultaneous hydrogen sulfide removal from biogas and nitrogen removal from swine slurry (Ssu-Nir) process. Anaerobic sludge, aerobic sludge, and water were used as inocula, and Na2S and biogas were used as a sulfide substrate, respectively. Additionally, 454 pyrosequencing of the 16S rRNA gene was used to explore the bacterial diversity. The results showed that sulfur-oxidizing bacteria (Thiobacillus, 42.2-84.4 %) were dominant in Ssu-Nir process and led to the excellent performance. Aerobic sludge was more suitable for inoculation of the Ssu-Nir process because it is better for rapidly enriching dominant sulfur-oxidizing bacteria (Thiobacillus, 54.4 %), denitrifying sulfur-oxidizing bacteria (40.0 %) and denitrifiers (23.9 %). Lower S(2-) removal efficiency (72.6 %) and NO3 (-) removal efficiency (<90 %) of the Ssu-Nir process were obtained using biogas as a sulfide substrate than when Na2S was used. For the Ssu-Nir process with biogas as the sulfide substrate, limiting H2S absorption caused a high relative abundance of sulfur-oxidizing bacteria, Thiobacillus (84.8 %) and Thiobacillus sayanicus (39.6 %), which in turn led to low relative abundance of denitrifiers (1.6 %) and denitrifying sulfur-oxidizing bacteria (24.4 %), low NO3 (-) removal efficiency, and eventually poor performance.

Improvement of conspicuity of trailblazing signs, Phase III : evaluation of fluorescent colors.

DOT National Transportation Integrated Search

2001-01-01

This report represents a Phase III effort to design and evaluate a new sign design for incident route trailblazing. The colors evaluated were fluorescent coral, fluorescent purple, fluorescent yellow-green, and non-fluorescent purple. The results ind...

Transcriptome sequencing of purple petal spot region in tree peony reveals differentially expressed anthocyanin structural genes

PubMed Central

Zhang, Yanzhao; Cheng, Yanwei; Ya, Huiyuan; Xu, Shuzhen; Han, Jianming

2015-01-01

The pigmented cells in defined region of a petal constitute the petal spots. Petal spots attract pollinators and are found in many angiosperm families. Several cultivars of tree peony contain a single red or purple spot at the base of petal that makes the flower more attractive for the ornamental market. So far, the understanding of the molecular mechanism of spot formation is inadequate. In this study, we sequenced the transcriptome of the purple spot and the white non-spot of tree peony flower. We assembled and annotated 67,892 unigenes. Comparative analyses of the two transcriptomes showed 1,573 differentially expressed genes, among which 933 were up-regulated, and 640 were down-regulated in the purple spot. Subsequently, we examined four anthocyanin structural genes, including PsCHS, PsF3′H, PsDFR, and PsANS, which expressed at a significantly higher level in the purple spot than in the white non-spot. We further validated the digital expression data using quantitative real-time PCR. Our result uncovered transcriptome variance between the spot and non-spot of tree peony flower, and revealed that the co-expression of four anthocyanin structural genes was responsible for spot pigment in tree peony. The data will further help to unravel the genetic mechanism of peony flower spot formation. PMID:26583029

Cytochrome bc1-cy Fusion Complexes Reveal the Distance Constraints for Functional Electron Transfer Between Photosynthesis Components*

PubMed Central

Lee, Dong-Woo; Öztürk, Yavuz; Osyczka, Artur; Cooley, Jason W.; Daldal, Fevzi

2008-01-01

Photosynthetic (Ps) growth of purple non-sulfur bacteria such as Rhodobacter capsulatus depends on the cyclic electron transfer (ET) between the ubihydroquinone (QH2): cytochrome (cyt) c oxidoreductases (cyt bc1 complex), and the photochemical reaction centers (RC), mediated by either a membrane-bound (cyt cy) or a freely diffusible (cyt c2) electron carrier. Previously, we constructed a functional cyt bc1-cy fusion complex that supported Ps growth solely relying on membrane-confined ET (Lee, D.-W., Ozturk, Y., Mamedova, A., Osyczka, A., Cooley, J. W., and Daldal, F. (2006) Biochim. Biophys. Acta1757 ,346 -35216781662). In this work, we further characterized this cyt bc1-cy fusion complex, and used its derivatives with shorter cyt cy linkers as “molecular rulers” to probe the distances separating the Ps components. Comparison of the physicochemical properties of both membrane-embedded and purified cyt bc1-cy fusion complexes established that these enzymes were matured and assembled properly. Light-activated, time-resolved kinetic spectroscopy analyses revealed that their variants with shorter cyt cy linkers exhibited fast, native-like ET rates to the RC via the cyt bc1. However, shortening the length of the cyt cy linker decreased drastically this electronic coupling between the cyt bc1-cy fusion complexes and the RC, thereby limiting Ps growth. The shortest and still functional cyt cy linker was about 45 amino acids long, showing that the minimal distance allowed between the cyt bc1-cy fusion complexes and the RC and their surrounding light harvesting proteins was very short. These findings support the notion that membrane-bound Ps components form large, active structural complexes that are “hardwired” for cyclic ET. PMID:18343816

Photodynamic inactivation of Staphylococcus aureus and Escherichia coli using a new bacteriochlorin as photosensitizer

NASA Astrophysics Data System (ADS)

Barboza, Diego D.; Martins, Laura C. A.; Corrêa, Thaila Quatrini; Geralde, Mariana Carreira; Pratavieira, Sebastião.; de Oliveira, Kleber Thiago; Uliana, Marciana P.; de Souza, Clovis W.

2018-02-01

In this study, we used bacteriochlorin as a photosensitizer, characterized by their low toxicity in the absence of light, presenting absorption around 780 nm, with the objective of evaluating their photodynamic inactivation potential on Staphylococcus aureus and Escherichia coli. Bacteriochlorins were synthesized from the extraction of bacteriochlorophylls from non-sulfurous purple bacteria and were then converted to bacteriochlorins. S. aureus and E. coli microorganisms were used in the planktonic and biofilm forms. For the formation of biofilms on glass coverslips, suspensions of the microorganisms at the concentration of 106 CFU/mL were inoculated into each well of a microplate. There was an exchange of culture medium (Tryptic Soy Broth - TSB) every 24 hours for 7 days, pre-washing the coverslips with a phosphate-buffered saline (PBS), to ensure that only adhered microorganisms were grown and then incubated at (36 +/- 1)°C between the middle exchanges. After 7 days of induction, the biofilm was mature, like those normally found in nature, and then it was applied different treatments (light doses associated with FS concentrations). At the end of the treatment, the coverslips underwent an ultrasonic disintegration, and the quantitative evaluation of viable cells was performed by plate counting using the plate method in Tryptic Soy Agar (TSA), incubating at (36 +/- 1)°C for 24 hours. The results showed that the PDI for E. coli was not successful even when it was more susceptible to the planktonic form, whereas for S. aureus the results showed a reduction in cell viability 6 logs for the planktonic forms, but lower to 1 log in biofilms. Therefore, novel studies using bacteriochlorins and surfactants will be performed to verify the potential of this alternative treatment method.

Phytoplasma-host interactions: tomato gibberellin homeostasis and its role in defense against potato purple top phytoplasma infection

USDA-ARS?s Scientific Manuscript database

Phytoplasmas are cell wall-less bacteria that parasitize plant phloem sieve cells and cause numerous diseases in diverse plant species. Plants infected by phytoplasmas often exhibit symptoms such as general stunting, excessive shoot proliferation, witches’-broom growth, rapid senescence, and a...

Compositions of constructed microbial mats

DOEpatents

Bender, Judith A.; Phillips, Peter C.

1999-01-01

Compositions and methods of use of constructed microbial mats, comprising cyanobacteria and purple autotrophic bacteria and an organic nutrient source, in a laminated structure, are described. The constructed microbial mat is used for bioremediation of different individual contaminants and for mixed or multiple contaminants, and for production of beneficial compositions and molecules.

Leaching of Zinc Sulfide by Thiobacillus ferrooxidans: Bacterial Oxidation of the Sulfur Product Layer Increases the Rate of Zinc Sulfide Dissolution at High Concentrations of Ferrous Ions

PubMed Central

Fowler, T. A.; Crundwell, F. K.

1999-01-01

This paper reports the results of leaching experiments conducted with and without Thiobacillus ferrooxidans at the same conditions in solution. The extent of leaching of ZnS with bacteria is significantly higher than that without bacteria at high concentrations of ferrous ions. A porous layer of elemental sulfur is present on the surfaces of the chemically leached particles, while no sulfur is present on the surfaces of the bacterially leached particles. The analysis of the data using the shrinking-core model shows that the chemical leaching of ZnS is limited by the diffusion of ferrous ions through the sulfur product layer at high concentrations of ferrous ions. The analysis of the data shows that diffusion through the product layer does not limit the rate of dissolution when bacteria are present. This suggests that the action of T. ferrooxidans in oxidizing the sulfur formed on the particle surface is to remove the barrier to diffusion by ferrous ions. PMID:10583978

Synthesis of the sulfur amino acids: cysteine and methionine.

PubMed

Wirtz, Markus; Droux, Michel

2005-12-01

This review will assess new features reported for the molecular and biochemical aspects of cysteine and methionine biosynthesis in Arabidopsis thaliana with regards to early published data from other taxa including crop plants and bacteria (Escherichia coli as a model). By contrast to bacteria and fungi, plant cells present a complex organization, in which the sulfur network takes place in multiple sites. Particularly, the impact of sulfur amino-acid biosynthesis compartmentalization will be addressed in respect to localization of sulfur reduction. To this end, the review will focus on regulation of sulfate reduction by synthesis of cysteine through the cysteine synthase complex and the synthesis of methionine and its derivatives. Finally, regulatory aspects of sulfur amino-acid biosynthesis will be explored with regards to interlacing processes such as photosynthesis, carbon and nitrogen assimilation.

Excitation energy transfer from the bacteriochlorophyll Soret band to carotenoids in the LH2 light-harvesting complex from Ectothiorhodospira haloalkaliphila is negligible.

PubMed

Razjivin, A P; Lukashev, E P; Kompanets, V O; Kozlovsky, V S; Ashikhmin, A A; Chekalin, S V; Moskalenko, A A; Paschenko, V Z

2017-09-01

Pathways of intramolecular conversion and intermolecular electronic excitation energy transfer (EET) in the photosynthetic apparatus of purple bacteria remain subject to debate. Here we experimentally tested the possibility of EET from the bacteriochlorophyll (BChl) Soret band to the singlet S 2 level of carotenoids using femtosecond pump-probe measurements and steady-state fluorescence excitation and absorption measurements in the near-ultraviolet and visible spectral ranges. The efficiency of EET from the Soret band of BChl to S 2 of the carotenoids in light-harvesting complex LH2 from the purple bacterium Ectothiorhodospira haloalkaliphila appeared not to exceed a few percent.

Metabolic Capabilities of Microorganisms Involved in and Associated with the Anaerobic Oxidation of Methane

PubMed Central

Wegener, Gunter; Krukenberg, Viola; Ruff, S. Emil; Kellermann, Matthias Y.; Knittel, Katrin

2016-01-01

In marine sediments the anaerobic oxidation of methane with sulfate as electron acceptor (AOM) is responsible for the removal of a major part of the greenhouse gas methane. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. The physiology of these organisms is poorly understood, which is due to their slow growth with doubling times in the order of months and the phylogenetic diversity in natural and in vitro AOM enrichments. Here we study sediment-free long-term AOM enrichments that were cultivated from seep sediments sampled off the Italian Island Elba (20°C; hereon called E20) and from hot vents of the Guaymas Basin, Gulf of California, cultivated at 37°C (G37) or at 50°C (G50). These enrichments were dominated by consortia of ANME-2 archaea and Seep-SRB2 partner bacteria (E20) or by ANME-1, forming consortia with Seep-SRB2 bacteria (G37) or with bacteria of the HotSeep-1 cluster (G50). We investigate lipid membrane compositions as possible factors for the different temperature affinities of the different ANME clades and show autotrophy as characteristic feature for both ANME clades and their partner bacteria. Although in the absence of additional substrates methane formation was not observed, methanogenesis from methylated substrates (methanol and methylamine) could be quickly stimulated in the E20 and the G37 enrichment. Responsible for methanogenesis are archaea from the genus Methanohalophilus and Methanococcoides, which are minor community members during AOM (1–7‰ of archaeal 16S rRNA gene amplicons). In the same two cultures also sulfur disproportionation could be quickly stimulated by addition of zero-valent colloidal sulfur. The isolated partner bacteria are likewise minor community members (1–9‰ of bacterial 16S rRNA gene amplicons), whereas the dominant partner bacteria (Seep-SRB1a, Seep-SRB2, or HotSeep-1) did not grow on elemental sulfur. Our results support a functioning of AOM as syntrophic interaction of obligate methanotrophic archaea that transfer non-molecular reducing equivalents (i.e., via direct interspecies electron transfer) to obligate sulfate-reducing partner bacteria. Additional katabolic processes in these enrichments but also in sulfate methane interfaces are likely performed by minor community members. PMID:26870011

Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis

PubMed Central

Wang, Minxiao; Liu, Yuan; Hui, Min

2017-01-01

For deep-sea hydrothermal vent crabs, recent investigations have revealed some epibiotic bacteria, but no study has described the bacterial community associated with the gill and intestine. In this study, the microbiota attached to the gill and intestine of the hydrothermal vent crab Austinograea sp. and two shallow-water crab species (Eriocheir sinensis and Portunus trituberculatus) were compared by high-throughput sequencing of 16S rDNA genes. The highest and lowest diversity in bacterial communities were observed in the gill and intestine of Austinograea sp., respectively. Non-metric multidimensional scaling (NMDS) analysis indicated that Austinograea sp. harbored a distinct microbial community. Operational taxonomic units (OTUs) for phylum Fusobacteria, class Epsilonproteobacteria, and genera Leucothrix, Polaribacter, Fusibacter, etc. were dominant in Austinograea sp. Of these, Leucothrix, Sulfurospirillum, and Arcobacter may be involved in oxidizing reduced sulfur compounds and sulfur metabolism; Marinomonas, Polaribacter adapted to the low temperature, and Fusibacter and Psychrilyobacter may survive well under hypoxic conditions. Bacteria commonly present in seawater were dominant in the gill, whereas anaerobic bacteria showed strikingly high abundance in the intestine. Interestingly, Firmicutes and Epsilonproteobacteria may complement each other in Austinograea sp., forming an internal environment. The diversified microbial community of Austinograea sp. reveals adaptation to the hydrothermal vent environment. PMID:29121118

Sulfur Upwelling off the African Coast

NASA Technical Reports Server (NTRS)

2002-01-01

Though these aquamarine clouds in the waters off the coast of northern Namibia may look like algae blooms, they are in fact clouds of sulfur produced by anaerobic bacteria on the ocean's floor. This image of the sulfur-filled water was taken on April 24, 2002, by the Sea-viewing Wide Field-of-View Sensor (SeaWiFS), flying aboard the Orbview-2 satellite. The anaerobic bacteria (bacteria that can live without oxygen) feed upon algae carcasses that exist in abundance on the ocean's floor off of Namibia. As the bacteria ingest the algae husks, they produce hydrogen sulfide, which slowly builds up in the sea-floor sediments. Eventually, the hydrogen sulfide reaches the point where the sediment can no longer contain it, and it bubbles forth. When this poisonous chemical reaches the surface, it combines with the oxygen in the upper layers of the ocean to create clouds of pure sulfur. The sulfur causes the Namibian coast to smell like rotten eggs, and the hydrogen sulfide will often kill fish and drive lobsters away. For more information, read: A Bloom By Any Other Name A high-resolution (250 meters per pixel) image earlier on the 24th taken from the Moderate-Resolution Imaging Spectroradiometer (MODIS) shows additional detail in the plumes. Image courtesy the SeaWiFS Project, NASA/Goddard Space Flight Center, and ORBIMAGE. MODIS image courtesy Jacques Descloitres, MODIS Land Rapid Response Team at NASA GSFC

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh

PubMed Central

Salman, Verena; Yang, Tingting; Berben, Tom; Klein, Frieder; Angert, Esther; Teske, Andreas

2015-01-01

Large sulfur bacteria of the genus Achromatium are exceptional among Bacteria and Archaea as they can accumulate high amounts of internal calcite. Although known for more than 100 years, they remain uncultured, and only freshwater populations have been studied so far. Here we investigate a marine population of calcite-accumulating bacteria that is primarily found at the sediment surface of tide pools in a salt marsh, where high sulfide concentrations meet oversaturated oxygen concentrations during the day. Dynamic sulfur cycling by phototrophic sulfide-oxidizing and heterotrophic sulfate-reducing bacteria co-occurring in these sediments creates a highly sulfidic environment that we propose induces behavioral differences in the Achromatium population compared with reported migration patterns in a low-sulfide environment. Fluctuating intracellular calcium/sulfur ratios at different depths and times of day indicate a biochemical reaction of the salt marsh Achromatium to diurnal changes in sedimentary redox conditions. We correlate this calcite dynamic with new evidence regarding its formation/mobilization and suggest general implications as well as a possible biological function of calcite accumulation in large bacteria in the sediment environment that is governed by gradients. Finally, we propose a new taxonomic classification of the salt marsh Achromatium based on their adaptation to a significantly different habitat than their freshwater relatives, as indicated by their differential behavior as well as phylogenetic distance on 16S ribosomal RNA gene level. In future studies, whole-genome characterization and additional ecophysiological factors could further support the distinctive position of salt marsh Achromatium. PMID:25909974

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh.

PubMed

Salman, Verena; Yang, Tingting; Berben, Tom; Klein, Frieder; Angert, Esther; Teske, Andreas

2015-11-01

Large sulfur bacteria of the genus Achromatium are exceptional among Bacteria and Archaea as they can accumulate high amounts of internal calcite. Although known for more than 100 years, they remain uncultured, and only freshwater populations have been studied so far. Here we investigate a marine population of calcite-accumulating bacteria that is primarily found at the sediment surface of tide pools in a salt marsh, where high sulfide concentrations meet oversaturated oxygen concentrations during the day. Dynamic sulfur cycling by phototrophic sulfide-oxidizing and heterotrophic sulfate-reducing bacteria co-occurring in these sediments creates a highly sulfidic environment that we propose induces behavioral differences in the Achromatium population compared with reported migration patterns in a low-sulfide environment. Fluctuating intracellular calcium/sulfur ratios at different depths and times of day indicate a biochemical reaction of the salt marsh Achromatium to diurnal changes in sedimentary redox conditions. We correlate this calcite dynamic with new evidence regarding its formation/mobilization and suggest general implications as well as a possible biological function of calcite accumulation in large bacteria in the sediment environment that is governed by gradients. Finally, we propose a new taxonomic classification of the salt marsh Achromatium based on their adaptation to a significantly different habitat than their freshwater relatives, as indicated by their differential behavior as well as phylogenetic distance on 16S ribosomal RNA gene level. In future studies, whole-genome characterization and additional ecophysiological factors could further support the distinctive position of salt marsh Achromatium.

Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

PubMed Central

Zheng, Chenkang; Black, Katherine A.; Dos Santos, Patricia C.

2017-01-01

Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes. PMID:28327539

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle.

PubMed

Jensen, Sigmund; Fortunato, Sofia A V; Hoffmann, Friederike; Hoem, Solveig; Rapp, Hans Tore; Øvreås, Lise; Torsvik, Vigdis L

2017-04-01

During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.

Compositions and method of use of constructed microbial mats

DOEpatents

Bender, Judith A.; Phillips, Peter C.

1997-01-01

Compositions and methods of use of constructed microbial mats, comprising cyanobacteria and purple autotrophic bacteria and an organic nutrient source, in a laminated structure, are described. The constructed microbial mat is used for bioremediation of different individual contaminants and for mixed or multiple contaminants, and for production of beneficial compositions and molecules.

A new energy transfer channel from carotenoids to chlorophylls in purple bacteria.

PubMed

Feng, Jin; Tseng, Chi-Wei; Chen, Tingwei; Leng, Xia; Yin, Huabing; Cheng, Yuan-Chung; Rohlfing, Michael; Ma, Yuchen

2017-07-10

It is unclear whether there is an intermediate dark state between the S 2 and S 1 states of carotenoids. Previous two-dimensional electronic spectroscopy measurements support its existence and its involvement in the energy transfer from carotenoids to chlorophylls, but there is still considerable debate on the origin of this dark state and how it regulates the energy transfer process. Here we use ab initio calculations on excited-state dynamics and simulated two-dimensional electronic spectrum of carotenoids from purple bacteria to provide evidence supporting that the dark state may be assigned to a new A g + state. Our calculations also indicate that groups on the conjugation backbone of carotenoids may substantially affect the excited-state levels and the energy transfer process. These results contribute to a better understanding of carotenoid excited states.Carotenoids harvest energy from light and transfer it to chlorophylls during photosynthesis. Here, Feng et al. perform ab initio calculations on excited-state dynamics and simulated 2D electronic spectrum of carotenoids, supporting the existence of a new excited state in carotenoids.

Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method.

PubMed

Shrestha, Kushal; Jakubikova, Elena

2015-08-20

Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.

Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome

PubMed Central

Brito, José A.; Gutierres, André; Denkmann, Kevin; Dahl, Christiane; Archer, Margarida

2014-01-01

The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacterium Allochromatium vinosum was recombinantly expressed in Escherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 79.2, b = 69.9, c = 57.9 Å, β = 129.3°, contained one monomer per asymmetric unit and diffracted to a resolution of 1.98 Å. PMID:25286955

Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.

PubMed

Han, Yifan; Ma, Xiaomei; Zhao, Wei; Chang, Yunkang; Zhang, Xiaoxia; Wang, Xingbiao; Wang, Jingjing; Huang, Zhiyong

2013-10-01

The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae

PubMed Central

2018-01-01

ABSTRACT Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the other host species examined. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harbors cooccurring gamma-, alpha-, and deltaproteobacterial symbionts, while all other known host species harbor gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic sulfur oxidizer “Candidatus Thiosymbion” that occurs in all other gutless phallodriline hosts does not appear to be present in I. exumae. Instead, I. exumae harbors a bacterial endosymbiont that resembles “Ca. Thiosymbion” morphologically and metabolically but originates from a novel lineage within the class Gammaproteobacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA gene sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from that of “Ca. Thiosymbion.” Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), indicate that this symbiont is a chemoautotrophic sulfur oxidizer. Our results suggest that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae and appears to have displaced the “Ca. Thiosymbion” symbionts originally associated with these hosts. IMPORTANCE All 22 gutless marine phallodriline species examined to date live in a highly specific association with endosymbiotic, chemoautotrophic sulfur oxidizers called “Ca. Thiosymbion.” These symbionts evolved from a single common ancestor and represent the ancestral trait for this host group. They are transmitted vertically and assumed to be in transition to becoming obligate endosymbionts. It is therefore surprising that despite this ancient, evolutionary relationship between phallodriline hosts and “Ca. Thiosymbion,” these symbionts are apparently no longer present in Inanidrilus exumae. They appear to have been displaced by a novel lineage of sulfur-oxidizing bacteria only very distantly related to “Ca. Thiosymbion.” Thus, this study highlights the remarkable plasticity of both animals and bacteria in establishing beneficial associations: the phallodriline hosts were able to acquire and maintain symbionts from two very different lineages of bacteria, while sulfur-oxidizing bacteria from two very distantly related lineages were able to independently establish symbiotic relationships with phallodriline hosts. PMID:29330187

Supraglacial sulfur springs and associated biological activity in the Canadian high arctic - signs of life beneath the ice

USGS Publications Warehouse

Grasby, Stephen E.; Allen, Carlton C.; Longazo, Teresa G.; Lisle, John T.; Griffin, Dale W.; Beauchamp, Benoit

2003-01-01

Unique springs, discharging from the surface of an arctic glacier, release H2S and deposit native sulfur, gypsum, and calcite. The presence of sulfur in three oxidation states indicates a complex series of redox reactions. Physical and chemical conditions of the spring water and surrounding environment, as well as mineralogical and isotopic signatures, suggest biologically mediated reactions. Cell counts and DNA analyses confirm bacteria are present in the spring system, and a limited number of sequenced isolates suggests that complex communities of bacteria live within the glacial system.

Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry

PubMed Central

Houghton, J.L.; Foustoukos, D.; Flynn, T.M.; Vetriani, C.; Bradley, A.S.; Fike, D.A.

2017-01-01

Summary Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here we present reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise. At pH 8.0, thiosulfate is stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation are extracellular elemental sulfur and sulfate. We were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reports of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway (soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observe in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling. PMID:26914243

Thiosulfate oxidation by Thiomicrospira thermophila: Metabolic flexibility in response to ambient geochemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Houghton, J. L.; Foustoukos, D. I.; Flynn, T. M.

Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. Here, we were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reportsmore » of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway ( soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.« less

Thiosulfate oxidation by Thiomicrospira thermophila: Metabolic flexibility in response to ambient geochemistry

DOE PAGES

Houghton, J. L.; Foustoukos, D. I.; Flynn, T. M.; ...

2016-03-21

Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. Here, we were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reportsmore » of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway ( soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.« less

Transcriptome of the Australian Mollusc Dicathais orbita Provides Insights into the Biosynthesis of Indoles and Choline Esters

PubMed Central

Baten, Abdul; Ngangbam, Ajit Kumar; Waters, Daniel L. E.; Benkendorff, Kirsten

2016-01-01

Dicathais orbita is a mollusc of the Muricidae family and is well known for the production of the expensive dye Tyrian purple and its brominated precursors that have anticancer properties, in addition to choline esters with muscle-relaxing properties. However, the biosynthetic pathways that produce these secondary metabolites in D. orbita are not known. Illumina HiSeq 2000 transcriptome sequencing of hypobranchial glands, prostate glands, albumen glands, capsule glands, and mantle and foot tissues of D. orbita generated over 201 million high quality reads that were de novo assembled into 219,437 contigs. Annotation with reference to the Nr, Swiss-Prot and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases identified candidate-coding regions in 76,152 of these contigs, with transcripts for many enzymes in various metabolic pathways associated with secondary metabolite biosynthesis represented. This study revealed that D. orbita expresses a number of genes associated with indole, sulfur and histidine metabolism pathways that are relevant to Tyrian purple precursor biosynthesis, and many of which were not found in the fully annotated genomes of three other molluscs in the KEGG database. However, there were no matches to known bromoperoxidase enzymes within the D. orbita transcripts. These transcriptome data provide a significant molecular resource for gastropod research in general and Tyrian purple producing Muricidae in particular. PMID:27447649

Immobilized OBOC combinatorial bead array to facilitate multiplicative screening.

PubMed

Xiao, Wenwu; Bononi, Fernanda C; Townsend, Jared; Li, Yuanpei; Liu, Ruiwu; Lam, Kit S

2013-07-01

One-bead-one-compound (OBOC) combinatorial library screening has been broadly utilized for the last two decades to identify small molecules, peptides or peptidomimetics targeting variable screening probes such as cell surface receptors, bacteria, protein kinases, phosphatases, proteases etc. In previous screening methods, library beads were suspended in solution and screened against one single probe. Only the positive beads were tracked and isolated for additional screens and finally selected for chemical decoding. During this process, the remaining negative beads were not tracked and discarded. Here we report a novel bead immobilization method such that a bead library array can be conveniently prepared and screened in its entirety, sequentially many times with a series of distinct probes. This method not only allows us to increase the screening efficiency but also permits us to determine the binding profile of each and every library bead against a large number of target receptors. As proof of concept, we serially screened a random OBOC disulfide containing cyclic heptapeptide library with three water soluble dyes as model probes: malachite green, bromocresol purple and indigo carmine. This multiplicative screening approach resulted in a rapid determination of the binding profile of each and every bead respective to each of the three dyes. Beads that interacted with malachite green only, bromocresol purple only, or both indigo carmine and bromocresol purple were isolated, and their peptide sequences were determined with microsequencer. Ultimately, the novel OBOC multiplicative screening approach could play a key role in the enhancement of existing on-bead assays such as whole cell binding, bacteria binding, protein binding, posttranslational modifications etc. with increased efficiency, capacity, and specificity.

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment

PubMed Central

Lipsewers, Yvonne A.; Vasquez-Cardenas, Diana; Seitaj, Dorina; Schauer, Regina; Hidalgo-Martinez, Silvia; Meysman, Filip J. R.

2017-01-01

ABSTRACT Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae. The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H2S, S0, and S2O32−) and electron acceptors (O2 and NO3−) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments. PMID:28314724

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment.

PubMed

Lipsewers, Yvonne A; Vasquez-Cardenas, Diana; Seitaj, Dorina; Schauer, Regina; Hidalgo-Martinez, Silvia; Sinninghe Damsté, Jaap S; Meysman, Filip J R; Villanueva, Laura; Boschker, Henricus T S

2017-05-15

Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria ( Thiotrichales ) and Epsilonproteobacteria ( Campylobacterales ) were prevalent during spring, whereas Deltaproteobacteria ( Desulfobacterales ) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H 2 S, S 0 , and S 2 O 3 2- ) and electron acceptors (O 2 and NO 3 - ) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae ). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments. Copyright © 2017 American Society for Microbiology.

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MedlinePlus

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Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture.

PubMed

Den Uyl, Paul A; Richardson, Laurie L; Jain, Sunit; Dick, Gregory J

2016-01-01

Black band disease (BBD) is a cyanobacterial-dominated polymicrobial mat that propagates on and migrates across coral surfaces, necrotizing coral tissue. Culture-based laboratory studies have investigated cyanobacteria and heterotrophic bacteria isolated from BBD, but the metabolic potential of various BBD microbial community members and interactions between them remain poorly understood. Here we report genomic insights into the physiological and metabolic potential of the BBD-associated cyanobacterium Geitlerinema sp. BBD 1991 and six associated bacteria that were also present in the non-axenic culture. The essentially complete genome of Geitlerinema sp. BBD 1991 contains a sulfide quinone oxidoreductase gene for oxidation of sulfide, suggesting a mechanism for tolerating the sulfidic conditions of BBD mats. Although the operon for biosynthesis of the cyanotoxin microcystin was surprisingly absent, potential relics were identified. Genomic evidence for mixed-acid fermentation indicates a strategy for energy metabolism under the anaerobic conditions present in BBD during darkness. Fermentation products may supply carbon to BBD heterotrophic bacteria. Among the six associated bacteria in the culture, two are closely related to organisms found in culture-independent studies of diseased corals. Their metabolic pathways for carbon and sulfur cycling, energy metabolism, and mechanisms for resisting coral defenses suggest adaptations to the coral surface environment and biogeochemical roles within the BBD mat. Polysulfide reductases were identified in a Flammeovirgaceae genome (Bacteroidetes) and the sox pathway for sulfur oxidation was found in the genome of a Rhodospirillales bacterium (Alphaproteobacteria), revealing mechanisms for sulfur cycling, which influences virulence of BBD. Each genomic bin possessed a pathway for conserving energy from glycerol degradation, reflecting adaptations to the glycerol-rich coral environment. The presence of genes for detoxification of reactive oxygen species and resistance to antibiotics suggest mechanisms for combating coral defense strategies. This study builds upon previous research on BBD and provides new insights into BBD disease etiology.

Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture

PubMed Central

Den Uyl, Paul A.; Richardson, Laurie L.; Jain, Sunit

2016-01-01

Black band disease (BBD) is a cyanobacterial-dominated polymicrobial mat that propagates on and migrates across coral surfaces, necrotizing coral tissue. Culture-based laboratory studies have investigated cyanobacteria and heterotrophic bacteria isolated from BBD, but the metabolic potential of various BBD microbial community members and interactions between them remain poorly understood. Here we report genomic insights into the physiological and metabolic potential of the BBD-associated cyanobacterium Geitlerinema sp. BBD 1991 and six associated bacteria that were also present in the non-axenic culture. The essentially complete genome of Geitlerinema sp. BBD 1991 contains a sulfide quinone oxidoreductase gene for oxidation of sulfide, suggesting a mechanism for tolerating the sulfidic conditions of BBD mats. Although the operon for biosynthesis of the cyanotoxin microcystin was surprisingly absent, potential relics were identified. Genomic evidence for mixed-acid fermentation indicates a strategy for energy metabolism under the anaerobic conditions present in BBD during darkness. Fermentation products may supply carbon to BBD heterotrophic bacteria. Among the six associated bacteria in the culture, two are closely related to organisms found in culture-independent studies of diseased corals. Their metabolic pathways for carbon and sulfur cycling, energy metabolism, and mechanisms for resisting coral defenses suggest adaptations to the coral surface environment and biogeochemical roles within the BBD mat. Polysulfide reductases were identified in a Flammeovirgaceae genome (Bacteroidetes) and the sox pathway for sulfur oxidation was found in the genome of a Rhodospirillales bacterium (Alphaproteobacteria), revealing mechanisms for sulfur cycling, which influences virulence of BBD. Each genomic bin possessed a pathway for conserving energy from glycerol degradation, reflecting adaptations to the glycerol-rich coral environment. The presence of genes for detoxification of reactive oxygen species and resistance to antibiotics suggest mechanisms for combating coral defense strategies. This study builds upon previous research on BBD and provides new insights into BBD disease etiology. PMID:27336619

Absorption and fluorescence spectroscopic characterization of BLUF domain of AppA from Rhodobacter sphaeroides

NASA Astrophysics Data System (ADS)

Zirak, P.; Penzkofer, A.; Schiereis, T.; Hegemann, P.; Jung, A.; Schlichting, I.

2005-08-01

The BLUF domain of the transcriptional anti-repressor protein AppA from the non-sulfur anoxyphototrophic purple bacterium Rhodobacter sphaeroides was characterized by absorption and emission spectroscopy. The BLUF domain constructs AppA 148 (consisting of amino-acid residues 1-148) and AppA 126 (amino-acid residues 1-126) are investigated. The cofactor of the investigated domains is found to consist of a mixture of the flavins riboflavin, FMN, and FAD. The dark-adapted domains exist in two different active receptor conformations (receptor states) with different sub-nanosecond fluorescence lifetimes (BLUF r,f and BLUF r,sl) and a small non-interacting conformation (BLUF nc). The active receptor conformations are transformed to putative signalling states (BLUF s,f and BLUF s,sl) of low fluorescence efficiency and picosecond fluorescence lifetime by blue-light excitation (light-adapted domains). In the dark at room temperature both signalling states recover back to the initial receptor states with a time constant of about 17 min. A quantum yield of signalling state formation of about 25% was determined by intensity dependent transmission measurements. A photo-cycle scheme is presented including photo-induced charge transfer complex formation, charge recombination, and protein binding pocket reorganisation.

Light energy transduction by the purple membrane of halophilic bacteria; Proceedings of the Symposium, San Francisco, Calif., June 6, 1976

NASA Technical Reports Server (NTRS)

1977-01-01

Several aspects of bacteriorhodopsin, the retinal protein component of the purple membranes of Halobacterium halobium, are discussed. Structural studies are presented. Photochemical properties of the protein complex and of its chromophore are described. Proton translocation of bacteriorhodopsin is compared to that of a protein from a thermophilic bacterium. Ionophore activity of bacteriorhodopsin is considered with attention to conformational changes, light dependency, and electrical potential. Amino acid transport is also examined and the light-energy budget is investigated. Bacteriorhodopsin is of interest because of its similarity to rhodopsin, which plays a major role in mammalian vision, and also because its attainability and distinctive characteristics will facilitate studies of certain bacterial physiological functions, such as ion transport and membrane organization.

Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage

PubMed Central

Aida, Azrina A.; Kuroda, Kyohei; Yamamoto, Masamitsu; Nakamura, Akinobu; Hatamoto, Masashi; Yamaguchi, Takashi

2015-01-01

We herein analyzed the diversity of microbes involved in anaerobic sulfur oxidation in an upflow anaerobic sludge blanket (UASB) reactor used for treating municipal sewage under low-temperature conditions. Anaerobic sulfur oxidation occurred in the absence of oxygen, with nitrite and nitrate as electron acceptors; however, reactor performance parameters demonstrated that anaerobic conditions were maintained. In order to gain insights into the underlying basis of anaerobic sulfur oxidation, the microbial diversity that exists in the UASB sludge was analyzed comprehensively to determine their identities and contribution to sulfur oxidation. Sludge samples were collected from the UASB reactor over a period of 2 years and used for bacterial 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing analyses. T-RFLP and sequencing results both showed that microbial community patterns changed markedly from day 537 onwards. Bacteria belonging to the genus Desulforhabdus within the phylum Proteobacteria and uncultured bacteria within the phylum Fusobacteria were the main groups observed during the period of anaerobic sulfur oxidation. Their abundance correlated with temperature, suggesting that these bacterial groups played roles in anaerobic sulfur oxidation in UASB reactors. PMID:25817585

The fate of dissolved dimethylsulfoniopropionate (DMSP) in seawater: tracer studies using 35S-DMSP

NASA Astrophysics Data System (ADS)

Kiene, Ronald P.; Linn, Laura J.

2000-08-01

The algal osmolyte dimethylsulfoniopropionate (DMSP) is distributed globally in the marine euphotic zone, where it represents a major form of reduced sulfur. Previous investigations of DMSP cycling have focused mainly on its degradation to the volatile sulfur species dimethylsulfide (DMS) and little is known about the other possible fates of the sulfur. In this study 35S-DMSP was used to trace the biogeochemical fate of sulfur in the natural pool of dissolved DMSP in seawater. Dissolved 35S-DMSP added to seawater was degraded within hours, with the 35S partitioning into three major, relatively stable, operational pools: particulates, dissolved non-volatile degradation products (DNVS), and volatiles. The mean values for partitioning of DMSP obtained from 20 different seawater incubations were (in terms of sulfur): particulates (33%; range 6-85%;); DNVS (46%; range 21-74%); and volatiles (9%; range 2-21%). Oceanic water samples had lower incorporation of DMSP-S into particulates and higher incorporation into DNVS as compared with coastal-shelf samples. Transient accumulation of untransformed 35S-DMSP in bacteria accounted for some of the particulate 35S, but most of the cell-associated DMSP was rapidly transformed and the sulfur incorporated into relatively stable macromolecules. 35S-labeled DNVS accumulated steadily during DMSP metabolism and approximately half of this pool was confirmed to be sulfate, implying that oxidation of DMSP-sulfur takes place on time scales of minutes to hours. Volatile products were produced rapidly from 35S-DMSP, but most were consumed within 1-3 h. Experiments showed that methanethiol (MeSH) was the major volatile compound produced from tracer DMSP, with longer-lived DMS formed in lower amounts. Tracer additions of 35S-MeSH to seawater resulted in incorporation of sulfur into cellular macromolecules and DNVS, suggesting MeSH was an intermediate in the conversion of DMSP into these pools. Experiments with 35S-DMS revealed that turnover of DMS was much slower than for DMSP or MeSH, and the retention of the DMS-sulfur in particles was only a minor fraction of the total amount metabolized. The majority of the 35S-DMS was transformed into DNVS including sulfate. Temperature and DMSP concentration significantly affected the partitioning of sulfur during DMSP degradation, with lower temperatures and higher substrate concentrations causing a shift from particulate into volatile and non-volatile dissolved products. Our work demonstrates that natural turnover of dissolved DMSP results in minor net production of sulfur gases, and substantial production of previously unrecognized products (particulate and dissolved non-volatile sulfur). The main fates of DMSP are tied to assimilation and oxidation of the reduced sulfur by microorganisms, both of which may act as important controls on the production of climatically active DMS.

Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA

PubMed Central

Miranda, Priscilla J.; McLain, Nathan K.; Hatzenpichler, Roland; Orphan, Victoria J.; Dillon, Jesse G.

2016-01-01

The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing is known about the in situ diversity and activity of the microorganisms in these habitats. We studied the diversity, micron-scale spatial associations and metabolic activity of the mat community via sequence analysis of 16S rRNA and aprA genes, fluorescence in situ hybridization (FISH) microscopy and sulfate reduction rate (SRR) measurements. Sequence analysis revealed a diverse group of bacteria, dominated by sulfur cycling gamma-, epsilon-, and deltaproteobacterial lineages such as Marithrix, Sulfurovum, and Desulfuromusa. FISH microscopy suggests a close physical association between sulfur-oxidizing and sulfur-reducing genotypes, while radiotracer studies showed low, but detectable, SRR. Comparative 16S rRNA gene sequence analyses indicate the WP sulfur vent microbial mat community is similar, but distinct from other hydrothermal vent communities representing a range of biotopes and lithologic settings. These findings suggest a complete biological sulfur cycle is operating in the WP mat ecosystem mediated by diverse bacterial lineages, with some similarity with deep-sea hydrothermal vent communities. PMID:27512390

A simple evaluation of soil quality of waterlogged purple paddy soils with different productivities.

PubMed

Liu, Zhanjun; Zhou, Wei; Lv, Jialong; He, Ping; Liang, Guoqing; Jin, Hui

2015-01-01

Evaluation of soil quality can be crucial for designing efficient farming systems and ensuring sustainable agriculture. The present study aimed at evaluating the quality of waterlogged purple paddy soils with different productivities in Sichuan Basin. The approach involved comprehensive analyses of soil physical and chemical properties, as well as enzyme activities and microbial community structure measured by phospholipid fatty acid analysis (PLFA). A total of 36 soil samples were collected from four typical locations, with 12 samples representing high productivity purple paddy soil (HPPS), medium productivity purple paddy soil (MPPS) and low productivity purple paddy soil (LPPS), respectively. Most measured soil properties showed significant differences (P ≤ 0.05) among HPPS, MPPS and LPPS. Pearson correlation analysis and principal component analysis were used to identify appropriate soil quality indicators. A minimum data set (MDS) including total nitrogen (TN), available phosphorus (AP), acid phosphatase (ACP), total bacteria (TB) and arbuscular mycorrhizal fungi was established and accounted for 82.1% of the quality variation among soils. A soil quality index (SQI) was developed based on the MDS method, whilst HPPS, MPPS and LPPS received mean SQI scores of 0.725, 0.536 and 0.425, respectively, with a ranking of HPPS > MPPS > LPPS. HPPS showed relatively good soil quality characterized by optimal nutrient availability, enzymatic and microbial activities, but the opposite was true of LPPS. Low levels of TN, AP and soil microbial activities were considered to be the major constraints limiting the productivity in LPPS. All soil samples collected were rich in available N, K, Si and Zn, but deficient in available P, which may be the major constraint for the studied regions. Managers in our study area should employ more appropriate management in the LPPS to improve its rice productivity, and particularly to any potential limiting factor.

Effect of pH buffering capacity and sources of dietary sulfur on rumen fermentation, sulfide production, methane production, sulfate reducing bacteria, and total Archaea in in vitro rumen cultures.

PubMed

Wu, Hao; Meng, Qingxiang; Yu, Zhongtang

2015-06-01

The effects of three types of dietary sulfur on in vitro fermentation characteristics, sulfide production, methane production, and microbial populations at two different buffer capacities were examined using in vitro rumen cultures. Addition of dry distilled grain with soluble (DDGS) generally decreased total gas production, degradation of dry matter and neutral detergent fiber, and concentration of total volatile fatty acids, while increasing ammonia concentration. High buffering capacity alleviated these adverse effects on fermentation. Increased sulfur content resulted in decreased methane emission, but total Archaea population was not changed significantly. The population of sulfate reducing bacteria was increased in a sulfur type-dependent manner. These results suggest that types of dietary sulfur and buffering capacity can affect rumen fermentation and sulfide production. Diet buffering capacity, and probably alkalinity, may be increased to alleviate some of the adverse effects associated with feeding DDGS at high levels. Copyright © 2015 Elsevier Ltd. All rights reserved.

Polysulfides as Intermediates in the Oxidation of Sulfide to Sulfate by Beggiatoa spp.

PubMed Central

Schwedt, Anne; Kreutzmann, Anne-Christin; Kuypers, Marcel M. M.; Milucka, Jana

2014-01-01

Zero-valent sulfur is a key intermediate in the microbial oxidation of sulfide to sulfate. Many sulfide-oxidizing bacteria produce and store large amounts of sulfur intra- or extracellularly. It is still not understood how the stored sulfur is metabolized, as the most stable form of S0 under standard biological conditions, orthorhombic α-sulfur, is most likely inaccessible to bacterial enzymes. Here we analyzed the speciation of sulfur in single cells of living sulfide-oxidizing bacteria via Raman spectroscopy. Our results showed that under various ecological and physiological conditions, all three investigated Beggiatoa strains stored sulfur as a combination of cyclooctasulfur (S8) and inorganic polysulfides (Sn2−). Linear sulfur chains were detected during both the oxidation and reduction of stored sulfur, suggesting that Sn2− species represent a universal pool of bioavailable sulfur. Formation of polysulfides due to the cleavage of sulfur rings could occur biologically by thiol-containing enzymes or chemically by the strong nucleophile HS− as Beggiatoa migrates vertically between oxic and sulfidic zones in the environment. Most Beggiatoa spp. thus far studied can oxidize sulfur further to sulfate. Our results suggest that the ratio of produced sulfur and sulfate varies depending on the sulfide flux. Almost all of the sulfide was oxidized directly to sulfate under low-sulfide-flux conditions, whereas only 50% was oxidized to sulfate under high-sulfide-flux conditions leading to S0 deposition. With Raman spectroscopy we could show that sulfate accumulated in Beggiatoa filaments, reaching intracellular concentrations of 0.72 to 1.73 M. PMID:24212585

Overall energy conversion efficiency of a photosynthetic vesicle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sener, Melih; Strumpfer, Johan; Singharoy, Abhishek

The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytbc1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in amore » quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12-0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination.« less

Overall energy conversion efficiency of a photosynthetic vesicle

PubMed Central

Sener, Melih; Strumpfer, Johan; Singharoy, Abhishek; Hunter, C Neil; Schulten, Klaus

2016-01-01

The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytb⁢c1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12–0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination. DOI: http://dx.doi.org/10.7554/eLife.09541.001 PMID:27564854

Elevated ground-level O(3) changes the diversity of anoxygenic purple phototrophic bacteria in paddy field.

PubMed

Feng, Youzhi; Lin, Xiangui; Yu, Yongchang; Zhu, Jianguo

2011-11-01

The knowledge of the impact of elevated ground-level O(3) below ground the agro-ecosystem is limited. A field experiment in China Ozone Free-Air Concentration Enrichment (FACE-O(3)) facility on a rice-wheat rotation system was carried out to investigate responses of anoxygenic phototrophic purple bacteria (AnPPB) to elevated ground-level O(3). AnPPB community structures and sizes in paddy soil were monitored by molecular approaches including PCR-DGGE and real-time quantitative PCR based upon the pufM gene on three typical rice growth stages. Repetitive sequence-based PCR (rep-PCR) in combination with culture-reliant method was conducted to reveal changes in genotypic diversity. Elevated ground-level O(3) statistically reduce AnPPB abundance and percentage in total bacterial community in flooded rice soil via decreasing their genotypic diversity and metabolic versatility. Concomitantly, their community composition changed after rice anthesis stage under elevated ground-level O(3). Our results from AnPPB potential responses imply that continuously elevated ground-level O(3) in the future would eventually harm the health of paddy ecosystem through negative effect on soil microorganisms.

Overall energy conversion efficiency of a photosynthetic vesicle

DOE PAGES

Sener, Melih; Strumpfer, Johan; Singharoy, Abhishek; ...

2016-08-26

The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytbc1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in amore » quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12-0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination.« less

Purple: a modular system for developing and deploying behavioral intervention technologies.

PubMed

Schueller, Stephen M; Begale, Mark; Penedo, Frank J; Mohr, David C

2014-07-30

The creation, deployment, and evaluation of Web-based and mobile-based applications for health, mental health, and wellness within research settings has tended to be siloed, with each research group developing their own systems and features. This has led to technological features and products that are not sharable across research teams, thereby limiting collaboration, reducing the speed of dissemination, and raising the bar for entry into this area of research. This paper provides an overview of Purple, an extensible, modular, and repurposable system created for the development of Web-based and mobile-based applications for health behavior change. Purple contains features required to construct applications and to manage and evaluate research trials using these applications. Core functionality of Purple includes elements that support user management, content authorship, content delivery, and data management. We discuss the history and development of the Purple system guided by the rationale of producing a system that allows greater collaboration and understanding across research teams interested in investigating similar questions and using similar methods. Purple provides a useful tool to meet the needs of stakeholders involved in the creation, provision, and usage of eHealth and mHealth applications. Housed in a non-profit, academic institution, Purple also offers the potential to facilitate the diffusion of knowledge across the research community and improve our capacity to deliver useful and usable applications that support the behavior change of end users.

Purple: A Modular System for Developing and Deploying Behavioral Intervention Technologies

PubMed Central

Schueller, Stephen M; Begale, Mark; Penedo, Frank J

2014-01-01

The creation, deployment, and evaluation of Web-based and mobile-based applications for health, mental health, and wellness within research settings has tended to be siloed, with each research group developing their own systems and features. This has led to technological features and products that are not sharable across research teams, thereby limiting collaboration, reducing the speed of dissemination, and raising the bar for entry into this area of research. This paper provides an overview of Purple, an extensible, modular, and repurposable system created for the development of Web-based and mobile-based applications for health behavior change. Purple contains features required to construct applications and to manage and evaluate research trials using these applications. Core functionality of Purple includes elements that support user management, content authorship, content delivery, and data management. We discuss the history and development of the Purple system guided by the rationale of producing a system that allows greater collaboration and understanding across research teams interested in investigating similar questions and using similar methods. Purple provides a useful tool to meet the needs of stakeholders involved in the creation, provision, and usage of eHealth and mHealth applications. Housed in a non-profit, academic institution, Purple also offers the potential to facilitate the diffusion of knowledge across the research community and improve our capacity to deliver useful and usable applications that support the behavior change of end users. PMID:25079298

Gram staining.

PubMed

Coico, Richard

2005-10-01

Named after Hans Christian Gram who developed the method in 1884, the Gram stain allows one to distinguish between Gram-positive and Gram-negative bacteria on the basis of differential staining with a crystal violet-iodine complex and a safranin counterstain. The cell walls of Gram-positive organisms retain this complex after treatment with alcohol and appear purple, whereas gram-negative organisms decolorize following such treatment and appear pink. The method described here is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures.

Gram staining.

PubMed

Coico, R

2001-05-01

Named after Hans Christian Gram who developed the method in 1884, the Gram stain allows one to distinguish between Gram-positive and Gram-negative bacteria on the basis of differential staining with a crystal violet-iodine complex and a safranin counterstain. The cell walls of Gram-positive organisms retain this complex after treatment with alcohol and appear purple, whereas gram-negative organisms decolorize following such treatment and appear pink. The method described here is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures.

Generalized Master Equation with Non-Markovian Multichromophoric Förster Resonance Energy Transfer for Modular Exciton Densities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jang, Seogjoo; Hoyer, Stephan; Fleming, Graham

2014-10-31

A generalized master equation (GME) governing quantum evolution of modular exciton density (MED) is derived for large scale light harvesting systems composed of weakly interacting modules of multiple chromophores. The GME-MED offers a practical framework to incorporate real time coherent quantum dynamics calculations of small length scales into dynamics over large length scales, and also provides a non-Markovian generalization and rigorous derivation of the Pauli master equation employing multichromophoric Förster resonance energy transfer rates. A test of the GME-MED for four sites of the Fenna-Matthews-Olson complex demonstrates how coherent dynamics of excitonic populations over coupled chromophores can be accurately describedmore » by transitions between subgroups (modules) of delocalized excitons. Application of the GME-MED to the exciton dynamics between a pair of light harvesting complexes in purple bacteria demonstrates its promise as a computationally efficient tool to investigate large scale exciton dynamics in complex environments.« less

Elemental sulfur in Eddy County, New Mexico

USGS Publications Warehouse

Hinds, Jim S.; Cunningham, Richard R.

1970-01-01

Sulfur has been reported in Eddy County, N. Mex., in rocks ranging from Silurian to Holocene in age at depths of 0-15,020 feet. Targets of present exploration are Permian formations in the Delaware Basin and northwest shelf areas at depths of less than 4,000 feet. Most of the reported sulfur occurrences in the shelf area are in the 'Abo' (as used by some subsurface geologists), Yeso, and San Andres Formations and the Artesia Group. Sulfur deposition in the dense dolomites of the 'Abo,' Yeso, and San Andres Formations is attributed to the reduction of ionic sulfate by hydrogen sulfide in formation waters in zones of preexisting porosity and permeability. A similar origin accounts for most of the sulfur deposits in the formations of the Artesia Group, but some of the sulfur in these formations may have originated in place through the alteration of anhydrite to carbonate and sulfur by the metabolic processes of bacteria in the presence of hydrocarbons. Exploration in the Delaware Basin area is directed primarily toward the Castile Formation. Sulfur deposits in the Castile Formation are found in irregular masses of cavernous brecciated secondary carbonate rock enveloped by impermeable anhydrite. The carbonate masses, or 'castiles,' probably originated as collapse features resulting from subsurface solution and upward stopping. Formation of carbonate rock and sulfur in the castiles is attributed to the reduction of brecciated anhydrite by bacteria and hydrocarbons in the same process ascribed to the formation of carbonate and sulfur in the caprocks of salt domes.

Biosorption of heavy metal ions on Rhodobacter sphaeroides and Alcaligenes eutrophus H16

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seki, Hideshi; Suzuki, Akira; Mitsueda, Shinichiro

1998-01-15

A fundamental study of the application of bacteria to the recovery of toxic heavy metals from aqueous environments was carried out. The biosorption characteristics of cadmium and lead ions were determined with purple nonsulfur bacteria, Rhodobacter sphaeroides and hydrogen bacteria, Alcaligenes eutrophus H16 that were inactivated by steam sterilization. A simplified version of the metal binding model proposed by Plette et al. was used for the description of meal binding data. The results showed that the biosorption of bivalent metal ions to whole cell bodies of the bacteria was due to monodentate binding to two different types of acidic sites:more » carboxilic and phosphatic-type sites. The number of metal binding sites of A. eutrophus was 2.4-fold larger than that of R. sphaeroides.« less

Organic geochemistry of the early Toarcian oceanic anoxic event in Hawsker Bottoms, Yorkshire, England

NASA Astrophysics Data System (ADS)

French, K. L.; Sepúlveda, J.; Trabucho-Alexandre, J.; Gröcke, D. R.; Summons, R. E.

2014-03-01

A comprehensive organic geochemical investigation of the Hawsker Bottoms outcrop section in Yorkshire, England has provided new insights about environmental conditions leading into and during the Toarcian oceanic anoxic event (T-OAE; ∼183 Ma). Rock-Eval and molecular analyses demonstrate that the section is uniformly within the early oil window. Hydrogen index (HI), organic petrography, polycyclic aromatic hydrocarbon (PAH) distributions, and tricyclic terpane ratios mark a shift to a lower relative abundance of terrigenous organic matter supplied to the sampling locality during the onset of the T-OAE and across a lithological transition. Unlike other ancient intervals of anoxia and extinction, biomarker indices of planktonic community structure do not display major changes or anomalous values. Depositional environment and redox indicators support a shift towards more reducing conditions in the sediment porewaters and the development of a seasonally stratified water column during the T-OAE. In addition to carotenoid biomarkers for green sulfur bacteria (GSB), we report the first occurrence of okenane, a marker of purple sulfur bacteria (PSB), in marine samples younger than ∼1.64 Ga. Based on modern observations, a planktonic source of okenane's precursor, okenone, would require extremely shallow photic zone euxinia (PZE) and a highly restricted depositional environment. However, due to coastal vertical mixing, the lack of planktonic okenone production in modern marine sulfidic environments, and building evidence of okenone production in mat-dwelling Chromatiaceae, we propose a sedimentary source of okenone as an alternative. Lastly, we report the first parallel compound-specific δC13 record in marine- and terrestrial-derived biomarkers across the T-OAE. The δC13 records of short-chain n-alkanes, acyclic isoprenoids, and long-chain n-alkanes all encode negative carbon isotope excursions (CIEs), and together, they support an injection of isotopically light carbon that impacted both the atmospheric and marine carbon reservoirs. To date, molecular δC13 records of the T-OAE display a negative CIE that is smaller in magnitude compared to the bulk organic δC13 excursion. Although multiple mechanisms could explain this observation, our molecular, petrographic, and Rock-Eval data suggest that variable mixing of terrigenous and marine organic matter is an important factor affecting the bulk organic δC13 records of the T-OAE.

Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

PubMed Central

Ishoey, Thomas; Espinoza, Carola; Pérez-Pantoja, Danilo; Manghisi, Antonio; Morabito, Marina; Salas-Burgos, Alexis

2017-01-01

The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (ca. 6°S and ca. 36°S). Studies show that primeval sulfuretums held diverse prokaryotic life, and, while rare today, still sustain species-rich giant sulfur-oxidizing bacterial communities. We here present the genomic features of a new bacteria of the HS, “Candidatus Venteria ishoeyi” (“Ca. V. ishoeyi”) in the family Thiotrichaceae.Three identical filaments were micro-manipulated from reduced sediments collected off central Chile; their DNA was extracted, amplified, and sequenced by a Roche 454 GS FLX platform. Using three sequenced libraries and through de novo genome assembly, a draft genome of 5.7 Mbp, 495 scaffolds, and a N50 of 70 kbp, was obtained. The 16S rRNA gene phylogenetic analysis showed that “Ca. V. ishoeyi” is related to non-vacuolate forms presently known as Beggiatoa or Beggiatoa-like forms. The complete set of genes involved in respiratory nitrate-reduction to dinitrogen was identified in “Ca. V. ishoeyi”; including genes likely leading to ammonification. As expected, the sulfur-oxidation pathway reported for other sulfur-oxidizing bacteria were deduced and also, key inorganic and organic carbon acquisition related genes were identified. Unexpectedly, the genome of “Ca. V. ishoeyi” contained numerous CRISPR repeats and an I-F CRISPR-Cas type system gene coding array. Findings further show that, as a member of an eons-old marine ecosystem, “Ca. V. ishoeyi” contains the needed metabolic plasticity for life in an increasingly oxygenated and variable ocean. PMID:29236755

Microbial life in cold, sulfur-rich environments: Investigations of an Arctic ecosystem and implications for life detection at Europa

NASA Astrophysics Data System (ADS)

Gleeson, Damhnait Fagan

2009-12-01

Exobiological investigations require a detailed understanding of life's interactions with its environment here on Earth before we can confidently recognize signs of these interactions at other worlds such as Europa. Using a cold, sulfur-based ecosystem at Borup Fiord pass in the Canadian High Arctic as a study site, I investigated how the supraglacial non-ice materials are represented across different scales in spectral data, how microbiology is influencing the mineralogy of the site, and whether the products of microbial sulfide oxidation preserve indications of their biogenic origin. A systematic scale-integrated approach was applied to query orbital (Hyperion), field, and laboratory spectra to identify sulfur-rich materials precipitated on a glacier. While sulfur, the main constituent of the deposits, is well represented in Hyperion data, minor constituents such as calcite and gypsum are partially or entirely masked. Absorption features of sulfates, where present, are shifted in wavelength due to the effects of mixing or temperature. Autonomous detection methods were successfully applied to monitor the generation and extent of the deposits, which show spectral similarities to Europa's non-ice materials. Geomicrobiological cultivation of sulfide oxidizing bacteria succeeded in demonstrating that the microbiological community present at the site has the potential to catalyze the generation of sulfur deposits. Sulfur generated in culture is present as biomineralized structures comprised of microbial filaments and sheaths along which sulfur globules are deposited. Consortia producing these structures are dominated by gamma-Proteobacteria closely related to Marinobacter, not previously known to oxidize sulfide. The sulfur structures produced by these consortia are not observed in abiotic controls and have the potential to serve as morphological biosignatures. Investigations into the biogenicity of field deposits reveal mineral assemblages with similar morphologies to those generated in culture. X-ray diffraction analyses show some evidence for rosickyite, a metastable form of biogenic sulfur. Mid-infrared laboratory spectroscopy also indicates the presence of organic functional groups diagnostic of proteins and fatty acids within the sulfur deposits. These combined investigations suggest that sulfur minerals extruded onto Europa's near surface, analogous to those of Borup Fiord pass, have the potential to contain identifiable biosignatures which low-temperature conditions could help stabilize and preserve.

Multilayer-MCTDH approach to the energy transfer dynamics in the LH2 antenna complex

NASA Astrophysics Data System (ADS)

Shibl, Mohamed F.; Schulze, Jan; Al-Marri, Mohammed J.; Kühn, Oliver

2017-09-01

The multilayer multiconfiguration time-dependent Hartree method is used to study the coupled exciton-vibrational dynamics in a high-dimensional nonameric model of the LH2 antenna complex of purple bacteria. The exciton-vibrational coupling is parametrized within the Huang-Rhys model according to phonon and intramolecular vibrational modes derived from an experimental bacteriochlorophyll spectral density. In contrast to reduced density matrix approaches, the Schrödinger equation is solved explicitly, giving access to the full wave function. This facilitates an unbiased analysis in terms of the coupled dynamics of excitonic and vibrational degrees of freedom. For the present system, we identify spectator modes for the B800 to B800 transfer and we find a non-additive effect of phonon and intramolecular vibrational modes on the B800 to B850 exciton transfer.

Aptasensors for rapid detection of Escherichia coli O157:H7 and Salmonella typhimurium

NASA Astrophysics Data System (ADS)

Wu, Wen-he; Li, Min; Wang, Yue; Ouyang, Hou-xian; Wang, Lin; Li, Ci-xiu; Cao, Yu-chen; Meng, Qing-he; Lu, Jian-xin

2012-11-01

Herein we reported the development of aptamer-based biosensors (aptasensors) based on label-free aptamers and gold nanoparticles (AuNPs) for detection of Escherichia coli ( E. coli) O157:H7 and Salmonella typhimurium. Target bacteria binding aptamers are adsorbed on the surface of unmodified AuNPs to capture target bacteria, and the detection was accomplished by target bacteria-induced aggregation of the aptasensor which is associated as red-to-purple color change upon high-salt conditions. By employing anti- E. coli O157:H7 aptamer and anti- S. typhimurium aptamer, we developed a convenient and rapid approach that could selectively detect bacteria without specialized instrumentation and pretreatment steps such as cell lysis. The aptasensor could detect as low as 105colony-forming units (CFU)/ml target bacteria within 20 min or less and its specificity was 100%. This novel method has a great potential application in rapid detection of bacteria in the near future.

Growth of the facultative anaerobe Shewanella putrefaciens by elemental sulfur reduction

NASA Technical Reports Server (NTRS)

Moser, D. P.; Nealson, K. H.

1996-01-01

The growth of bacteria by dissimilatory elemental sulfur reduction is generally associated with obligate anaerobes and thermophiles in particular. Here we describe the sulfur-dependent growth of the facultatively anaerobic mesophile Shewanella putrefaciens. Six of nine representative S. putrefaciens isolates from a variety of environments proved able to grow by sulfur reduction, and strain MR-1 was chosen for further study. Growth was monitored in a minimal medium (usually with 0.05% Casamino Acids added as a growth stimulant) containing 30 mM lactate and limiting concentrations of elemental sulfur. When mechanisms were provided for the removal of the metabolic end product, H2S, measurable growth was obtained at sulfur concentrations of from 2 to 30 mM. Initial doubling times were ca. 1.5 h and substrate independent over the range of sulfur concentrations tested. In the cultures with the highest sulfur concentrations, cell numbers increased by greater than 400-fold after 48 h, reaching a maximum density of 6.8 x 10(8) cells ml-1. Yields were determined as total cell carbon and ranged from 1.7 to 5.9 g of C mol of S(0) consumed-1 in the presence of the amino acid supplement and from 0.9 to 3.4 g of C mol of S(0-1) in its absence. Several lines of evidence indicate that cell-to-sulfur contact is not required for growth. Approaches for the culture of sulfur-metabolizing bacteria and potential ecological implications of sulfur reduction in Shewanella-like heterotrophs are discussed.

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge.

PubMed

Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Bajic, Vladimir; Qian, Pei-Yuan

2014-11-01

Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

WHC Dose pump R&R

NASA Image and Video Library

2012-10-02

ISS033-E-009153 (2 Oct. 2012) --- Japan Aerospace Exploration Agency astronaut Aki Hoshide, Expedition 33 flight engineer, performs a removal and replacement of the DKiV water pump and the E-K pre-treat tank with its hose in the Tranquility node of the International Space Station. E-K contains five liters of pre-treat solution, i.e., a mix of H2SO4 (sulfuric acid), CrO3 (chromium oxide, for oxidation and purple color) and H2O (water). The pre-treat liquid is mixed with water in the DKiV dispenser and used for toilet flushing.

Homology modeling reveals the structural background of the striking difference in thermal stability between two related [NiFe]hydrogenases.

PubMed

Szilágyi, András; Kovács, Kornél L; Rákhely, Gábor; Závodszky, Péter

2002-02-01

Hydrogenases are redox metalloenzymes in bacteria that catalyze the uptake or production of molecular hydrogen. Two homologous nickel-iron hydrogenases, HupSL and HydSL from the photosynthetic purple sulfur bacterium Thiocapsa roseopersicina, differ substantially in their thermal stabilities despite the high sequence similarity between them. The optimum temperature of HydSL activity is estimated to be at least 50 degrees C higher than that of HupSL. In this work, homology models of both proteins were constructed and analyzed for a number of structural properties. The comparison of the models reveals that the higher stability of HydSL can be attributed to increased inter-subunit electrostatic interactions: the homology models reliably predict that HydSL contains at least five more inter-subunit ion pairs than HupSL. The subunit interface of HydSL is more polar than that of HupSL, and it contains a few extra inter-subunit hydrogen bonds. A more optimized cavity system and amino acid replacements resulting in increased conformational rigidity may also contribute to the higher stability of HydSL. The results are in accord with the general observation that with increasing temperature, the role of electrostatic interactions in protein stability increases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-001-0071-8.

Tracking photosynthetic sulfide oxidation in a meromictic lake using sulfate δ34S and δ18O

NASA Astrophysics Data System (ADS)

Gilhooly, W. P.; Reinhard, C.; Lyons, T. W.; Glass, J. B.

2012-12-01

Phototrophic sulfur bacteria oxidize sulfide and fix carbon dioxide in the presence of sunlight without producing oxygen. Environmental conditions in the Paleo- and Mesoproterozoic, when atmospheric oxygen concentrations were at low levels and portions of the oceans were anoxic and sulfidic (euxinic), were conducive to widespread carbon fixation by anoxygenic photosynthesis. This pathway may have helped sustain euxinic conditions in the Proterozoic water column. With limited organic biomarker and geochemical evidence for widespread production of anoxygenic phototrophs, however, additional proxies are needed to fingerprint paleoecological and biogeochemical signals associated with photic zone euxinia. Paired δ34S and δ18O from ancient sulfates (gypsum, barite, or CAS) may offer an added constraint on the history and ecological dominance of photosynthetic S-oxidation. Sulfate-oxygen can fractionate during sulfate reduction, but the extent of isotopic enrichment is controlled either by kinetic isotope effects imparted during intracellular enzymatic steps or equilibrium oxygen exchange with ambient water. An improved understanding of these processes can be gained from modern natural environments. Mahoney Lake is a density-stratified lake located within the White Lake Basin of British Columbia. The euxinic water column supports a dense plate of purple sulfur bacteria (Amoebobacter purpureus) that thrives where free sulfide intercepts the photic zone at ~7 m water depth. We analyzed the isotopic composition of sulfate (δ34SSO4 and δ18OSO4), sulfide (δ34SH2S), and water (δ18OH2O) to track the potentially coupled processes of dissimilatory sulfate reduction and phototrophic sulfide oxidation within this meromictic lake. Large isotopic offsets observed between sulfate and sulfide within the monimolimnion (δ34SSO4-H2S = 51‰) and within pore waters along the oxic margin (δ34SSO4-H2S >50‰) are consistent with sulfate reduction in both the sediments and the anoxic water column. Given the high sulfide concentrations of the lake ([H2S] = 30 mM), sulfur disproportionation is likely inoperable, and so the large instantaneous fractionations are best explained by single-step sulfate reduction. The offset between sulfate and sulfide decreases at the chemocline (δ34SSO4-H2S = 37‰), a trend possibly explained by sulfide oxidation or decreasing sulfate reduction rates. Sulfate exhibits a curvilinear response in δ18OSO4/δ34SSO4 that approaches δ18OSO4 values (~24-33‰) in equilibrium with ambient water (δ18OH2O = -2.2‰). Although an inverse relationship between δ18OSO4/δ18OH2O is inconsistent with chemical sulfide oxidation (typically a positive relationship), fine-scale variations in δ34SSO4 and δ18OSO4 at the chemocline imply sulfate reduction coupled with near quantitative reoxidation by A. purpureus. Although observed within the microbial plate, this photosynthetic S-bacteria biosignature is restricted to the oxic/anoxic transition zone and is apparently swamped by the more prevalent process of sulfate reduction operative throughout the anoxic water column and sediment pore waters.

Towards a semiquantitative non invasive characterisation of Tyrian purple dye composition: Convergence of UV-Visible reflectance spectroscopy and fast-high temperature-high performance liquid chromatography with photodiode array detection.

PubMed

Clementi, Catia; Nowik, Witold; Romani, Aldo; Cardon, Dominique; Trojanowicz, Marek; Davantès, Athénaïs; Chaminade, Pierre

2016-07-05

In this paper, partial least square (PLS) regression is innovatively applied for a semi-quantitative non invasive study of the most precious dye of Antiquity: Tyrian purple. This original approach for the study of organic dyes in the cultural heritage field, is based on the correlation of spectrophotometric (UV-Visible) and chromatographic (Fast-HT-HPLC-PDA) data from an extensive set of textiles prepared with different snail species according to historical recipes. A cross-validated PLS model, based on the quantity of 6,6'-dibromoindigotin, displays an excellent correlation factor (R(2)Y = 0.987) between values determined by chromatography and those predicted from reflectance spectra. This indicates that the spectral features of Tyrian purple on textile fibre is strictly related to the amount of this indigoid component whose content may be non invasively predicted from reflectance spectrum. The studied correlation also highlights that, independently of the dyeing method and nature of the textile fibre used, the relative content of 6,6'-dibromindigotin may be used as a parameter to distinguish samples prepared with Hexaplex trunculus L. snails from those prepared with further mollusc species. To validate this model, archaeological textile fragments dating from the Roman period were successfully examined. The results achieved open an absolutely new way in Tyrian purple analysis in cultural heritage by non invasive spectroscopic techniques attesting their convergence with HPLC and giving them a semi-quantitative value. Copyright © 2016 Elsevier B.V. All rights reserved.

On the transformation of sulfur-containing amino acids and peptides to volatile sulfur compounds (VSC) in the human mouth.

PubMed

Wåler, S M

1997-10-01

Halitosis is most often caused by oral conditions. Volatile sulfur compounds (VSC), constituting the major components of oral malodor, are produced by anaerobic, gram-negative bacteria retained mainly in periodontal pockets or on the tongue dorsum. Sulfur-containing amino acids serve as substrate for these bacteria. VSC have also been found to have unfavorable effect on the tissue. The aim of this study was to examine whether normal, healthy individuals with no history of halitosis were able to produce VSC from cysteine, when applied as a mouthrinse. A further aim of the study was to investigate and compare the potential of other sulfur-containing amino acids and peptides as substrates for oral VSC production and to localize the odor-production sites. A portable sulfide monitor was used for VSC registration. Results showed that all test subjects produced high oral concentrations of VSC upon rinses with cysteine, which thus seems to be a major substrate for VSC production. The other sulfur-containing substrates had much less effect. It was found that the tongue was the major site for VSC production, and that saliva per se caused low VSC production.

Characterization of sulfur oxidizing bacteria related to biogenic sulfuric acid corrosion in sludge digesters.

PubMed

Huber, Bettina; Herzog, Bastian; Drewes, Jörg E; Koch, Konrad; Müller, Elisabeth

2016-07-18

Biogenic sulfuric acid (BSA) corrosion damages sewerage and wastewater treatment facilities but is not well investigated in sludge digesters. Sulfur/sulfide oxidizing bacteria (SOB) oxidize sulfur compounds to sulfuric acid, inducing BSA corrosion. To obtain more information on BSA corrosion in sludge digesters, microbial communities from six different, BSA-damaged, digesters were analyzed using culture dependent methods and subsequent polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). BSA production was determined in laboratory scale systems with mixed and pure cultures, and in-situ with concrete specimens from the digester headspace and sludge zones. The SOB Acidithiobacillus thiooxidans, Thiomonas intermedia, and Thiomonas perometabolis were cultivated and compared to PCR-DGGE results, revealing the presence of additional acidophilic and neutrophilic SOB. Sulfate concentrations of 10-87 mmol/L after 6-21 days of incubation (final pH 1.0-2.0) in mixed cultures, and up to 433 mmol/L after 42 days (final pH <1.0) in pure A. thiooxidans cultures showed huge sulfuric acid production potentials. Additionally, elevated sulfate concentrations in the corroded concrete of the digester headspace in contrast to the concrete of the sludge zone indicated biological sulfur/sulfide oxidation. The presence of SOB and confirmation of their sulfuric acid production under laboratory conditions reveal that these organisms might contribute to BSA corrosion within sludge digesters. Elevated sulfate concentrations on the corroded concrete wall in the digester headspace (compared to the sludge zone) further indicate biological sulfur/sulfide oxidation in-situ. For the first time, SOB presence and activity is directly relatable to BSA corrosion in sludge digesters.

Sulfur and oxygen isotope fractionation during benzene, toluene, ethyl benzene, and xylene degradation by sulfate-reducing bacteria.

PubMed

Knöller, Kay; Vogt, Carsten; Richnow, Hans-Herrmann; Weise, Stephan M

2006-06-15

We examined the oxygen and sulfur isotope fractionation of sulfate during anaerobic degradation of toluene by sulfate-reducing bacteria in culture experiments with Desulfobacula toluolica as a type strain and with an enrichment culture Zz5-7 obtained from a benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated aquifer. Sulfur isotope fractionation can show considerable variation upon sulfate reduction and may react extremely sensitively to changes in environmental conditions. In contrast, oxygen isotope fractionation seems to be less sensitive to environmental changes. Our results clearly indicate that oxygen isotope fractionation is dominated by isotope exchange with ambient water. To verify our experimental results and to test the applicability of oxygen and sulfur isotope investigations under realistic field conditions, we evaluated isotope data from two BTEX-contaminated aquifers presented in the recent literature. On a field scale, bacterial sulfate reduction may be superimposed by processes such as dispersion, adsorption, reoxidation, or mixing. The dual isotope approach enables the identification of such sulfur transformation processes. This identification is vital for a general qualitative evaluation of the natural attenuation potential of the contaminated aquifer.

Use of the gram stain in microbiology.

PubMed

Beveridge, T J

2001-05-01

The Gram stain differentiates bacteria into two fundamental varieties of cells. Bacteria that retain the initial crystal violet stain (purple) are said to be "gram-positive," whereas those that are decolorized and stain red with carbol fuchsin (or safranin) are said to be "gram-negative." This staining response is based on the chemical and structural makeup of the cell walls of both varieties of bacteria. Gram-positives have a thick, relatively impermeable wall that resists decolorization and is composed of peptidoglycan and secondary polymers. Gram-negatives have a thin peptidoglycan layer plus an overlying lipid-protein bilayer known as the outer membrane, which can be disrupted by decolorization. Some bacteria have walls of intermediate structure and, although they are officially classified as gram-positives because of their linage, they stain in a variable manner. One prokaryote domain, the Archaea, have such variability of wall structure that the Gram stain is not a useful differentiating tool.

Conformational Complexity in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum Revealed by Hole-Burning Spectroscopy.

PubMed

Kell, Adam; Jassas, Mahboobe; Acharya, Khem; Hacking, Kirsty; Cogdell, Richard J; Jankowiak, Ryszard

2017-06-15

This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800 R and B800 B . The energy differences between average site energies of conformations 1 and 2, and B800 R and B800 B are similar (∼200 cm -1 ), suggesting weak and strong hydrogen bonds linking two major subpopulations of BChls and the protein scaffolding. Although conformations 1 and 2 of the B850 chromophores, and B800 R and B800 B , exist in the ground state, selective excitation leads to 1 → 2 and B800 R → B800 B phototransformations. Different static inhomogeneous broadening is revealed for the lowest energy exciton states of B850 (fwhm ∼195 cm -1 ) and B800 R (fwhm ∼140 cm -1 ). To describe the 5 K absorption spectrum and the above-mentioned conformations, we employ an exciton model with dichotomous protein conformation disorder. We show that both experimental data and the modeling study support a two-site model with strongly and weakly hydrogen-bonded B850 and B800 BChls, which under illumination undergo conformational changes, most likely caused by proton dynamics.

Location and magnetic relaxation properties of the stable tyrosine radical in photosystem II.

PubMed

Innes, J B; Brudvig, G W

1989-02-07

Dipolar interactions with neighboring metal ions can cause enhanced spin-lattice relaxation of free radicals. We have applied the theory of dipolar relaxation enhancement and shown that the dependence of the enhanced relaxation on the protein structure surrounding the free radical can be used to obtain distances from the free radical to the protein surface. To test the theoretical predictions, we have examined the effect of added Dy3+ complexes on the microwave power saturation of free radicals in two protein complexes of known structure: myoglobin nitroxide and the reaction center from Rhodobacter sphaeroides. Three cases have been considered: (1) metal ions bound to a specific site, (2) metal ions bound randomly over the protein surface, and (3) metal ions distributed randomly in solution. Only case 3, which assumes no specific binding, gave good agreement between the distances obtained by using the two model systems. The effect of added Dy3+ complexes on the microwave power saturation of signal IIslow from photosystem II (PSII) was used to determine the location of the stable tyrosine radical giving rise to signal IIslow. Assuming that the surface of a membrane-bound protein can be approximated as planar, we have obtained distances from the tyrosine radical to the membrane surface in thylakoids, in PSII membranes, and in Tris-washed PSII membranes. The distances we have determined are in good agreement with those predicted on the basis of a structural homology between the D1 and D2 subunits of PSII and the structurally characterized L and M subunits of the reaction center from purple non-sulfur bacteria. We have also examined the temperature dependence of the microwave power at half-saturation (P1/2) of signal IIslow from 4 to 200 K in dark-adapted PSII membranes. Above 70 K, the P1/2 increases as T2.5, which is consistent with a Raman relaxation mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)

Biohydrogen, biomethane and bioelectricity as crucial components of biorefinery of organic wastes: a review.

PubMed

Poggi-Varaldo, Héctor M; Munoz-Paez, Karla M; Escamilla-Alvarado, Carlos; Robledo-Narváez, Paula N; Ponce-Noyola, M Teresa; Calva-Calva, Graciano; Ríos-Leal, Elvira; Galíndez-Mayer, Juvencio; Estrada-Vázquez, Carlos; Ortega-Clemente, Alfredo; Rinderknecht-Seijas, Noemí F

2014-05-01

Biohydrogen is a sustainable form of energy as it can be produced from organic waste through fermentation processes involving dark fermentation and photofermentation. Very often biohydrogen is included as a part of biorefinery approaches, which reclaim organic wastes that are abundant sources of renewable and low cost substrate that can be efficiently fermented by microorganisms. The aim of this work was to critically assess selected bioenergy alternatives from organic solid waste, such as biohydrogen and bioelectricity, to evaluate their relative advantages and disadvantages in the context of biorefineries, and finally to indicate the trends for future research and development. Biorefining is the sustainable processing of biomass into a spectrum of marketable products, which means: energy, materials, chemicals, food and feed. Dark fermentation of organic wastes could be the beach-head of complete biorefineries that generate biohydrogen as a first step and could significantly influence the future of solid waste management. Series systems show a better efficiency than one-stage process regarding substrate conversion to hydrogen and bioenergy. The dark fermentation also produces fermented by-products (fatty acids and solvents), so there is an opportunity for further combining with other processes that yield more bioenergy. Photoheterotrophic fermentation is one of them: photosynthetic heterotrophs, such as non-sulfur purple bacteria, can thrive on the simple organic substances produced in dark fermentation and light, to give more H2. Effluents from photoheterotrophic fermentation and digestates can be processed in microbial fuel cells for bioelectricity production and methanogenic digestion for methane generation, thus integrating a diverse block of bioenergies. Several digestates from bioenergies could be used for bioproducts generation, such as cellulolytic enzymes and saccharification processes, leading to ethanol fermentation (another bioenergy), thus completing the inverse cascade. Finally, biohydrogen, biomethane and bioelectricity could contribute to significant improvements for solid organic waste management in agricultural regions, as well as in urban areas.

Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments.

PubMed

Boschker, Henricus T S; Vasquez-Cardenas, Diana; Bolhuis, Henk; Moerdijk-Poortvliet, Tanja W C; Moodley, Leon

2014-01-01

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, The Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m(-2) d(-1). Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)(-1), which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.

Distribution and abundance of organic thiols

NASA Technical Reports Server (NTRS)

Fahey, R.

1985-01-01

The role of glutathione (GSH) in protecting against the toxicity of oxygen and oxygen by products is well established for all eukaryotes studied except Entamoeba histolytica which lacks mitochrondria, chloroplasts, and microtubules. The GSH is not universal among prokaryotes. Entamoeba histolytica does not produce GSH or key enzymes of GSH metabolism. A general method of thiol analysis based upon fluorescent labeling with monobromobimane and HPLC separation of the resulting thiol derivatives was developed to determine the occurrence of GSH and other low molecular weight thiols in bacteria. Glutathione is the major thiol in cyanobacteria and in most bacteria closely related to the purple photosynthetic bacteria, but GSH was not found in archaebacteria, green bacteria, or GRAM positive bacteria. It suggested that glutathione metabolism was incorporated into eukaryotes at the time that mitochondria and chloroplasts were acquired by endosymbiosis. In Gram positive aerobes, coenzyme A occurs at millimolar levels and CoA disulfide reductases are identified. The CoA, rather than glutathione, may function in the oxygen detoxification processes of these organisms.

GEOCHEMISTRY OF SULFUR IN IRON CORROSION SCALES FOUND IN DRINKING WATER DISTRIBUTION SYSTEMS

EPA Science Inventory

Iron-sulfur geochemistry is important in many natural and engineered environments, including drinking water systems. In the anaerobic environment beneath scales of corroding iron drinking water distribution system pipes, sulfate reducing bacteria (SRB) produce sulfide from natu...

Enrichment of sulfidogenic bacteria from the human intestinal tract.

PubMed

Feng, Yuan; Stams, Alfons J M; de Vos, Willem M; Sánchez-Andrea, Irene

2017-02-01

Hydrogen sulfide is formed in the human intestinal tract as the end product of the anaerobic microbial degradation of sulfur compounds present in mucus, bile or proteins. Since human gut microbial sulfur metabolism has been poorly characterized, we aimed to identify and isolate the microorganisms involved in sulfide formation. Fresh fecal samples from one healthy donor and one diagnosed with irritable bowel syndrome were used as inocula for enrichments that were supplemented with sulfate or sulfite as electron acceptors in combination with different electron donors. After two transfers, cultures with high sulfide production were selected and the phylogenetic composition of the enriched microbial communities was determined. Sulfite respiration and cysteine degradation were the dominant sulfidogenic processes, and the most abundant bacteria enriched belonged to Bilophila and Clostridium cluster XIVa. Different isolates were obtained and remarkably included a novel sulfite reducer, designated strain 2C. Strain 2C belongs to the Veillonellaceae family of Firmicutes phylum and showed limited (91%) 16S rRNA gene sequence similarity with that of known Sporomusa species and hence may represent a novel genus. This study indicates that bacteria that utilize sulfite and organic sulfur compounds rather than merely sulfate are relevant for human intestinal sulfur metabolism. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evaluating the Nature of So-Called S*-State Feature in Transient Absorption of Carotenoids in Light-Harvesting Complex 2 (LH2) from Purple Photosynthetic Bacteria.

PubMed

Niedzwiedzki, Dariusz M; Hunter, C Neil; Blankenship, Robert E

2016-11-03

Carotenoids are a class of natural pigments present in all phototrophic organisms, mainly in their light-harvesting proteins in which they play roles of accessory light absorbers and photoprotectors. Extensive time-resolved spectroscopic studies of these pigments have revealed unexpectedly complex photophysical properties, particularly for carotenoids in light-harvesting LH2 complexes from purple bacteria. An ambiguous, optically forbidden electronic excited state designated as S* has been postulated to be involved in carotenoid excitation relaxation and in an alternative carotenoid-to-bacteriochlorophyll energy transfer pathway, as well as being a precursor of the carotenoid triplet state. However, no definitive and satisfactory origin of the carotenoid S* state in these complexes has been established, despite a wide-ranging series of studies. Here, we resolve the ambiguous origin of the carotenoid S* state in LH2 complex from Rba. sphaeroides by showing that the S* feature can be seen as a combination of ground state absorption bleaching of the carotenoid pool converted to cations and the Stark spectrum of neighbor neutral carotenoids, induced by temporal electric field brought by the carotenoid cation-bacteriochlorophyll anion pair. These findings remove the need to assign an S* state, and thereby significantly simplify the photochemistry of carotenoids in these photosynthetic antenna complexes.

Phylogenetic diversity and position of the genus Campylobacter

NASA Technical Reports Server (NTRS)

Lau, P. P.; DeBrunner-Vossbrinck, B.; Dunn, B.; Miotto, K.; MacDonnell, M. T.; Rollins, D. M.; Pillidge, C. J.; Hespell, R. B.; Colwell, R. R.; Sogin, M. L.;

Vegetation successfully prevents oxidization of sulfide minerals in mine tailings.

PubMed

Li, Yang; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

2016-07-15

The oxidization of metal sulfide in tailings causes acid mine drainage. However, it remains unclear whether vegetation prevents the oxidization of metal sulfides. The oxidization characteristics and microbial indices of the tailings in the presence of various plant species were investigated to explore the effects of vegetation on the oxidization of sulfide minerals in tailings. The pH, reducing sulfur, free iron oxides (Fed), chemical oxygen consumption (COC) and biological oxygen consumption (BOC) were measured. Key iron- and sulfur-oxidizing bacteria (Acidithiobacillus spp., Leptospirillum spp. and Thiobacillus spp.) were quantified using real-time PCR. The results indicate that vegetation growing on tailings can effectively prevent the oxidization of sulfide minerals in tailings. A higher pH and reducing-sulfur content and lower Fed were observed in the 0-30 cm depth interval in the presence of vegetation compared to bare tailings (BT). The COC gradually decreased with depth in all of the soil profiles; specifically, the COC rapidly decreased in the 10-20 cm interval in the presence of vegetation but gradually decreased in the BT profiles. Imperata cylindrica (IC) and Chrysopogon zizanoides (CZ) profiles contained the highest BOC in the 10-20 cm interval. The abundance of key iron- and sulfur-oxidizing bacteria in the vegetated tailings were significantly lower than in the BT; in particular, IC was associated with the lowest iron- and sulfur-oxidizing bacterial abundance. In conclusion, vegetation successfully prevented the oxidization of sulfide minerals in the tailings, and Imperata cylindrica is the most effective in reducing the number of iron- and sulfur-oxidizing bacteria and helped to prevent the oxidization of sulfide minerals in the long term. Copyright © 2016 Elsevier Ltd. All rights reserved.

The global sulfur cycle

NASA Technical Reports Server (NTRS)

Sagan, D. (Editor)

1985-01-01

The results of the planetary biology microbial ecology's 1984 Summer Research Program, which examined various aspects of the global sulfur cycle are summarized. Ways in which sulfur flows through the many living and chemical species that inhabit the surface of the Earth were investigated. Major topics studied include: (1) sulfur cycling and metabolism of phototropic and filamentous sulfur bacteria; (2) sulfur reduction in sediments of marine and evaporite environments; (3) recent cyanobacterial mats; (4) microanalysis of community metabolism in proximity to the photic zone in potential stromatolites; and (5) formation and activity of microbial biofilms on metal sulfides and other mineral surfaces. Relationships between the global sulfur cycle and the understanding of the early evolution of the Earth and biosphere and current processes that affect global habitability are stressed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wronkiewicz, David; Paul, Varum; Abousif, Alsedik

The most effective mechanism to limit CO 2 release from underground Geologic Carbon Sequestration (GCS) sites over multi-century time scales will be to convert the CO 2 into solid carbonate minerals. This report describes the results from four independent research investigations on carbonate mineralization: 1) Colloidal calcite particles forming in Maramec Spring, Missouri, provide a natural analog to evaluate reactions that may occur in a leaking GCS site. The calcite crystals form as a result of physiochemical changes that occur as the spring water rises from a depth of more than 190'. The resultant pressure decrease induces a loss ofmore » CO 2 from the water, rise in pH, lowering of the solubility of Ca 2+ and CO 3 2-, and calcite precipitation. Equilibrium modelling of the spring water resulted in a calculated undersaturated state with respect to calcite. The discontinuity between the observed occurrence of calcite and the model result predicting undersaturated conditions can be explained if bicarbonate ions (HCO 3 -) are directly involved in precipitation process rather than just carbonate ions (CO 3 2-). 2) Sedimentary rocks in the Oronto Group of the Midcontinent Rift (MCR) system contain an abundance of labile Ca-, Mg-, and Fe-silicate minerals that will neutralize carbonic acid and provide alkaline earth ions for carbonate mineralization. One of the challenges in using MCR rocks for GCS results from their low porosity and permeability. Oronto Group samples were reacted with both CO 2-saturated deionized water at 90°C, and a mildly acidic leachant solution in flow-through core-flooding reactor vessels at room temperature. Resulting leachate solutions often exceeded the saturation limit for calcite. Carbonate crystals were also detected in as little as six days of reaction with Oronto Group rocks at 90oC, as well as experiments with forsterite-olivine and augite, both being common minerals this sequence. The Oronto Group samples have poor reservoir rock characteristics, none ever exceeded a permeability value of 2.0 mD even after extensive dissolution of calcite cement during the experiments. The overlying Bayfield Group – Jacobsville Formation sandstones averaged 13.4 ± 4.3% porosity and a single sample tested by core-flooding revealed a permeability of ~340 mD. The high porosity-permeability characteristics of these sandstones will allow them to be used for GCS as a continuous aquifer unit with the overlying Mt. Simon Formation. 3) Anaerobic sulfate reducing bacteria (SRB) can enhance the conversion rate of CO 2 into solid minerals and thereby improve long-term storage. SRB accelerated carbonate mineralization reactions between pCO 2 values of 0.0059 and 14.7 psi. Hydrogen, lactate and formate served as suitable electron donors for SRB metabolism. The use of a 13CO 2 spiked gas source also produced carbonate minerals with ~53% of the carbon being derived from the gas phase. The sulfate reducing activity of the microbial community was limited, however, at 20 psi pCO 2 and carbonate mineralization did not occur. Inhibition of bacterial metabolism may have resulted from the acidic conditions or CO 2 toxicity. 4) Microbialite communities forming in the high turbidity and hypersaline water of Storrs’ Lake, San Salvador Island, The Bahamas, were investigated for their distribution, mineralogy and microbial diversity. Molecular analysis of the organic mats on the microbialites indicate only a trace amount of cyanobacteria, while anaerobic and photosynthetic non-sulfur bacteria of the phyla Chloroflexi and purple sulfur bacteria of class Gammaproteobacteria were abundant.« less

Sulfur redox chemistry governs diurnal antimony and arsenic cycles at Champagne Pool, Waiotapu, New Zealand

NASA Astrophysics Data System (ADS)

Ullrich, Maria K.; Pope, James G.; Seward, Terry M.; Wilson, Nathaniel; Planer-Friedrich, Britta

2013-07-01

Champagne Pool, a sulfidic hot spring in New Zealand, exhibits distinct diurnal variations in antimony (Sb) and arsenic (As) concentrations, with daytime high and night-time low concentrations. To identify the underlying mobilization mechanisms, five sites along the drainage channel of Champagne Pool were sampled every 2 h during a 24 h period. Temporal variations in elemental concentrations and Sb, As, and sulfur (S) speciation were monitored in the discharging fluid. Total trace element concentrations in filtered and unfiltered samples were analyzed using ICP-MS, and Sb, As and S species were determined by IC-ICP-MS. Sulfur speciation in the drainage channel was dominated by thiosulfate and sulfide at night, while sulfate dominated during the day. The distinct diurnal changes suggest that the transformations are caused by phototrophic sulfur-oxidizing bacteria. These bacteria metabolize thiosulfate and sulfide in daylight to form sulfate and, as suggested by modeling with PhreeqC, elemental sulfur. Sulfide consumption during the day results in undersaturation of antimony sulfides, which triggers the additional release of dissolved Sb. For As, diurnal cycles were much more pronounced in speciation than in total concentrations, with di- and trithioarsenate forming at night due to excess sulfide, and monothioarsenate forming from arsenite and elemental sulfur during the day. Sulfur speciation was thus found to control Sb and As in terms of both solubility and speciation.

Use of purple durum wheat to produce naturally functional fresh and dry pasta.

PubMed

Ficco, Donatella Bianca Maria; De Simone, Vanessa; De Leonardis, Anna Maria; Giovanniello, Valentina; Del Nobile, Matteo Alessandro; Padalino, Lucia; Lecce, Lucia; Borrelli, Grazia Maria; De Vita, Pasquale

2016-08-15

In this study, the effects of different milling procedures (roller-milling vs. stone-milling) and pasta processing (fresh vs. dried spaghetti), and cooking on the antioxidant components and sensory properties of purple durum wheat were investigated. Milling and pasta processing were performed using one purple and one conventional non-pigmented durum wheat genotypes, and the end-products were compared with commercial pasta. The results show that the stone milling process preserved more compounds with high health value (total fibre and carotenoids, and in the purple genotype, also anthocyanins) compared to roller-milling. The drying process significantly (p<0.05) reduced the content of anthocyanins (21.42 μg/g vs. 46.32 μg/g) and carotenoids (3.77 μg/g vs. 4.04 μg/g) with respect to the pasteurisation process involved in fresh pasta production. The sensory properties of pasta from the purple genotype did not significantly differ from commercial wholemeal pasta, and its in vitro glycemic index was even lower. Thus, it is possible to consider this genetic material as a good ingredient for the production of functional foods from cereals naturally rich in bioactive compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

Applications of the Phytomedicine Echinacea purpurea (Purple Coneflower) in Infectious Diseases

PubMed Central

Hudson, James B.

2012-01-01

Extracts of Echinacea purpurea (EP, purple coneflower) have been used traditionally in North America for the treatment of various types of infections and wounds, and they have become very popular herbal medicines globally. Recent studies have revealed that certain standardized preparations contain potent and selective antiviral and antimicrobial activities. In addition, they display multiple immune-modulatory activities, comprising stimulation of certain immune functions such as phagocytic activity of macrophages and suppression of the proinflammatory responses of epithelial cells to viruses and bacteria, which are manifested as alterations in secretion of various cytokines and chemokines. These immune modulations result from upregulation or downregulation of the relevant genes and their transcription factors. All these bioactivities can be demonstrated at noncytotoxic concentrations of extract and appear to be due to multiple components rather than the individual chemical compounds that characterize Echinacea extracts. Potential applications of the bioactive extracts may go beyond their traditional uses. PMID:22131823

Nitrogen and Sulfur Requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on Cellulosic Substrates in Minimal Nutrient Media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kridelbaugh, Donna M; Nelson, Josh C; Engle, Nancy L

2013-01-01

Growth media for cellulolytic Clostridium thermocellum and Caldicellulosiruptor bescii bacteria usually contain excess nutrients that would increase costs for consolidated bioprocessing for biofuel production and create a waste stream with nitrogen, sulfur and phosphate. C. thermocellum was grown on crystalline cellulose with varying concentrations of nitrogen and sulfur compounds, and growth rate and alcohol production response curves were determined. Both bacteria assimilated sulfate in the presence of ascorbate reductant, increasing the ratio of oxidized to reduced fermentation products. From these results, a low ionic strength, defined minimal nutrient medium with decreased nitrogen, sulfur, phosphate and vitamin supplements was developed formore » the fermentation of cellobiose, cellulose and acid-pretreated Populus. Carbon and electron balance calculations indicate the unidentified residual fermentation products must include highly reduced molecules. Both bacterial populations were maintained in co-cultures with substrates containing xylan or hemicellulose in defined medium with sulfate and basal vitamin supplements.« less

Succession of Sulfur-Oxidizing Bacteria in the Microbial Community on Corroding Concrete in Sewer Systems† ▿

PubMed Central

Okabe, Satoshi; Odagiri, Mitsunori; Ito, Tsukasa; Satoh, Hisashi

2007-01-01

Microbially induced concrete corrosion (MICC) in sewer systems has been a serious problem for a long time. A better understanding of the succession of microbial community members responsible for the production of sulfuric acid is essential for the efficient control of MICC. In this study, the succession of sulfur-oxidizing bacteria (SOB) in the bacterial community on corroding concrete in a sewer system in situ was investigated over 1 year by culture-independent 16S rRNA gene-based molecular techniques. Results revealed that at least six phylotypes of SOB species were involved in the MICC process, and the predominant SOB species shifted in the following order: Thiothrix sp., Thiobacillus plumbophilus, Thiomonas intermedia, Halothiobacillus neapolitanus, Acidiphilium acidophilum, and Acidithiobacillus thiooxidans. A. thiooxidans, a hyperacidophilic SOB, was the most dominant (accounting for 70% of EUB338-mixed probe-hybridized cells) in the heavily corroded concrete after 1 year. This succession of SOB species could be dependent on the pH of the concrete surface as well as on trophic properties (e.g., autotrophic or mixotrophic) and on the ability of the SOB to utilize different sulfur compounds (e.g., H2S, S0, and S2O32−). In addition, diverse heterotrophic bacterial species (e.g., halo-tolerant, neutrophilic, and acidophilic bacteria) were associated with these SOB. The microbial succession of these microorganisms was involved in the colonization of the concrete and the production of sulfuric acid. Furthermore, the vertical distribution of microbial community members revealed that A. thiooxidans was the most dominant throughout the heavily corroded concrete (gypsum) layer and that A. thiooxidans was most abundant at the highest surface (1.5-mm) layer and decreased logarithmically with depth because of oxygen and H2S transport limitations. This suggested that the production of sulfuric acid by A. thiooxidans occurred mainly on the concrete surface and the sulfuric acid produced penetrated through the corroded concrete layer and reacted with the sound concrete below. PMID:17142362

Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens.

PubMed

Woodhams, Douglas C; LaBumbard, Brandon C; Barnhart, Kelly L; Becker, Matthew H; Bletz, Molly C; Escobar, Laura A; Flechas, Sandra V; Forman, Megan E; Iannetta, Anthony A; Joyce, Maureen D; Rabemananjara, Falitiana; Gratwicke, Brian; Vences, Miguel; Minbiole, Kevin P C

2018-05-01

Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.

Bioreactor for acid mine drainage control

DOEpatents

Zaluski, Marek H.; Manchester, Kenneth R.

2001-01-01

A bioreactor for reacting an aqueous heavy metal and sulfate containing mine drainage solution with sulfate reducing bacteria to produce heavy metal sulfides and reduce the sulfuric acid content of the solution. The reactor is an elongated, horizontal trough defining an inlet section and a reaction section. An inlet manifold adjacent the inlet section distributes aqueous mine drainage solution into the inlet section for flow through the inlet section and reaction section. A sulfate reducing bacteria and bacteria nutrient composition in the inlet section provides sulfate reducing bacteria that with the sulfuric acid and heavy metals in the solution to form solid metal sulfides. The sulfate reducing bacteria and bacteria nutrient composition is retained in the cells of a honeycomb structure formed of cellular honeycomb panels mounted in the reactor inlet section. The honeycomb panels extend upwardly in the inlet section at an acute angle with respect to the horizontal. The cells defined in each panel are thereby offset with respect to the honeycomb cells in each adjacent panel in order to define a tortuous path for the flow of the aqueous solution.

Metaproteome of the viral concentrates from the deep chlorophyll maximum of the South China Sea

NASA Astrophysics Data System (ADS)

Xie, Zhang-Xian; Chen, Feng; Zhang, Shu-Feng; Wang, Ming-Hua; Zhang, Hao; Kong, Ling-Fen; Dai, Min-Han; Hong, Hua-Sheng; Lin, Lin; Wang, Da-Zhi

2016-04-01

Viral concentrates (VCs) have been commonly used for studying viral diversity, viral metagenomics and virus-host interactions in the natural ecosystem. However, the protein characteristics of VCs have not been explored. Here, we applied shotgun proteomics to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum of the South China Sea. We found that 34% of the identified proteins were assigned to the viruses, mainly being those of SAR11 related bacteria, cyanobacteria and picophytoeukaryotes. The remaining 66% were non-viral proteins mostly originating from diverse bacteria, such as SAR324, SAR11 and the Alteromonadales, and were functionally dominated by transport, translation, sulfur metabolism and one-carbon metabolism. Among the non-viral proteins, 28% were extracellular proteins and 10% were identified exclusively in the VCs, suggesting that non-viral entities might exist in the VCs. This study demonstrated that metaproteomics provides a valuable avenue to explore not only the diversity and structure of a viral community but also the novel ecological functions affiliated with microbes in the natural environment.

Mathematical modeling of simultaneous carbon-nitrogen-sulfur removal from industrial wastewater.

PubMed

Xu, Xi-Jun; Chen, Chuan; Wang, Ai-Jie; Ni, Bing-Jie; Guo, Wan-Qian; Yuan, Ye; Huang, Cong; Zhou, Xu; Wu, Dong-Hai; Lee, Duu-Jong; Ren, Nan-Qi

2017-01-05

A mathematical model of carbon, nitrogen and sulfur removal (C-N-S) from industrial wastewater was constructed considering the interactions of sulfate-reducing bacteria (SRB), sulfide-oxidizing bacteria (SOB), nitrate-reducing bacteria (NRB), facultative bacteria (FB), and methane producing archaea (MPA). For the kinetic network, the bioconversion of C-N by heterotrophic denitrifiers (NO 3 - →NO 2 - →N 2 ), and that of C-S by SRB (SO 4 2- →S 2- ) and SOB (S 2- →S 0 ) was proposed and calibrated based on batch experimental data. The model closely predicted the profiles of nitrate, nitrite, sulfate, sulfide, lactate, acetate, methane and oxygen under both anaerobic and micro-aerobic conditions. The best-fit kinetic parameters had small 95% confidence regions with mean values approximately at the center. The model was further validated using independent data sets generated under different operating conditions. This work was the first successful mathematical modeling of simultaneous C-N-S removal from industrial wastewater and more importantly, the proposed model was proven feasible to simulate other relevant processes, such as sulfate-reducing, sulfide-oxidizing process (SR-SO) and denitrifying sulfide removal (DSR) process. The model developed is expected to enhance our ability to predict the treatment of carbon-nitrogen-sulfur contaminated industrial wastewater. Copyright © 2016 Elsevier B.V. All rights reserved.

The role of bacteria and mycorrhiza in plant sulfur supply

PubMed Central

Gahan, Jacinta; Schmalenberger, Achim

2014-01-01

Plant growth is highly dependent on bacteria, saprophytic, and mycorrhizal fungi which facilitate the cycling and mobilization of nutrients. Over 95% of the sulfur (S) in soil is present in an organic form. Sulfate-esters and sulfonates, the major forms of organo-S in soils, arise through deposition of biological material and are transformed through subsequent humification. Fungi and bacteria release S from sulfate-esters using sulfatases, however, release of S from sulfonates is catalyzed by a bacterial multi-component mono-oxygenase system. The asfA gene is used as a key marker in this desulfonation process to study sulfonatase activity in soil bacteria identified as Variovorax, Polaromonas, Acidovorax, and Rhodococcus. The rhizosphere is regarded as a hot spot for microbial activity and recent studies indicate that this is also the case for the mycorrhizosphere where bacteria may attach to the fungal hyphae capable of mobilizing organo-S. While current evidence is not showing sulfatase and sulfonatase activity in arbuscular mycorrhiza, their effect on the expression of plant host sulfate transporters is documented. A revision of the role of bacteria, fungi and the interactions between soil bacteria and mycorrhiza in plant S supply was conducted. PMID:25566295

Femtosecond spectroscopy of native and carotenoidless purple-bacterial LH2 clarifies functions of carotenoids.

PubMed

Theiss, Christoph; Leupold, Dieter; Moskalenko, Andrei A; Razjivin, Andrei P; Eichler, Hans J; Lokstein, Heiko

2008-06-01

EET between the two circular bacteriochlorophyll compartments B800 and B850 in native (containing the carotenoid rhodopin) and carotenoidless LH2 isolated from the photosynthetic purple sulfur bacterium Allochromatium minutissimum was investigated by femtosecond time-resolved transient absorption spectroscopy. Both samples were excited with 120-fs laser pulses at 800 nm, and spectral evolution was followed in the 720-955 nm range at different delay times. No dependence of transient absorption in the B800 band on the presence of the carotenoid rhodopin was found. Together with the likewise virtually unchanged absorption spectra in the bacteriochlorophyll Q(y) region, these observations suggest that absence of rhodopin does not significantly alter the structure of the pigment-protein complex including interactions between bacteriochlorophylls. Apparently, rhodopin does also not accelerate B800 to B850 EET in LH2, contrary to what has been suggested previously. Moreover, "carotenoid-catalyzed internal conversion" can also be excluded for the bacteriochlorophylls in LH2 of A. minutissimum. Together with previous results obtained with two-photon fluorescence excitation spectroscopy, it can also be concluded that there is neither EET from rhodopin to B800 nor (back-)EET from B800 to rhodopin.

Growth of Leptospirillum ferriphilum in sulfur medium in co-culture with Acidithiobacillus caldus.

PubMed

Smith, Sarah L; Johnson, D Barrie

2018-03-01

Leptospirillum ferriphilum and Acidithiobacillus caldus are both thermotolerant acidophilic bacteria that frequently co-exist in natural and man-made environments, such as biomining sites. Both are aerobic chemolithotrophs; L. ferriphilum is known only to use ferrous iron as electron donor, while A. caldus can use zero-valent and reduced sulfur, and also hydrogen, as electron donors. It has recently been demonstrated that A. caldus reduces ferric iron to ferrous when grown aerobically on sulfur. Experiments were carried out which demonstrated that this allowed L. ferriphilum to be sustained for protracted periods in media containing very little soluble iron, implying that dynamic cycling of iron occurred in aerobic mixed cultures of these two bacteria. In contrast, numbers of viable L. ferriphilum rapidly declined in mixed cultures that did not contain sulfur. Data also indicated that growth of A. caldus was partially inhibited in the presence of L. ferriphilum. This was shown to be due to greater sensitivity of the sulfur-oxidizer to ferric than to ferrous iron, and to highly positive redox potentials, which are characteristic of cultures containing Leptospirillum spp. The implications of these results in the microbial ecology of extremely acidic environments and in commercial bioprocessing applications are discussed.

Long-distance electron transport occurs globally in marine sediments

NASA Astrophysics Data System (ADS)

Burdorf, Laurine D. W.; Tramper, Anton; Seitaj, Dorina; Meire, Lorenz; Hidalgo-Martinez, Silvia; Zetsche, Eva-Maria; Boschker, Henricus T. S.; Meysman, Filip J. R.

2017-02-01

Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements.

Bio-desulfurization and denitrification by anaerobic-anoxic process for the treatment of wastewater from flue gas washing.

PubMed

Song, Ziyu; Zhou, Xuemei; Li, Yuguang; Yang, Maohua; Xing, Jianmin

2013-01-01

For amine-based carbon dioxide capture, nitrogen oxides and sulfur oxides were the main pollutants that had a negative effect on the regeneration of solvent. Before carbon dioxide capture, the sulfur oxides in flue gas should be removed by the method of calcium salt, and then washed by alkaline solution to eliminate the residual nitrogen oxides and sulfur oxides. The washing wastewater containing sulfate and nitrate needs to be treated. In this study, a novel anaerobic-anoxic process was built up for the treatment of this washing wastewater. Nitrate was reduced to nitrogen by denitrifying bacteria. Sulfate was firstly reduced to sulfide by sulfate reducing bacteria, and then selectively oxidized to element sulfur by sulfide oxidizing bacteria. The treated liquid could be reused as absorption after the adjustment of pH value. The performances of this bioprocess were investigated under various pH values and S/N ratios. It was found that the optimal pH value of influent was 6.0, the percentages of denitrification and sulfate reducing could reach 90 and 89%, respectively. Seventy-six percent of sulfate was transformed into element sulfur. Nitrate significantly had a negative effect on sulfate reduction above 10 mM. As 20 mM nitrate, the sulfate reducing percentage would drop to 67%. These results showed that the anaerobic-anoxic process was feasible for the treatment of flue gas washing wastewater. It would be prospectively applied to other wastewater with the higher ratio of SO4(2-)/NO3(-).

B. subtilis as a Model for Studying the Assembly of Fe-S Clusters in Gram-Positive Bacteria.

PubMed

Dos Santos, Patricia C

2017-01-01

Complexes of iron and sulfur (Fe-S clusters) are widely distributed in nature and participate in essential biochemical reactions. The biological formation of Fe-S clusters involves dedicated pathways responsible for the mobilization of sulfur, the assembly of Fe-S clusters, and the transfer of these clusters to target proteins. Genomic analysis of Bacillus subtilis and other Gram-positive bacteria indicated the presence of only one Fe-S cluster biosynthesis pathway, which is distinct in number of components and organization from previously studied systems. B. subtilis has been used as a model system for the characterization of cysteine desulfurases responsible for sulfur mobilization reactions in the biogenesis of Fe-S clusters and other sulfur-containing cofactors. Cysteine desulfurases catalyze the cleavage of the C-S bond from the amino acid cysteine and subsequent transfer of sulfur to acceptor molecules. These reactions can be monitored by the rate of alanine formation, the first product in the reaction, and sulfide formation, a byproduct of reactions performed under reducing conditions. The assembly of Fe-S clusters on protein scaffolds and the transfer of these clusters to target acceptors are determined through a combination of spectroscopic methods probing the rate of cluster assembly and transfer. This chapter provides a description of reactions promoting the assembly of Fe-S clusters in bacteria as well as methods used to study functions of each biosynthetic component and identify mechanistic differences employed by these enzymes across different pathways. © 2017 Elsevier Inc. All rights reserved.

Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.

PubMed

Castresana, J; Lübben, M; Saraste, M; Higgins, D G

1994-06-01

Cytochrome oxidase is a key enzyme in aerobic metabolism. All the recorded eubacterial (domain Bacteria) and archaebacterial (Archaea) sequences of subunits 1 and 2 of this protein complex have been used for a comprehensive evolutionary analysis. The phylogenetic trees reveal several processes of gene duplication. Some of these are ancient, having occurred in the common ancestor of Bacteria and Archaea, whereas others have occurred in specific lines of Bacteria. We show that eubacterial quinol oxidase was derived from cytochrome c oxidase in Gram-positive bacteria and that archaebacterial quinol oxidase has an independent origin. A considerable amount of evidence suggests that Proteobacteria (Purple bacteria) acquired quinol oxidase through a lateral gene transfer from Gram-positive bacteria. The prevalent hypothesis that aerobic metabolism arose several times in evolution after oxygenic photosynthesis, is not sustained by two aspects of the molecular data. First, cytochrome oxidase was present in the common ancestor of Archaea and Bacteria whereas oxygenic photosynthesis appeared in Bacteria. Second, an extant cytochrome oxidase in nitrogen-fixing bacteria shows that aerobic metabolism is possible in an environment with a very low level of oxygen, such as the root nodules of leguminous plants. Therefore, we propose that aerobic metabolism in organisms with cytochrome oxidase has a monophyletic and ancient origin, prior to the appearance of eubacterial oxygenic photosynthetic organisms.

Preliminary Analysis of Lipids and Fatty Acids of Green Bacteria and Chloroflexus aurantiacus

PubMed Central

Kenyon, Christine N.; Gray, Alane M.

1974-01-01

The complex lipids and fatty acids of the seven type species of green bacteria and three strains of Chloroflexus aurantiacus were analyzed. The green bacteria contained lipids that behaved as cardiolipin and phosphatidylglycerol on thin-layer chromatography. They did not contain phosphatidylethanolamine or phosphatidylserine. Similarly, Chloroflexus contained lipids that behaved as phosphatidylglycerol and phosphatidylinositol on thin-layer chromatography and did not contain phosphatidylethanolamine or phosphatidylserine. The green bacteria contained glycolipids I and II of Constantopoulos and Bloch (monogalactosyldiglyceride and a galactose- and rhamnose-containing diglyceride). Chloroflexus exhibited galactose-containing glycolipids that behaved identically with the mono- and digalactosyldiglycerides of spinach on thin-layer chromatography, and each contained galactose as well as at least one other sugar. The fatty acids of both groups of bacteria consisted entirely of saturated and monounsaturated fatty acids. In the green bacteria, myristic, palmitic, and hexadecenoic acids predominated. In Chloroflexus, palmitic, stearic, and oleic acids predominated. The positions of the double bonds in the monounsaturated fatty acids of Chloroflexus indicated synthesis by the anaerobic pathway. The lipid analyses suggest a close relationship between the green bacteria and Chloroflexus and further suggest that these groups of photosynthetic bacteria are more closely related to the blue-green algae than are the purple bacteria. Images PMID:4421249

High-pressure and stark hole-burning studies of chlorosome antennas from Chlorobium tepidum.

PubMed

Wu, H M; Rätsep, M; Young, C S; Jankowiak, R; Blankenship, R E; Small, G J

2000-09-01

Results from high-pressure and Stark hole-burning experiments on isolated chlorosomes from the green sulfur bacterium Chlorobium tepidum are presented, as well as Stark hole-burning data for bacteriochlorophyll c (BChl c) monomers in a poly(vinyl butyral) copolymer film. Large linear pressure shift rates of -0.44 and -0.54 cm(-1)/MPa were observed for the chlorosome BChl c Q(y)-band at 100 K and the lowest Q(y)-exciton level at 12 K, respectively. It is argued that approximately half of the latter shift rate is due to electron exchange coupling between BChl c molecules. The similarity between the above shift rates and those observed for the B875 and B850 BChl a rings of the light-harvesting complexes of purple bacteria is emphasized. For BChl c monomer, fDeltamu++ = 0.35 D, where Deltamu+ is the dipole moment change for the Q(y) transition and f is the local field correction factor. The data establish that Deltamu+ is dominated by the matrix-induced contribution. The change in polarizability (Deltaalpha) for the Q(y) transition of the BChl c monomer is estimated at 19 A(3), which is essentially identical to that of the Chl a monomer. Interestingly, no Stark effects were observed for the lowest exciton level of the chlorosomes (maximum Stark field of 10(5) V/cm). Possible explanations for this are given, and these include consideration of structural models for the chlorosome BChl c aggregates.

Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase–rhodanese fusion protein functions in sulfur assimilation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motl, Nicole; Skiba, Meredith A.; Kabil, Omer

Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO–rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans. The crystal structures ofmore » wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.« less

Extremophiles and chemotrophs as contributors to astrobiological signatures on Europa: a review of biomarkers of sulfate-reducers and other microorganisms

NASA Astrophysics Data System (ADS)

Seckbach, Joseph; Chela-Flores, Julian

2007-09-01

Microorganisms occupy almost every habitable niche on Earth. Some of them may use inorganic or organic substances rather than light as energy sources. We refer to this group as chemotrophs in order to distinguish them from those organisms that use light as an energy source (phototrophs). Both chemotrophs and phototrophs are abundant in environments where one or more physical, or chemical parameters show values far from the lower or upper limits known for life. These ambient habitats are referred to as normal environments. When microorganisms succeed in adapting themselves to harsh niches they are referred to collectively as extremophiles (Seckbach 2004, 2006). We review arguments that militate in favor of microorganisms that in the past and present may have occupied other niches in the Solar System. Among the extremophiles we find representatives of the three domains of life (Bacteria, Archaea, and Eukarya). Some of the possible candidates for life in the Solar System are the extremophiles including chemotrophs, especially sulfur-reducing bacteria (SRB). Another example of chemotrophs are the methanogens. Those microbes are capable of producing methane as a metabolic byproduct of the reduction of carbon dioxide, a process that is called methanogenesis. Searching for new forms of life (within the extraterrestrial regions) is the object of planning within the Cosmic Vision Program of ESA, in collaboration with NASA, and other space agencies. Indeed, sulfur traces on Jupiter's moon Europa detected by the Galileo mission have been conjectured to be endogenic, most likely of cryovolcanic origin, due to their non-uniform distribution in patches. The Galileo space probe first detected the sulfur compounds, as well as revealing that this moon almost certainly has a volcanically heated and potentially habitable ocean hiding beneath Europa surface layer of icy water. In this paper we restrict our attention to possible biomarkers that could signal on Europa the presence extremophiles in general and chemotrophs, especially the presence of sulfur reducers.

Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria.

PubMed

Kikuchi, Yo; Umekage, So

2018-02-01

Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Denitrifying sulfur conversion-associated EBPR: The effect of pH on anaerobic metabolism and performance.

PubMed

Guo, Gang; Wu, Di; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Chen, Guanghao

2017-10-15

The performance of the denitrifying sulfur conversion-associated enhanced biological phosphorus removal (DS-EBPR) process tends to be unstable and requires further study and development. This in turn requires extensive study of the anaerobic metabolism in terms of its stoichiometry and kinetics. This study evaluates the corresponding responses of DS-EBPR to pH, as it significantly influences both stoichiometry and biochemical kinetics. The impacts of five representative pH values ranging between 6.5 and 8.5 on the anaerobic metabolism were investigated, followed by identification of the optimal pH for performance optimization. A mature DS-EBPR sludge was used in the study, enriched with approximately 30% sulfate-reducing bacteria (SRB) and 33% sulfide-oxidizing bacteria (SOB). Through a series of batch tests, the optimal pH range was determined as 7.0-7.5. In this pH range, the anaerobic stoichiometry of phosphorus released/volatile fatty acid (VFA) uptake ratio, sulfate reduction, and internal polymer production (including poly-β-hydroxyalkanoates and polysulfide and/or elemental sulfur) all increased along with the anaerobic kinetics of the VFA uptake ratio. Consequently, phosphorus removal was maximized at this pH range (≥95% vs. 84-93% at other pH values), as was sulfur conversion (16 mg S/L vs. 10-13 mg S/L). This pH range therefore favors the activity and synergy of the key functional bacteria (i.e. SRB and SOB). Anaerobic maintenance tests showed these bacteria required 38-61% less energy for maintenance than that reported for GAOs regardless of pH changes, improving their ability to cope with anaerobic starvation. Adversely, both bacteria showed much lower VFA uptake rates than that of GAOs at all tested pH values (0.03-0.06 vs. 0.2-0.24 mol-C/C-mol biomass/h), possibly revealing the primary cause of frequent instability in the DS-EBPR process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Response to copper of Acidithiobacillus ferrooxidans ATCC 23270 grown in elemental sulfur.

PubMed

Almárcegui, Rodrigo J; Navarro, Claudio A; Paradela, Alberto; Albar, Juan Pablo; von Bernath, Diego; Jerez, Carlos A

2014-11-01

The response of Acidithiobacillus ferrooxidans ATCC 23270 to copper was analyzed in sulfur-grown cells by using quantitative proteomics. Forty-seven proteins showed altered levels in cells grown in the presence of 50 mM copper sulfate. Of these proteins, 24 were up-regulated and 23 down-regulated. As seen before in ferrous iron-grown cells, there was a notorious up-regulation of RND-type Cus systems and different RND-type efflux pumps, indicating that these proteins are very important in copper resistance. Copper also triggered the down-regulation of the major outer membrane porin of A. ferrooxidans in sulfur-grown bacteria, suggesting they respond to the metal by decreasing the influx of cations into the cell. On the contrary, copper in sulfur-grown cells caused an overexpression of putative TadA and TadB proteins known to be essential for biofilm formation in bacteria. Surprisingly, sulfur-grown microorganisms showed increased levels of proteins related with energy generation (rus and petII operons) in the presence of copper. Although rus operon is overexpressed mainly in cells grown in ferrous iron, the up-regulation of rusticyanin in sulfur indicates a possible role for this protein in copper resistance as well. Finally, copper response in A. ferrooxidans appears to be influenced by the substrate being oxidized by the microorganism. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Denitrifying sulfur conversion-associated EBPR: Effects of temperature and carbon source on anaerobic metabolism and performance.

PubMed

Guo, Gang; Wu, Di; Ekama, George A; Hao, Tianwei; Mackey, Hamish Robert; Chen, Guanghao

2018-04-16

The recently developed Denitrifying Sulfur conversion-associated Enhanced Biological Phosphorus Removal (DS-EBPR) process has demonstrated simultaneous removal of organics, nitrogen and phosphorus with minimal sludge production in the treatment of saline/brackish wastewater. Its performance, however, is sensitive to operating and environmental conditions. In this study, the effects of temperature (20, 25, 30 and 35 °C) and the ratio of influent acetate to propionate (100-0, 75-25, 50-50, 25-75 and 0-100%) on anaerobic metabolism were investigated, and their optimal values/controls for performance optimization were identified. A mature DS-EBPR sludge enriched with approximately 30% sulfate-reducing bacteria (SRB) and 33% sulfide-oxidizing bacteria (SOB) was used in this study. The anaerobic stoichiometry of this process was insensitive to temperature or changes in the carbon source. However, an increase in temperature from 20 to 35 °C accelerated the kinetic reactions of the functional bacteria (i.e. SRB and SOB) and raised the energy requirement for their anaerobic maintenance, while a moderate temperature (25-30 °C) resulted in better P removal (≥93%, 18.6 mg P/L removal from total 20 mg P/L in the influent) with a maximum sulfur conversion of approximately 16 mg S/L. These results indicate that the functional bacteria are likely to be mesophilic. When a mixed carbon source (75-25 and 50-50% acetate to propionate ratios) was supplied, DS-EBPR achieved a stable P removal (≥89%, 17.8 mg P/L for 400 mg COD/L in the influent) with sulfur conversions at around 23 mg S/L, suggesting the functional bacteria could effectively adapt to changes in acetate or propionate as the carbon source. The optimal temperatures or carbon source conditions maximized the functional bacteria competition against glycogen-accumulating organisms by favoring their activity and synergy. Therefore, the DS-EBPR process can be optimized by setting the temperature in the appropriate range (25-30 °C) and/or manipulating influent carbon sources. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of Simulated Human Gastrointestinal Digestion of Two Purple-Fleshed Potato Cultivars on Anthocyanin Composition and Cytotoxicity in Colonic Cancer and Non-Tumorigenic Cells

PubMed Central

Kubow, Stan; Iskandar, Michèle M.; Melgar-Bermudez, Emiliano; Sleno, Lekha; Sabally, Kebba; Azadi, Behnam; How, Emily; Prakash, Satya; Burgos, Gabriela; zum Felde, Thomas

2017-01-01

A dynamic human gastrointestinal (GI) model was used to digest cooked tubers from purple-fleshed Amachi and Leona potato cultivars to study anthocyanin biotransformation in the stomach, small intestine and colonic vessels. Colonic Caco-2 cancer cells and non-tumorigenic colonic CCD-112CoN cells were tested for cytotoxicity and cell viability after 24 h exposure to colonic fecal water (FW) digests (0%, 10%, 25%, 75% and 100% FW in culture media). After 24 h digestion, liquid chromatography-mass spectrometry identified 36 and 15 anthocyanin species throughout the GI vessels for Amachi and Leona, respectively. The total anthocyanin concentration was over thirty-fold higher in Amachi compared to Leona digests but seven-fold higher anthocyanin concentrations were noted for Leona versus Amachi in descending colon digests. Leona FW showed greater potency to induce cytotoxicity and decrease viability of Caco-2 cells than observed with FW from Amachi. Amachi FW at 100% caused cytotoxicity in non-tumorigenic cells while FW from Leona showed no effect. The present findings indicate major variations in the pattern of anthocyanin breakdown and release during digestion of purple-fleshed cultivars. The differing microbial anthocyanin metabolite profiles in colonic vessels between cultivars could play a significant role in the impact of FW toxicity on tumor and non-tumorigenic cells. PMID:28850070

Exploring the Sulfur Nutrient Cycle Using the Winogradsky Column

ERIC Educational Resources Information Center

Rogan, Brian; Lemke, Michael; Levandowsky, Michael; Gorrell, Thomas

2005-01-01

The Winogradsky column demonstrates how the metabolic diversity of prokaryotes transforms sulfur to different forms with varying redox states and hence, supplies nutrients and/or energy to the organism. The Winogardsky column is an excellent way to show that not all bacteria are pathogens and they have an important role in the geochemical cycling…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tabita, Fred Robert

The overall objective of this project is to determine the mechanism by which a transcriptional activator protein affects CO 2 fixation (cbb) gene expression in nonsulfur purple photosynthetic bacteria, with special emphasis to Rhodobacter sphaeroides and with comparison to Rhodopseudomonas palustris. These studies culminated in several publications which indicated that additional regulators interact with the master regulator CbbR in both R. sphaeroides and R. palustris. In addition, the interactive control of the carbon and nitrogen assimilatory pathways was studied and unique regulatory signals were discovered.

Evaluating the Nature of So-Called S*-State Feature in Transient Absorption of Carotenoids in Light-Harvesting Complex 2 (LH2) from Purple Photosynthetic Bacteria

PubMed Central

2016-01-01

Carotenoids are a class of natural pigments present in all phototrophic organisms, mainly in their light-harvesting proteins in which they play roles of accessory light absorbers and photoprotectors. Extensive time-resolved spectroscopic studies of these pigments have revealed unexpectedly complex photophysical properties, particularly for carotenoids in light-harvesting LH2 complexes from purple bacteria. An ambiguous, optically forbidden electronic excited state designated as S* has been postulated to be involved in carotenoid excitation relaxation and in an alternative carotenoid-to-bacteriochlorophyll energy transfer pathway, as well as being a precursor of the carotenoid triplet state. However, no definitive and satisfactory origin of the carotenoid S* state in these complexes has been established, despite a wide-ranging series of studies. Here, we resolve the ambiguous origin of the carotenoid S* state in LH2 complex from Rba. sphaeroides by showing that the S* feature can be seen as a combination of ground state absorption bleaching of the carotenoid pool converted to cations and the Stark spectrum of neighbor neutral carotenoids, induced by temporal electric field brought by the carotenoid cation–bacteriochlorophyll anion pair. These findings remove the need to assign an S* state, and thereby significantly simplify the photochemistry of carotenoids in these photosynthetic antenna complexes. PMID:27726397

Toward extending photosynthetic biosignatures: quantum dynamics calculation of light harvesting complexes

NASA Astrophysics Data System (ADS)

Komatsu, Yu; Umemura, Masayuki; Shoji, Mitsuo; Kayanuma, Megumi; Yabana, Kazuhiro; Shiraishi, Kenji

For detecting life from reflectance spectra on extrasolar planets, several indicators called surface biosignatures have been proposed. One of them is the vegetation red edge (VRE) which derives from surface vegetation. VRE is observed in 700-750 nm on the Earth, but there is no guarantee that exovegetation show the red edge in this wavelength. Therefore it is necessary to check the validity of current standards of VRE as the signatures. In facts, M stars (cooler than Sun) will be the main targets in future missions, it is significantly important to know on the fundamental mechanisms in photosynthetic organism such as purple bacteria which absorb longer wavelength radiation. We investigated light absorptions and excitation energy transfers (EETs) in light harvesting complexes in purple bacteria (LH2s) by using quantum dynamics simulations. In LH2, effective EET is accomplished by corporative electronic excitation of the pigments. In our theoretical model, a dipole-dipole approximation was used for the electronic interactions between pigment excitations. Quantum dynamics simulations were performed according to Liouville equation to examine the EET process. The calculated oscillator strength and the transfer time between LH2 were good agreement with the experimental values. As the system size increases, the absorption bands shifted longer and the transfer velocities became larger. When two pigments in a LHC were exchanged to another pigments with lower excitation energy, faster and intensive light collection were observed.

The Modulatory Effect of Anthocyanins from Purple Sweet Potato on Human Intestinal Microbiota in Vitro.

PubMed

Zhang, Xin; Yang, Yang; Wu, Zufang; Weng, Peifang

2016-03-30

In order to investigate the modulatory effect of purple sweet potato anthocyanins (PSPAs) on human intestinal microbiota, PSPAs were prepared by column chromatography and their influence on intestinal microbiota was analyzed by monitoring the bacterial populations and analyzing short-chain fatty acid (SCFA) concentrations at different time points. The numbers (log10 cell/mL) of Bifidobacterium and Lactobacillus/Enterococcus spp., Bacteroides-Prevotella, Clostridium histolyticum, and total bacteria after 24 h of culture in anaerobic fermentation broth containing PSPAs were 8.44 ± 0.02, 8.30 ± 0.01, 7.80 ± 0.03, 7.60 ± 0.03, and 9.00 ± 0.02, respectively, compared with 8.21 ± 0.03, 8.12 ± 0.02, 7.95 ± 0.02, 7.77 ± 0.02, and 9.01 ± 0.03, respectively, in the controls. The results showed that PSPAs induced the proliferation of Bifidobacterium and Lactobacillus/Enterococcus spp., inhibited the growth of Bacteroides-Prevotella and Clostridium histolyticum, and did not affect the total bacteria number. Total SCFA concentrations in the cultures with PSPAs were significantly higher than in the controls (P < 0.05). Moreover, during the fermentation, the PSPAs were partially fragmented to phenolic acids, which may exert a better effect on intestinal microecology, suggesting that PSPAs may have prebiotic-like activity by generating SCFAs and modulating the intestinal microbiota, contributing to improvements in human health.

Evaluating the nature of so-called S*-State feature in transient absorption of carotenoids in light-harvesting complex 2 (LH2) from purple photosynthetic bacteria

DOE PAGES

Niedzwiedzki, Dariusz M.; Hunter, C. Neil; Blankenship, Robert E.

2016-10-11

Carotenoids are a class of natural pigments present in all phototrophic organisms, mainly in their light-harvesting proteins in which they play roles of accessory light absorbers and photoprotectors. Extensive time-resolved spectroscopic studies of these pigments have revealed unexpectedly complex photophysical properties, particularly for carotenoids in light-harvesting LH2 complexes from purple bacteria. An ambiguous, optically forbidden electronic excited state designated as S* has been postulated to be involved in carotenoid excitation relaxation and in an alternative carotenoid-to-bacteriochlorophyll energy transfer pathway, as well as being a precursor of the carotenoid triplet state. However, no definitive and satisfactory origin of the carotenoid S*more » state in these complexes has been established, despite a wide-ranging series of studies. Here, we resolve the ambiguous origin of the carotenoid S* state in LH2 complex from Rba. sphaeroides by showing that the S* feature can be seen as a combination of ground state absorption bleaching of the carotenoid pool converted to cations and the Stark spectrum of neighbor neutral carotenoids, induced by temporal electric field brought by the carotenoid cation- bacteriochlorophyll anion pair. Lastly, these findings remove the need to assign an S* state, and thereby significantly simplify the photochemistry of carotenoids in these photosynthetic antenna complexes.« less

Evaluating the nature of so-called S*-State feature in transient absorption of carotenoids in light-harvesting complex 2 (LH2) from purple photosynthetic bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niedzwiedzki, Dariusz M.; Hunter, C. Neil; Blankenship, Robert E.

Carotenoids are a class of natural pigments present in all phototrophic organisms, mainly in their light-harvesting proteins in which they play roles of accessory light absorbers and photoprotectors. Extensive time-resolved spectroscopic studies of these pigments have revealed unexpectedly complex photophysical properties, particularly for carotenoids in light-harvesting LH2 complexes from purple bacteria. An ambiguous, optically forbidden electronic excited state designated as S* has been postulated to be involved in carotenoid excitation relaxation and in an alternative carotenoid-to-bacteriochlorophyll energy transfer pathway, as well as being a precursor of the carotenoid triplet state. However, no definitive and satisfactory origin of the carotenoid S*more » state in these complexes has been established, despite a wide-ranging series of studies. Here, we resolve the ambiguous origin of the carotenoid S* state in LH2 complex from Rba. sphaeroides by showing that the S* feature can be seen as a combination of ground state absorption bleaching of the carotenoid pool converted to cations and the Stark spectrum of neighbor neutral carotenoids, induced by temporal electric field brought by the carotenoid cation- bacteriochlorophyll anion pair. Lastly, these findings remove the need to assign an S* state, and thereby significantly simplify the photochemistry of carotenoids in these photosynthetic antenna complexes.« less

Optimization of biological sulfide removal in a CSTR bioreactor.

PubMed

Roosta, Aliakbar; Jahanmiri, Abdolhossein; Mowla, Dariush; Niazi, Ali; Sotoodeh, Hamidreza

2012-08-01

In this study, biological sulfide removal from natural gas in a continuous bioreactor is investigated for estimation of the optimal operational parameters. According to the carried out reactions, sulfide can be converted to elemental sulfur, sulfate, thiosulfate, and polysulfide, of which elemental sulfur is the desired product. A mathematical model is developed and was used for investigation of the effect of various parameters on elemental sulfur selectivity. The results of the simulation show that elemental sulfur selectivity is a function of dissolved oxygen, sulfide load, pH, and concentration of bacteria. Optimal parameter values are calculated for maximum elemental sulfur selectivity by using genetic algorithm as an adaptive heuristic search. In the optimal conditions, 87.76% of sulfide loaded to the bioreactor is converted to elemental sulfur.

New Targets and Inhibitors of Mycobacterial Sulfur Metabolism§

PubMed Central

Paritala, Hanumantharao; Carroll, Kate S.

2015-01-01

The identification of new antibacterial targets is urgently needed to address multidrug resistant and latent tuberculosis infection. Sulfur metabolic pathways are essential for survival and the expression of virulence in many pathogenic bacteria, including Mycobacterium tuberculosis. In addition, microbial sulfur metabolic pathways are largely absent in humans and therefore, represent unique targets for therapeutic intervention. In this review, we summarize our current understanding of the enzymes associated with the production of sulfated and reduced sulfur-containing metabolites in Mycobacteria. Small molecule inhibitors of these catalysts represent valuable chemical tools that can be used to investigate the role of sulfur metabolism throughout the Mycobacterial lifecycle and may also represent new leads for drug development. In this light, we also summarize recent progress made in the development of inhibitors of sulfur metabolism enzymes. PMID:23808874

Speciation of sulfur from filamentous microbial mats from sulfidic cave springs using X-ray absorption near-edge spectroscopy.

PubMed

Engel, Annette Summers; Lichtenberg, Henning; Prange, Alexander; Hormes, Josef

2007-04-01

Most transformations within the sulfur cycle are controlled by the biosphere, and deciphering the abiotic and biotic nature and turnover of sulfur is critical to understand the geochemical and ecological changes that have occurred throughout the Earth's history. Here, synchrotron radiation-based sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy is used to examine sulfur speciation in natural microbial mats from two aphotic (cave) settings. Habitat geochemistry, microbial community compositions, and sulfur isotope systematics were also evaluated. Microorganisms associated with sulfur metabolism dominated the mats, including members of the Epsilonproteobacteria and Gammaproteobacteria. These groups have not been examined previously by sulfur K-edge XANES. All of the mats consisted of elemental sulfur, with greater contributions of cyclo-octasulfur (S8) compared with polymeric sulfur (Smicro). While this could be a biological fingerprint for some bacteria, the signature may also indicate preferential oxidation of Smicro and S8 accumulation. Higher sulfate content correlated to less S8 in the presence of Epsilonproteobacteria. Sulfur isotope compositions confirmed that sulfur content and sulfur speciation may not correlate to microbial metabolic processes in natural samples, thereby complicating the interpretation of modern and ancient sulfur records.

Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms

PubMed Central

Gruber-Vodicka, Harald Ronald; Dirks, Ulrich; Leisch, Nikolaus; Stoecker, Kilian; Bulgheresi, Silvia; Heindl, Niels Robert; Horn, Matthias; Lott, Christian; Loy, Alexander; Wagner, Michael; Ott, Jörg

2011-01-01

Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria—the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as “Candidatus Riegeria galateiae” based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal–chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells. PMID:21709249

Isotopic Approaches to Allying Productivity and Sulfur Metabolism in Three Symbiotic Hydrothermal Vent Molluscs

NASA Astrophysics Data System (ADS)

Beinart, R.; Gartman, A.; Sanders, J. G.; Luther, G. W.; Girguis, P. R.

2012-12-01

Symbioses between animals and chemosynthetic bacteria predominate at hydrothermal vents. In these associations, the endosymbiotic bacteria utilize chemical reductants for the energy to support autotrophy, providing primary nutrition for the host. Despite their ubiquity at vents worldwide, little is known about the rates of productivity of these symbioses under different physico-chemical regimes or how their metabolism effects the local geochemical environment. To address this matter, we used high-pressure flow through incubations and stable isotopic tracers to maintain three genera of symbiotic mollusc - the gastropods Alviniconcha and Ifremeria, and the mussel Bathymodiolus - at vent-like conditions. Via the incorporation of isotopically labeled compounds, we assessed their productivity when using different reduced sulfur species as reductants. Using cyclic voltammetry, mass spectrometry and discrete geochemical analyses, we concurrently measured their effect on sulfur flux from the vessels. We found that the symbionts of all three genera can support autotrophy with hydrogen sulfide and thiosulfate, though at different rates. Additionally, by examining the rate of isotopic incorporation into biomass, we revealed intra-generic variability in productivity among the individuals in our experimental assemblages that are likely related to differences in the geochemical regime along the length of reactor. These geochemical gradients are due to the activity of other individuals within the vessel, since those organisms closest to the influent of the vent-like water had the highest measured carbon incorporation. Finally, we measured the uptake and excretion of sulfur species, which illustrate the degree to which these symbioses might impact local sulfur chemistry in situ. These experiments show that A) access to particular sulfur species differentially affects the productivity of vent symbioses, suggesting that competition for these substrates, both within and between host genera, could play a role in the structure of these communities, and B) that these symbioses could play a role in altering the local geochemical regime, influencing the activity and distribution of other associated microorganisms including free-living bacteria.

Hydrogen sulfide production from cysteine and homocysteine by periodontal and oral bacteria.

PubMed

Yoshida, Akihiro; Yoshimura, Mamiko; Ohara, Naoya; Yoshimura, Shigeru; Nagashima, Shiori; Takehara, Tadamichi; Nakayama, Koji

2009-11-01

Hydrogen sulfide is one of the predominant volatile sulfur compounds (VSCs) produced by oral bacteria. This study developed and evaluated a system for detecting hydrogen sulfide production by oral bacteria. L-methionine-alpha-deamino-gamma-mercaptomethane-lyase (METase) and beta carbon-sulfur (beta C-S) lyase were used to degrade homocysteine and cysteine, respectively, to produce hydrogen sulfide. Enzymatic reactions resulting in hydrogen sulfide production were assayed by reaction with bismuth trichloride, which forms a black precipitate when mixed with hydrogen sulfide. The enzymatic activities of various oral bacteria that result in hydrogen sulfide production and the capacity of bacteria from periodontal sites to form hydrogen sulfide in reaction mixtures containing L-cysteine or DL-homocysteine were assayed. With L-cysteine as the substrate, Streptococcus anginosus FW73 produced the most hydrogen sulfide, whereas Porphyromonas gingivalis American Type Culture Collection (ATCC) 33277 and W83 and Fusobacterium nucleatum ATCC 10953 produced approximately 35% of the amount produced by the P. gingivalis strains. Finally, the hydrogen sulfide found in subgingival plaque was analyzed. Using bismuth trichloride, the hydrogen sulfide produced by oral bacteria was visually detectable as a black precipitate. Hydrogen sulfide production by oral bacteria was easily analyzed using bismuth trichloride. However, further innovation is required for practical use.

Treatment of high-strength sulfate wastewater using an autotrophic biocathode in view of elemental sulfur recovery.

PubMed

Blázquez, Enric; Gabriel, David; Baeza, Juan Antonio; Guisasola, Albert

2016-11-15

Treatment of high-strength sulfate wastewaters is becoming a research issue not only for its optimal management but also for the possibility of recovering elemental sulfur. Moreover, sulfate-rich wastewater production is expected to grow due to the increased SO 2 emission contained in flue gases which are treated by chemical absorption in water. Bioelectrochemical systems (BESs) are a promising alternative for sulfate reduction with a lack of electron donor, since hydrogen can be generated in situ from electricity. However, complete sulfate reduction leads to hydrogen sulfide as final sulfur compound. This work is the first to demonstrate that, in addition to an efficient sulfate-rich wastewater treatment, elemental sulfur could be recovered in a biocathode of a BES under oxygen limiting conditions. The key of the process is the biological oxidation of sulfide to elemental sulfur simultaneously to the sulfate reduction in the cathode using the oxygen produced in the anode that diffuses through the membrane. High sulfate reduction rates (up to 388 mg S-SO 4 2-  L -1  d -1 ) were observed linked to a low production of sulfide. Accumulation of elemental sulfur over graphite fibers of the biocathode was demonstrated by energy dispersive spectrometry, discarding the presence of metal sulfides. Microbial community analysis of the cathode biofilm demonstrated the presence of sulfate-reducing bacteria (mainly Desulfovibrio sp.) and sulfide-oxidizing bacteria (mainly Sulfuricurvum sp.). Hence, this biocathode allows simultaneous biological sulfate reduction and biological sulfide oxidation to elemental sulfur, opening up a novel process for recovering sulfur from sulfate-rich wastewaters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Prediction of periodontopathic bacteria in dental plaque of periodontal healthy subjects by measurement of volatile sulfur compounds in mouth air.

PubMed

Kishi, Mitsuo; Ohara-Nemoto, Yuko; Takahashi, Masahiro; Kishi, Kayo; Kimura, Shigenobu; Aizawa, Fumie; Yonemitsu, Masami

2013-03-01

The aim of this study was to determine whether measurements of volatile sulfur compounds (VSCs) are useful to predict colonization of periodontopathic bacteria. For this purpose, we assessed the relationships among distributions of 4 species of periodontopathic bacteria in tongue coating and dental plaque, oral conditions including VSC concentration in mouth air, and smoking habit of periodontal healthy young subjects. The subjects were 108 young adults (mean age, 23.5±2.56 years) without clinical periodontal pockets. Information regarding smoking habit was obtained by interview. After VSC concentration in mouth, air was measured with a portable sulfide monitor (Halimeter(®)), non-stimulated saliva flow and dental caries status were assessed, and tongue coating and dental plaque samples were collected from the subjects. The tongue coating samples were weighed to determine the amount. The colonization of Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, and Treponema denticola in both tongue coating and plaque samples was investigated using species-specific polymerase chain reaction assays. Significant relationships were observed between the colonization of periodontopathic bacteria in tongue coating and plaque samples, especially that of P. gingivalis. VSC concentration showed the most significant association with colonization of P. gingivalis in both tongue coating and dental plaque. Logistic regression analysis demonstrated that the adjusted partial correlation coefficient [Exp(B)] values for VSC concentration with the colonization of P. gingivalis, P. intermedia, and T. denticola in dental plaque were 135, 35.4 and 10.4, respectively. In addition, smoking habit was also shown to be a significant variable in regression models [Exp(B)=6.19, 8.92 and 2.53, respectively]. Therefore, receiver operating characteristic analysis was performed to predict the colonization of periodontal bacteria in dental plaque in the subjects divided by smoking habit. Based on our results, we found cut-off values that indicated likelihood ratios (LR) within the efficient range for positive findings in both groups. The present results demonstrated that measurement of VSC concentration in mouth air is a useful method to predict the presence of colonization of some periodontopathic bacteria in dental plaque. Copyright © 2012 Elsevier Ltd. All rights reserved.

Plasma deposition of antimicrobial coating on organic polymer

NASA Astrophysics Data System (ADS)

Rżanek-Boroch, Zenobia; Dziadczyk, Paulina; Czajkowska, Danuta; Krawczyk, Krzysztof; Fabianowski, Wojciech

2013-02-01

Organic materials used for packing food products prevent the access of microorganisms or gases, like oxygen or water vapor. To prolong the stability of products, preservatives such as sulfur dioxide, sulfites, benzoates, nitrites and many other chemical compounds are used. To eliminate or limit the amount of preservatives added to food, so-called active packaging is sought for, which would limit the development of microorganisms. Such packaging can be achieved, among others, by plasma modification of a material to deposit on its surface substances inhibiting the growth of bacteria. In this work plasma modification was carried out in barrier discharge under atmospheric pressure. Sulfur dioxide or/and sodium oxide were used as the coating precursors. As a result of bacteriological studies it was found that sulfur containing coatings show a 16% inhibition of Salmonella bacteria growth and 8% inhibition of Staphylococcus aureus bacteria growth. Sodium containing coatings show worse (by 10%) inhibiting properties. Moreover, films with plasma deposited coatings show good sealing properties against water vapor. Contribution to the Topical Issue "13th International Symposium on High Pressure Low Temperature Plasma Chemistry (Hakone XIII)", Edited by Nicolas Gherardi, Henryca Danuta Stryczewska and Yvan Ségui.

Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan.

PubMed

Yang, Shan-Hua; Chiang, Pei-Wen; Hsu, Tin-Chang; Kao, Shuh-Ji; Tang, Sen-Lin

2016-01-01

Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75-4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems.

Isolation and Characterization of Strains CVO and FWKO B, Two Novel Nitrate-Reducing, Sulfide-Oxidizing Bacteria Isolated from Oil Field Brine

PubMed Central

Gevertz, Diane; Telang, Anita J.; Voordouw, Gerrit; Jenneman, Gary E.

2000-01-01

Bacterial strains CVO and FWKO B were isolated from produced brine at the Coleville oil field in Saskatchewan, Canada. Both strains are obligate chemolithotrophs, with hydrogen, formate, and sulfide serving as the only known energy sources for FWKO B, whereas sulfide and elemental sulfur are the only known electron donors for CVO. Neither strain uses thiosulfate as an energy source. Both strains are microaerophiles (1% O2). In addition, CVO grows by denitrification of nitrate or nitrite whereas FWKO B reduces nitrate only to nitrite. Elemental sulfur is the sole product of sulfide oxidation by FWKO B, while CVO produces either elemental sulfur or sulfate, depending on the initial concentration of sulfide. Both strains are capable of growth under strictly autotrophic conditions, but CVO uses acetate as well as CO2 as its sole carbon source. Neither strain reduces sulfate; however, FWKO B reduces sulfur and displays chemolithoautotrophic growth in the presence of elemental sulfur, hydrogen, and CO2. Both strains grow at temperatures between 5 and 40°C. CVO is capable of growth at NaCl concentrations as high as 7%. The present 16s rRNA analysis suggests that both strains are members of the epsilon subdivision of the division Proteobacteria, with CVO most closely related to Thiomicrospira denitrifcans and FWKO B most closely related to members of the genus Arcobacter. The isolation of these two novel chemolithotrophic sulfur bacteria from oil field brine suggests the presence of a subterranean sulfur cycle driven entirely by hydrogen, carbon dioxide, and nitrate. PMID:10831429

The Effect of Temperature and Hydrogen Limited Growth on the Fractionation of Sulfur Isotopes by Thermodesulfatator indicus, a Deep-sea Hydrothermal Vent Sulfate-Reducing Bacterium

NASA Astrophysics Data System (ADS)

Hoek, J.; Reysenbach, A.; Habicht, K.; Canfield, D. E.

2004-12-01

Sulfate-reducing bacteria fractionate sulfur isotopes during dissimilatory sulfate reduction, producing sulfide depleted in 34S. Although isotope fractionation during sulfate reduction of pure cultures has been extensively studied, most of the research to date has focused on mesophilic sulfate reducers, particularly for the species Desulfovibrio desulfuricans. Results from these studies show that: 1) fractionations range from 3-46‰ with an average around 18‰ , 2) when organic electron donors are utilized, the extent of fractionation is dependent on the rate of sulfate reduction, with decreasing fractionations observed with higher specific rates, 3) fractionations are suppressed with low sulfate concentrations, and when hydrogen is used as the electron donor. High specific sulfate-reduction rates are encountered when sulfate-reducing bacteria metabolize at their optimal temperature and under non-limiting substrate conditions. Changes in both temperature and substrate availability could shift fractionations from those expressed under optimal growth conditions. Sulfate reducers may frequently experience substrate limitation and sub-optimal growth temperatures in the environment. Therefore it is important to understand how sulfate-reducing bacteria fractionate sulfur isotopes under conditions that more closely resemble the restrictions imposed by the environment. In this study the fractionation of sulfur isotopes by Thermodesulfatator indicus was explored during sulfate reduction under a wide range of temperatures and with both hydrogen-saturating and hydrogen-limited conditions. T. indicus is a thermophilic (temperature optimum = 70° C) chemolithotrophic sulfate-reducing bacterium, which was recently isolated from a deep-sea hydrothermal vent on the Central Indian Ridge. This bacterium represents the type species of a new genus and to date is the most deeply branching sulfate-reducing bacterium known. T. indicus was grown in carbonate-buffered salt-water medium with H2 as the sole electron donor, and CO2 as primary carbon source. The fractionation of sulfur isotopes was measured in batch cultures and in a thermal gradient block over the full temperature range of growth (40-80° C). For experiments in the gradient block, cell-specific rates of sulfate reduction increased with increasing temperatures to 70° C after which sulfate-reduction rates rapidly decreased. The range of fractionations (1.5-10‰ ) was typical for growth with hydrogen as the electron donor. Fractionations decreased with increasing temperature from 40--60° C, and increased with increasing temperatures from 60-80° C. Growth under H2-limited conditions in a fed-batch culture revealed high fractionations of 24-37‰ . This is the first report of sulfur isotope fractionation under H2 limited growth and indicates that large fractionations are produced when H2 is supplied as a limiting substrate. Our results suggest that fractionation is controlled by the competition of forward and reverse enzymatic reaction rates during sulfate reduction and by sulfate transport into the cell.

Electricity generation by Rhodopseudomonas palustris DX-1.

PubMed

Xing, Defeng; Zuo, Yi; Cheng, Shaoan; Regan, John M; Logan, Bruce E

2008-06-01

Bacteria able to generate electricity in microbial fuel cells (MFCs) are of great interest, but there are few strains capable of high power production in these systems. Here we report that the phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris DX-1, isolated from an MFC, produced electricity at higher power densities (2720 +/- 60 mW/m2) than mixed cultures in the same device. While Rhodopseudomonas species are known for their ability to generate hydrogen, they have not previously been shown to generate power in an MFC, and current was generated without the need for light or hydrogen production. Strain DX-1 utilizes a wide variety of substrates (volatile acids, yeast extract, and thiosulfate) for power production in different metabolic modes, making it highly useful for studying power generation in MFCs and generating power from a range of simple and complex sources of organic matter. These results demonstrate that a phototrophic purple nonsulfur bacterium can efficiently generate electricity by direct electron transfer in MFCs, providing another model microorganism for MFC investigations.

Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay.

PubMed

Martínez, Patricio; Gálvez, Sebastián; Ohtsuka, Norimasa; Budinich, Marko; Cortés, María Paz; Serpell, Cristián; Nakahigashi, Kenji; Hirayama, Akiyoshi; Tomita, Masaru; Soga, Tomoyoshi; Martínez, Servet; Maass, Alejandro; Parada, Pilar

2013-02-01

In this study, we present the first metabolic profiles for two bioleaching bacteria using capillary electrophoresis coupled with mass spectrometry. The bacteria, Acidithiobacillus ferrooxidans strain Wenelen (DSM 16786) and Acidithiobacillus thiooxidans strain Licanantay (DSM 17318), were sampled at different growth phases and on different substrates: the former was grown with iron and sulfur, and the latter with sulfur and chalcopyrite. Metabolic profiles were scored from planktonic and sessile states. Spermidine was detected in intra- and extracellular samples for both strains, suggesting it has an important role in biofilm formation in the presence of solid substrate. The canonical pathway for spermidine synthesis seems absent as its upstream precursor, putrescine, was not present in samples. Glutathione, a catalytic activator of elemental sulfur, was identified as one of the most abundant metabolites in the intracellular space in A. thiooxidans strain Licanantay, confirming its participation in the sulfur oxidation pathway. Amino acid profiles varied according to the growth conditions and bioleaching species. Glutamic and aspartic acid were highly abundant in intra- and extracellular extracts. Both are constituents of the extracellular matrix, and have a probable role in cell detoxification. This novel metabolomic information validates previous knowledge from in silico metabolic reconstructions based on genomic sequences, and reveals important biomining functions such as biofilm formation, energy management and stress responses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0443-3) contains supplementary material, which is available to authorized users.

m-Cresol purple functionalized surface enhanced Raman scattering paper chips for highly sensitive detection of pH in the neutral pH range.

PubMed

Zou, Xinxin; Wang, Yunqing; Liu, Wanhui; Chen, Lingxin

2017-06-26

Herein, a pH sensitive paper SERS chip was prepared by selecting m-cresol purple, a molecule with halochromic properties in the neutral pH range as a Raman reporter. The adsorbed m-cresol purple underwent a reversible change in its electronic configuration from a non-resonant species to a resonant species, which resulted in a significant Raman signal intensity variation due to the transformation of the sensing mode from SERS to surface-enhanced resonance Raman scattering (SERRS). The chips have a sensitive pH range of 6.0 to 8.0 and exhibited good performance for the detection of natural water samples with detection precision of approximately 0.03 pH units, suggesting great potential for environmental pH monitoring applications.

Analysis of Ecological Distribution and Genomic Content from a Clade of Bacteroidetes Endemic to Sulfidic Environments

NASA Astrophysics Data System (ADS)

Zhou, K.; Sylvan, J. B.; Hallam, S. J.

2017-12-01

The Bacteroidetes are a ubiquitous phylum of bacteria found in a wide variety of habitats. Marine Bacteroidetes are known to utilize complex carbohydrates and have a potentially important role in the global carbon cycle through processing these compounds, which are not digestible by many other microbes. Some members of the phylum are known to perform denitrification and are facultative anaerobes, but Bacteroidetes are not known to participate in sulfur redox cycling. Recently, it was shown that a clade of uncultured Bacteroidetes, including the VC2.1_Bac22 group, appears to be endemic to sulfidic environments, including hydrothermal vent sulfide chimneys, sediments and marine water column oxygen minimum zones (OMZs). This clade, dubbed the Sulfiphilic Bacteroidetes, is not detected in 16S rRNA amplicon studies from non-sulfidic environments. To test the hypothesis that the Sulphiphilic Bacteroidetes are involved in sulfur redox chemistry, we updated our meta-analysis of the clade using 16s rRNA sequences from public databases and employed single-cell genomics to survey their genomic potential using 19 single amplified genomes (SAGs) isolated from the seasonally anoxic Saanich Inlet, a seasonally hypoxic basin in British Columbia. Initial analysis of these SAGs indicates the Sulphiphilic Bacteroidetes may perform sulfur redox reactions using a three gene psrABC operon encoding the polysulfide reductase enzyme complex with a thiosulfate sulfurtransferase (rhodanese), which putatively uses cyanide to convert thiosulfate to sulfite, just upstream. Interestingly, this is the same configuration as discovered recently in some Marine Group A bacteria. Further aspects of the Sulphiphilic Bacteroidetes' genomic potential will be presented in light of their presence in sulfidic environments.

Red-purple flower color and delphinidin-type pigments in the flowers of Pueraria lobata (Leguminosae).

PubMed

Tatsuzawa, Fumi; Tanikawa, Natsu; Nakayama, Masayoshi

2017-05-01

A previously undescribed acylated anthocyanin was extracted from the red-purple flowers of Pueraria lobata with 5% HOAc-H 2 O, and determined to be petunidin 3-O-(β-glucopyranoside)-5-O-[6-O-(malonyl)-β-glucopyranoside], by chemical and spectroscopic methods. In addition, two known acylated anthocyanins, delphinidin 3-O-(β-glucopyranoside)-5-O-[6-O-(malonyl)-β-glucopyranoside] and malvidin 3-O-(β-glucopyranoside)-5-O-[6-O-(malonyl)-β-glucopyranoside] were identified. Delphinidin 3,5-di-glucoside, petunidin 3,5-di-glucoside, and malvidin 3,5-di-glucoside, have been known as major components of P. lobata in the former study. However, malonyl esters amounts were detected over 10 times compared with non-malonyl esters amounts. In those anthocyanins the most abundant anthocyanin was petunidin 3-O-(β-glucopyranoside)-5-O-[6-O-(malonyl)-β-glucopyranoside] in total flowers. On the visible absorption spectral curve of fresh red-purple petals, one characteristic absorption maximum was observed at 520 nm, which is similar to those of flowers containing pelargonidin derivatives. In contrast, the absorption spectral curve of old violet petals was observed at 500(sh), 536, 564(sh), and 613(sh) nm, which are similar to those of violet flowers containing delphinidin-type pigments. Pressed juices of both fresh red-purple petals and old violet petals had pH5.2 and 5.5 respectively, and had the same flavonoid constitution. Crude fresh red-purple petal pigments extracted by pH 2.2 and pH 5.2 buffers exhibited the same color and spectral curves as fresh red-purple petals and old violet petals, respectively. Moreover, in a cross-TLC experiment of crude extracted pigments, red-purple color was exhibited by the anthocyanin region and the crossed region of anthocyanins and isoflavone. Thus, it may be assumed that the unusually low pH in the vacuole of fresh petals plays an important role to form red-purple flower color against weak acidic pH in the vacuole of old violet P. lobata petals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetically engineered acidophilic heterotrophic bacteria by bacteriophage transduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, T.E.; Bruhn, D.F.; Bulmer, D.F.

1989-05-10

A bacteriophage capable of infecting acidophilic heterotrophic bacteria and processes for genetically engineering acidophilic bacteria for biomining or sulfur removal from coal are disclosed. The bacteriophage is capable of growth in cells existing at pH at or below 3.0. Lytic forms of the phage introduced into areas experiencing acid drainage kill the bacteria causing such drainage. Lysogenic forms of the phage having genes for selective removal of metallic or nonmetallic elements can be introduced into acidophilic bacteria to effect removal of the desired element from ore or coal. 1 fig., 1 tab.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wrighton, Kelly C.; Thomas, Brian C.; Sharon, I.

BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like type II and III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO2 fixation, a pathway previously not described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-typemore » hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.« less

Bioaugmentation of Lactobacillus delbrueckii ssp. bulgaricus TISTR 895 to enhance bio-hydrogen production of Rhodobacter sphaeroides KKU-PS5.

PubMed

Laocharoen, Sucheera; Reungsang, Alissara; Plangklang, Pensri

2015-01-01

Bioaugmentation or an addition of the desired microorganisms or specialized microbial strains into the anaerobic digesters can enhance the performance of microbial community in the hydrogen production process. Most of the studies focused on a bioaugmentation of native microorganisms capable of producing hydrogen with the dark-fermentative hydrogen producers while information on bioaugmentation of purple non-sulfur photosynthetic bacteria (PNSB) with lactic acid-producing bacteria (LAB) is still limited. In our study, bioaugmentation of Rhodobacter sphaeroides KKU-PS5 with Lactobacillus delbrueckii ssp. bulgaricus TISTR 895 was conducted as a method to produce hydrogen. Unfortunately, even though well-characterized microorganisms were used in the fermentation system, a cultivation of two different organisms in the same bioreactor was still difficult because of the differences in their metabolic types, optimal conditions, and nutritional requirements. Therefore, evaluation of the physical and chemical factors affecting hydrogen production of PNSB augmented with LAB was conducted using a full factorial design followed by response surface methodology (RSM) with central composite design (CCD). A suitable LAB/PNSB ratio and initial cell concentration were found to be 1/12 (w/w) and 0.15 g/L, respectively. The optimal initial pH, light intensity, and Mo concentration obtained from RSM with CCD were 7.92, 8.37 klux and 0.44 mg/L, respectively. Under these optimal conditions, a cumulative hydrogen production of 3396 ± 66 mL H2/L, a hydrogen production rate (HPR) of 9.1 ± 0.2 mL H2/L h, and a hydrogen yield (HY) of 9.65 ± 0.23 mol H2/mol glucose were obtained. KKU-PS5 augmented with TISTR 895 produced hydrogen from glucose at a relatively high HY, 9.65 ± 0.23 mol H2/mol glucose, i.e., 80 % of the theoretical yield. The ratio of the strains TISTR 895/KKU-PS5 and their initial cell concentrations affected the rate of lactic acid production and its consumption. A suitable LAB/PNSB ratio and initial cell concentration could balance the lactic acid production rate and its consumption in order to avoid lactic acid accumulation in the fermentation system. Through use of appropriate environmental conditions for bioaugmentation of PNSB with LAB, a hydrogen production could be enhanced.

Microbial desulfurization of coal

NASA Technical Reports Server (NTRS)

Dastoor, M. N.; Kalvinskas, J. J.

1978-01-01

Experiments indicate that several sulfur-oxidizing bacteria strains have been very efficient in desulfurizing coal. Process occurs at room temperature and does not require large capital investments of high energy inputs. Process may expand use of abundant reserves of high-sulfur bituminous coal, which is currently restricted due to environmental pollution. On practical scale, process may be integrated with modern coal-slurry transportation lines.

Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus.

PubMed

Janosch, Claudia; Remonsellez, Francisco; Sand, Wolfgang; Vera, Mario

2015-10-21

The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an "archaeal like" enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293(T). The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the "thermophilic" nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293(T) was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant.

Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus

PubMed Central

Janosch, Claudia; Remonsellez, Francisco; Sand, Wolfgang; Vera, Mario

2015-01-01

The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293T. The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the “thermophilic” nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293T was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant. PMID:27682113

Removal of mercury from coal via a microbial pretreatment process

DOEpatents

Borole, Abhijeet P [Knoxville, TN; Hamilton, Choo Y [Knoxville, TN

2011-08-16

A process for the removal of mercury from coal prior to combustion is disclosed. The process is based on use of microorganisms to oxidize iron, sulfur and other species binding mercury within the coal, followed by volatilization of mercury by the microorganisms. The microorganisms are from a class of iron and/or sulfur oxidizing bacteria. The process involves contacting coal with the bacteria in a batch or continuous manner. The mercury is first solubilized from the coal, followed by microbial reduction to elemental mercury, which is stripped off by sparging gas and captured by a mercury recovery unit, giving mercury-free coal. The mercury can be recovered in pure form from the sorbents via additional processing.

Facultative anoxygenic photosynthesis in cyanobacteria driven by arsenite and sulfide with evidence for the support of nitrogen fixation

NASA Astrophysics Data System (ADS)

Wolfe-Simon, F.; Hoeft, S. E.; Baesman, S. M.; Oremland, R. S.

2010-12-01

The rise in atmospheric oxygen (O2) over geologic time is attributed to the evolution and widespread proliferation of oxygenic photosynthesis in cyanobacteria. However, cyanobacteria maintain a metabolic flexibility that may not always result in O2 release. In the environment, cyanobacteria may use a variety of alternative electron donors rather than water that are known to be used by other anoxygenic phototrophs (eg. purple sulfur bacteria) including reduced forms of sulfur, iron, nitrogen, and arsenic. Recent evidence suggests cyanobacteria actively take advantage of at least a few of these alternatives. We used a classical Winogradsky approach to enrich for cyanobacteria from the high salinity, elevated pH and arsenic-enriched waters of Mono Lake (CA). Experiments, optimized for cyanobacteria, revealed light-dependent, anaerobic arsenite-oxidation in sub-cultured sediment-free enrichments dominated by a filamentous cyanobacteria. We isolated and identified the dominant member of this enrichment to be a member of the Oscillatoriales by 16S rDNA. Addition of 1 mM arsenite induced facultative anoxygenic photosynthesis under continuous and circadian light. This isolate also oxidized sulfide under the same light-based conditions. Aerobic conditions elicited no arsenite oxidation in the light or dark and the isolate grew as a typical cyanobacterium using oxygenic photosynthesis. Under near-infrared light (700 nm) there was a direct correlation of enhanced growth with an increase in the rate arsenite or sulfide oxidation suggesting the use of photosystem I. Additionally, to test the wide-spread nature of this metabolism in the Oscillatoriales, we followed similar arsenite- and sulfide-driven facultative anoxygenic photosynthesis as well as nitrogen fixation (C2H2 reduction) in the axenic isolate Oscillatoria sp. CCMP 1731. Future characterization includes axenic isolation of the Mono Lake Oscillatoria sp. as well as the arsenite oxidase responsible for electron extraction and confirming the photosystem required for light capture. The geobiological implications of this phenomenon related to nitrogen-fixation and the evolution of O2 on Earth will be discussed.

Analysis of magnetite crystals and inclusion bodies inside magnetotactic bacteria from different environmental locations

NASA Astrophysics Data System (ADS)

Oestreicher, Z.; Lower, B.; Lower, S.; Bazylinski, D. A.

2011-12-01

Biomineralization occurs throughout the living world; a few common examples include iron oxide in chiton teeth, calcium carbonate in mollusk shells, calcium phosphate in animal bones and teeth, silica in diatom shells, and magnetite crystals inside the cells of magnetotactic bacteria. Biologically controlled mineralization is characterized by biominerals that have species-specific properties such as: preferential crystallographic orientation, consistent particle size, highly ordered spatial locations, and well-defined composition and structure. It is well known that magnetotactic bacteria synthesize crystals of magnetite inside of their cells, but how they mineralize the magnetite is poorly understood. Magnetosomes have a species-specific morphology that is due to specific proteins involved in the mineralization process. In addition to magnetite crystals, magnetotactic bacteria also produce inclusion bodies or granules that contain different elements, such as phosphorus, calcium, and sulfur. In this study we used the transmission electron microscope to analyze the structure of magnetite crystals and inclusion bodies from different species of magnetotactic bacteria in order to determine the composition of the inclusion bodies and to ascertain whether or not the magnetite crystals contain elements other than iron and oxygen. Using energy dispersive spectroscopy we found that different bacteria from different environments possess inclusion bodies that contain different elements such as phosphorus, calcium, barium, magnesium, and sulfur. These differences may reflect the conditions of the environment in which the bacteria inhabit.

The origin and evolution of sulfur in an Archean volcano-sedimentary basin, Deer Lake area, Minnesota. M.S. Thesis

NASA Technical Reports Server (NTRS)

Nicol, D. L.

1980-01-01

Rocks of the Deer Lake area, northcentral Minnesota, consist of Archean (age greater than 2.6 billion years) metasediments and metavolcanics intruded by mafic layered sills. Geologic and sulfur isotopic data suggest that sulfides in the sediments are bacteriogenic, having formed in response to the activity of sulfate reducing bacteria during diagenesis. Deposition of the sediments appears to have occurred in a deep marine basin with restricted circulation of sea water. The bulk of the sulfur in the igneous rocks is of deep seated origin, but basal contacts of the sills show evidence of assimilation of biogenic sulfur from the intruded sediments. This assimilation of biogenic sulfur is the primary geochemical control of local Cu-Ni sulfide mineralization.

[Corrosion of pipe steel samples and conjugated conversion of sulfur compounds by thiobacteria Halothiobacillus neapolitanus DSM 15147].

PubMed

Vatsurina, A V; Esikova, T Z; Kholodenko, V P; Vaĭnshteĭn, M B; Dubkova, V I

2005-01-01

The kinetics of conversion of sulfur compounds by Halothiobacillus neapolitanus DSM 15147 bacteria was studied in the presence of steel samples. It was shown that the presence of steel altered the known pathway of sulfur compound oxidation by thiobacteria. Production of atomic hydrogen via the interaction between biogenic sulfuric acid and steel enhanced secondary production of intermediates and decreased the content of sulfate produced previously. The process was accompanied by pH elevation and continuation of intense growth of the thiobacterium culture. Thiobacteria formed a corrosive medium, which caused metal destruction. The protective properties of anticorrosive coatings 225 LS and 640 mk were tested. It was shown that these coatings protected steel from the destructive effect of biogenic sulfuric acid.

The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria

PubMed Central

Yokoyama, Kenichi; Leimkühler, Silke

2016-01-01

Molybdenum is the only second row transition metal essential for biological systems, which is biologically available as molybdate ion. In eukarya, bacteria and archaea, molybdenum is bound to either to a tricyclic pyranopterin, thereby forming the molybdenum cofactor (Moco), or in some bacteria to the FeS cluster based iron-molybdenum cofactor (FeMoco), which forms the active site of nitrogenase. To date more than 50 Moco-containing enzymes have been purified and biochemically or structurally characterized. The physiological role of molybdenum in these enzymes is fundamental to organisms, since the reactions include the catalysis of key steps in carbon, nitrogen and sulfur metabolism. The catalyzed reactions are in most cases oxo-transfer reactions or the hydroxylation of carbon centers. The biosynthesis of Moco has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the biosynthesis and maturation of molybdoenzymes and the biosynthesis and distribution of FeS clusters has been identified in the last years: 1) The synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) The sulfurtransferase for the dithiolene group in Moco is common also for the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the modification of the active site with a sulfur atom additionally involves a sulfurtransferase, 4) most molybdoenzymes in bacteria require FeS clusters as additional redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer. PMID:25268953

[Thermoacidophilic micirobial community oxidizing the gold-bearing flotation concentrate of a pyrite-arsenopyrite ore].

PubMed

Paniushkina, A E; Tsaplina, I A; Grigor'eva, N V; Kondrat'eva, T F

2014-01-01

An aboriginal community of thermophilic acidophilic chemolithotrophic microorganisms (ACM) was isolated from a sample of pyrite gold-bearing flotation concentrateat 45-47 degrees C and pH 1.8-2.0. Compared to an experimental thermoacidophilic microbial consortium formed in the course of cultivation in parallel bioreactors, it had lower rates of iron leaching and oxidation, while its rate of sulfur oxidation was higher. A new thermophilic acidophilic microbial community was obtained by mutual enrichment with the micioorganisms from thie experimental and aboriginal communities during oxidation of sulfide ore flotation concentrate at 47 degrees C. The dominant bacteria of this new ACM community were Acidithiobacillus caldus strains (the most active sulfur oxidizers) and Sulfobacillus thermotolerans strains (active oxidizers of both iron and sulfur), while iron-oxidizing archaea of the family Ferroplasmaceae and heterotrophic bacteria Alicyclobacillus tolerans were the minor components. The new ACM community showed promise for leaching/oxidation of sulfides from flotation concentrates at high pulp density (S:L = 1:4).

Purple Pelisse: a specialty fingerling potato with purple skin and purple flesh

USDA-ARS?s Scientific Manuscript database

Purple Pelisse is a specialty fingerling potato with purple skin and dark purple flesh. It has medium maturity and sets a large number of smooth, small, fingerling-shaped tubers. The tubers have medium specific gravity and high levels of antioxidants. This potato variety is mainly intended for the f...

Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.

PubMed

Voordouw, G; Armstrong, S M; Reimer, M F; Fouts, B; Telang, A J; Shen, Y; Gevertz, D

1996-05-01

Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira, Arcobacter, Campylobacter, and Oceanospirillum spp.) were also detected. The first two were prominently amplified from uncultured production water DNA and represented 28 and 47% of all clones, respectively. Growth on media containing sulfide as the electron donor and nitrate as the electron acceptor and designed for the isolation of Thiomicrospira spp. gave only significant enrichment of the Campylobacter sp., which was shown to be present in different western Canadian oil fields. This newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction.

Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.

PubMed Central

Voordouw, G; Armstrong, S M; Reimer, M F; Fouts, B; Telang, A J; Shen, Y; Gevertz, D

1996-01-01

Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira, Arcobacter, Campylobacter, and Oceanospirillum spp.) were also detected. The first two were prominently amplified from uncultured production water DNA and represented 28 and 47% of all clones, respectively. Growth on media containing sulfide as the electron donor and nitrate as the electron acceptor and designed for the isolation of Thiomicrospira spp. gave only significant enrichment of the Campylobacter sp., which was shown to be present in different western Canadian oil fields. This newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction. PMID:8633860

Molecular analysis of the biomass of a fluidized bed reactor treating synthetic vinasse at anaerobic and micro-aerobic conditions.

PubMed

Rodríguez, Elisa; Lopes, Alexandre; Fdz-Polanco, María; Stams, Alfons J M; García-Encina, Pedro A

2012-03-01

The microbial communities (Bacteria and Archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. This study was focused on the competitive and syntrophic interactions between the different microbial groups at varying influent substrate to sulfate ratios of 8, 4, and 2 and anaerobic or micro-aerobic conditions. Acetogens detected along the anaerobic phases at substrate to sulfate ratios of 8 and 4 seemed to be mainly involved in the fermentation of glucose and betaine, but they were substituted by other sugar or betaine degraders after oxygen application. Typical fatty acid degraders that grow in syntrophy with methanogens were not detected during the entire reactor run. Likely, sugar and betaine degraders outnumbered them in the DGGE analysis. The detected sulfate-reducing bacteria (SRB) belonged to the hydrogen-utilizing Desulfovibrio. The introduction of oxygen led to the formation of elemental sulfur (S(0)) and probably other sulfur compounds by sulfide-oxidizing bacteria (γ-Proteobacteria). It is likely that the sulfur intermediates produced from sulfide oxidation were used by SRB and other microorganisms as electron acceptors, as was supported by the detection of the sulfur respiring Wolinella succinogenes. Within the Archaea population, members of Methanomethylovorans and Methanosaeta were detected throughout the entire reactor operation. Hydrogenotrophic methanogens mainly belonging to the genus Methanobacterium were detected at the highest substrate to sulfate ratio but rapidly disappeared by increasing the sulfate concentration.

Low-temperature growth and photoluminescence property of ZnS nanoribbons.

PubMed

Zhang, Zengxing; Wang, Jianxiong; Yuan, Huajun; Gao, Yan; Liu, Dongfang; Song, Li; Xiang, Yanjuan; Zhao, Xiaowei; Liu, Lifeng; Luo, Shudong; Dou, Xinyuan; Mou, Shicheng; Zhou, Weiya; Xie, Sishen

2005-10-06

At a low temperature of 450 degrees C, ZnS nanoribbons have been synthesized on Si and KCl substrates by a simple chemical vapor deposition (CVD) method with a two-temperature-zone furnace. Zinc and sulfur powders are used as sources in the different temperature zones. X-ray diffraction (XRD), selected area electron diffraction (SEAD), and transmission electron microscopy (TEM) analysis show that the ZnS nanoribbons are the wurtzite structure, and there are two types-single-crystal and bicrystal nanoribbons. Photoluminescence (PL) spectrum shows that the spectrum mainly includes two parts: a purple emission band centering at about 390 nm and a blue emission band centering at about 445 nm with a weak green shoulder around 510 nm.

A sandwich-type optical immunosensor based on the alkaline phosphatase enzyme for Salmonella thypimurium detection

NASA Astrophysics Data System (ADS)

Widyastuti, E.; Puspitasari Schonherr, M. F.; Masruroh, A.; Anggraeni, R. A.; Nisak, Y. K.; Mursidah, S.

2018-03-01

Salmonella is pathogenic bacteria that caused foodborne diseases which being called Salmonellosis. Prevalence of Salmonellosis that being caused by Salmonella thypimurium in Indonesia is quite high. However, detection of Salmonella bacteria in food still limited, complicated, and required a lot time. Sensitive optical assay for Salmonella thypimurium paper based detection has been developed by integrating sandwich assay between antibody-antigen complex and alkaline phosphatase enzyme that produce visible bluish-purple colour with presence of NBT-BCIP substrate. The results showed that Limit of Quantitation of detection is 105 CFU mL-1 with detection time 15 minutes. Linearity test between Colour intensity that produced from Salmonella concentration presence on samples showed that detection has good linearity. Selectivity test exhibited excellent sensitivity with good discrimination against Escherichia coli.

The stratified microbial community at Laguna Figueroa, Baja California, Mexico: A possible model for prephanerozoic laminated microbial communities preserved in cherts

NASA Astrophysics Data System (ADS)

Stolz, John F.; Margulis, Lynn

1984-12-01

The microbial mat community of the evaporite flat at North Pond, Laguna Figueroa (Baja California, Mexico) was actively involved in the production of laminated sediments prior to 1978. Heavy rains in 1979 and 1980 flooded the mat with 1 and 3 meters of meteoric water respectively. The flooding deposited up to 10 cm of silicoclastic sediment over theMicrocoleus-dominated mat and resulted in the cessation of laminated sediment deposition. In 1982, the surface had been recolonized by species of cyanobacteria (Spirulina, Oscillatoria) and purple photosynthetic bacteria (Chromatium, Thiocapsa). The silicoclastic sediments and residual evaporites, which overlaid the laminated sediment, had been reworked into an anaerobic, sulfide-rich mud and contained well preserved sheaths of filamentous and coccoid bacteria.

The Microbial Sulfur Cycle at Extremely Haloalkaline Conditions of Soda Lakes

PubMed Central

Sorokin, Dimitry Y.; Kuenen, J. Gijs; Muyzer, Gerard

2011-01-01

Soda lakes represent a unique ecosystem with extremely high pH (up to 11) and salinity (up to saturation) due to the presence of high concentrations of sodium carbonate in brines. Despite these double extreme conditions, most of the lakes are highly productive and contain a fully functional microbial system. The microbial sulfur cycle is among the most active in soda lakes. One of the explanations for that is high-energy efficiency of dissimilatory conversions of inorganic sulfur compounds, both oxidative and reductive, sufficient to cope with costly life at double extreme conditions. The oxidative part of the sulfur cycle is driven by chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria (SOB), which are unique for soda lakes. The haloalkaliphilic SOB are present in the surface sediment layer of various soda lakes at high numbers of up to 106 viable cells/cm3. The culturable forms are so far represented by four novel genera within the Gammaproteobacteria, including the genera Thioalkalivibrio, Thioalkalimicrobium, Thioalkalispira, and Thioalkalibacter. The latter two were only found occasionally and each includes a single species, while the former two are widely distributed in various soda lakes over the world. The genus Thioalkalivibrio is the most physiologically diverse and covers the whole spectrum of salt/pH conditions present in soda lakes. Most importantly, the dominant subgroup of this genus is able to grow in saturated soda brines containing 4 M total Na+ – a so far unique property for any known aerobic chemolithoautotroph. Furthermore, some species can use thiocyanate as a sole energy source and three out of nine species can grow anaerobically with nitrogen oxides as electron acceptor. The reductive part of the sulfur cycle is active in the anoxic layers of the sediments of soda lakes. The in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries using sulfate, thiosulfate, or elemental sulfur as electron acceptors demonstrated relatively high sulfate reduction rates only hampered by salt-saturated conditions. However, the highest rates of sulfidogenesis were observed not with sulfate, but with elemental sulfur followed by thiosulfate. Formate, but not hydrogen, was the most efficient electron donor with all three sulfur electron acceptors, while acetate was only utilized as an electron donor under sulfur-reducing conditions. The native sulfidogenic populations of soda lakes showed a typical obligately alkaliphilic pH response, which corresponded well to the in situ pH conditions. Microbiological analysis indicated a domination of three groups of haloalkaliphilic autotrophic sulfate-reducing bacteria belonging to the order Desulfovibrionales (genera Desulfonatronovibrio, Desulfonatronum, and Desulfonatronospira) with a clear tendency to grow by thiosulfate disproportionation in the absence of external electron donor even at salt-saturating conditions. Few novel representatives of the order Desulfobacterales capable of heterotrophic growth with volatile fatty acids and alcohols at high pH and moderate salinity have also been found, while acetate oxidation was a function of a specialized group of haloalkaliphilic sulfur-reducing bacteria, which belong to the phylum Chrysiogenetes. PMID:21747784

Characterization of extracellular polymeric substances in the biofilms of typical bacteria by the sulfur K-edge XANES spectroscopy.

PubMed

Lin, Huirong; Ye, Chengsong; Lv, Lu; Zheng, Clark Renjun; Zhang, Shenghua; Zheng, Lei; Zhao, Yidong; Yu, Xin

2014-08-01

A combined approach of physicochemical extraction and sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy was applied to characterize the extracellular polymeric substances (EPS) of typical bacterial biofilms in this study. Physicochemical analysis showed variation of the contents of DNA, polysaccharide and protein in different fractions of EPS in different mediums. The sulfur K-edge XANES analysis yielded a variety of spectra. Spectral fitting of the XANES spectra utilizing a large set of model compounds showed that there was more reduced sulfur in both LB-EPS (loosely bound EPS) and TB-EPS (tightly bound EPS) of all the biofilms in LB medium than in R2A medium. More oxidized sulfur was identified in LB-EPS than that in TB-EPS, suggesting different niches and physiological heterogeneity in the biofilms. Our results suggested that the sulfur K-edge XANES can be a useful tool to analyze the sulfur speciation in EPS of biofilms. Copyright © 2014. Published by Elsevier B.V.

Sugars, ascorbic acid, total phenolic content and total antioxidant activity in passion fruit (Passiflora) cultivars.

PubMed

Devi Ramaiya, Shiamala; Bujang, Japar Sidik; Zakaria, Muta Harah; King, Wong Sing; Shaffiq Sahrir, Muhd Arif

2013-03-30

The levels of sugars, ascorbic acid, total phenolic content (TPC) and total antioxidant activity (TAA) were determined in fruit juices from seven passion fruit (Passiflora spp.) cultivars: P. edulis cultivars Purple, Frederick, Yellow, Pink, P. edulis f. flavicarpa, P. maliformis and P. quadrangularis (we also tested this cultivar's mesocarp). Purple and Yellow P. edulis had significantly higher total sugar, 142.85 ± 0.17 g kg⁻¹ and 139.69 ± 0.12 g kg⁻¹, respectively, than other cultivars. Glucose and fructose content were higher in juice from vine-ripened fruits of Purple, Frederick and Yellow P. edulis, P. quadrangularis and P. maliformis. Sucrose content was significantly higher in juice of non-vine-ripened fruits of P. edulis (Pink) and P. edulis f. flavicarpa. Ascorbic acid, TPC and TAA were significantly higher in vine-ripened Purple and Yellow P. edulis; ranges were 0.22-0.33 g kg⁻¹, 342.80-382.00 mg gallic acid equivalent L⁻¹ and 409.13-586.70 µmol Trolox L⁻¹, respectively. Based on principal component analysis (PCA) and cluster analysis, the main variables - °Brix, total sugar, glucose, fructose, ascorbic acid, TPC and TAA - formed the characteristics for the group comprising Purple and Yellow P. edulis. Glucose, fructose, sucrose, ascorbic acid, TAA and TPC were quantified in passion fruit juices. Variation of the above variables in juices of Passiflora depends on the cultivar and ripeness. © 2012 Society of Chemical Industry.

Hydrogen Sulfide Emissions from Sow Farm Lagoons across Climates Zones.

PubMed

Grant, Richard H; Boehm, Matthew T; Lawrence, Alfred J; Heber, Albert J

2013-11-01

Hydrogen sulfide (HS) emissions were measured periodically over the course of 2 yr at three sow waste lagoons representing humid mesothermal (North Carolina, NC), humid microthermal (Indiana, IN), and semiarid (Oklahoma, OK) climates. Emissions were determined using a backward Lagrangian stochastic model in conjunction with line-sampled HS concentrations and measured turbulence. The median annual sow-specific (area-specific) lagoon emissions at the OK farm were approximately 1.6 g head [hd] d (5880 µg m s), whereas those at the IN and NC sow farms were 0.035 g hd d (130 µg m s), and 0.041 g hd d (260 µg m s), respectively. Hydrogen sulfide emissions generally increased with wind speed. The daily HS emissions from the OK lagoon were greatest during the first half of the year and decreased as the year progressed. Emissions were episodic at the NC and IN lagoons. The generally low emissions at the NC and IN lagoons were probably a result of significant populations of purple sulfur bacteria maintained in the humid mesothermal and humid microthermal climates. Most of the large HS emission events at the NC and IN lagoons appeared to be a result of either precipitation events or liquid pump-out events. The high emissions at the OK lagoon in a semiarid climate were largely a result of high wind speeds enhancing both lagoon and air boundary layer mixing. The climate (air temperature, winds, and precipitation) appeared to influence the HS emissions from lagoons. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Nonphotochemical Hole-Burning Studies of Energy Transfer Dynamics in Antenna Complexes of Photosynthetic Bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuzaki, Satoshi

2001-01-01

This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application ofmore » NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for understanding the energy transfer process associated within three lowest energy Q y-states of the complex. The results are compared with those obtained earlier on the FMO complex from Chlorobium tepidum. In Chapter 4, the energy transfer dynamics of the B800 molecules of intact LH2 and B800-deficient LH2 complexes of the purple bacterium Rhodopseudomonas acidophila are compared. New insights on the additional decay channel of the B800 ring of bacteriochlorophyll a (BChl a) molecules are provided. General conclusions are given in Chapter 5. A version of the hole spectrum simulation program written by the candidate for the FMO complex study (Chapter 3) is included as an appendix. The references for each chapter are given at the end of each chapter.« less

Distribution and size fractionation of elemental sulfur in aqueous environments: The Chesapeake Bay and Mid-Atlantic Ridge

NASA Astrophysics Data System (ADS)

Findlay, Alyssa J.; Gartman, Amy; MacDonald, Daniel J.; Hanson, Thomas E.; Shaw, Timothy J.; Luther, George W.

2014-10-01

Elemental sulfur is an important intermediate of sulfide oxidation and may be produced via abiotic and biotic pathways. In this study the concentration and size fractionation of elemental sulfur were measured in two different sulfidic marine environments: the Chesapeake Bay and buoyant hydrothermal vent plumes along the Mid-Atlantic Ridge. Nanoparticulate sulfur (<0.2 μm) was found to comprise up to 90% of the total elemental sulfur in anoxic deep waters of the Chesapeake Bay. These data were compared with previous studies of elemental sulfur, and represent one of the few reports of nanoparticulate elemental sulfur in the environment. Additionally, a strain of phototrophic sulfide oxidizing bacteria isolated from the Chesapeake Bay was shown to produce elemental sulfur as a product of sulfide oxidation. Elemental sulfur concentrations are also presented from buoyant hydrothermal vent plumes located along the Mid-Atlantic Ridge. In the Mid-Atlantic Ridge plume, S0 concentrations up to 33 μM were measured in the first meter of rising plumes at three different vent sites, and nanoparticulate S0 was up to 44% of total elemental sulfur present.

Mechanisms of volatile production from non-sulfur amino acids by irradiation

NASA Astrophysics Data System (ADS)

Ahn, Dong Uk; Lee, Eun Joo; Feng, Xi; Zhang, Wangang; Lee, Ji Hwan; Jo, Cheorun; Nam, Kichang

2016-02-01

Non-sulfur amino acid monomers were used to study the mechanisms of volatile production in meat by irradiation. Irradiation not only produced many volatiles but also increased the amounts of volatiles from non-sulfur amino acid monomers. The major reaction mechanisms involved in volatile production from each group of the amino acids by irradiation differ significantly. However, we speculate that the radiolysis of amino acid side chains were the major mechanism. In addition, Strecker degradation, especially the production of aldehydes from aliphatic group amino acids, and deamination, isomerization, decarboxylation, cyclic reaction and dehydrogenation of the initial radiolytic products were also contributed to the production of volatile compounds. Each amino acid monomers produced different odor characteristics, but the intensities of odor from all non-sulfur amino acid groups were very weak. This indicated that the contribution of volatiles produced from non-sulfur amino acids was minor. If the volatile compounds from non-sulfur amino acids, especially aldehydes, interact with other volatiles compounds such as sulfur compounds, however, they can contribute to the off-odor of irradiated meat significantly.

Microbial Thiocyanate Utilization under Highly Alkaline Conditions

PubMed Central

Sorokin, Dimitry Y.; Tourova, Tatyana P.; Lysenko, Anatoly M.; Kuenen, J. Gijs

2001-01-01

Three kinds of alkaliphilic bacteria able to utilize thiocyanate (CNS−) at pH 10 were found in highly alkaline soda lake sediments and soda soils. The first group included obligate heterotrophs that utilized thiocyanate as a nitrogen source while growing at pH 10 with acetate as carbon and energy sources. Most of the heterotrophic strains were able to oxidize sulfide and thiosulfate to tetrathionate. The second group included obligately autotrophic sulfur-oxidizing alkaliphiles which utilized thiocyanate nitrogen during growth with thiosulfate as the energy source. Genetic analysis demonstrated that both the heterotrophic and autotrophic alkaliphiles that utilized thiocyanate as a nitrogen source were related to the previously described sulfur-oxidizing alkaliphiles belonging to the gamma subdivision of the division Proteobacteria (the Halomonas group for the heterotrophs and the genus Thioalkalivibrio for autotrophs). The third group included obligately autotrophic sulfur-oxidizing alkaliphilic bacteria able to utilize thiocyanate as a sole source of energy. These bacteria could be enriched on mineral medium with thiocyanate at pH 10. Growth with thiocyanate was usually much slower than growth with thiosulfate, although the biomass yield on thiocyanate was higher. Of the four strains isolated, the three vibrio-shaped strains were genetically closely related to the previously described sulfur-oxidizing alkaliphiles belonging to the genus Thioalkalivibrio. The rod-shaped isolate differed from the other isolates by its ability to accumulate large amounts of elemental sulfur inside its cells and by its ability to oxidize carbon disulfide. Despite its low DNA homology with and substantial phenotypic differences from the vibrio-shaped strains, this isolate also belonged to the genus Thioalkalivibrio according to a phylogenetic analysis. The heterotrophic and autotrophic alkaliphiles that grew with thiocyanate as an N source possessed a relatively high level of cyanase activity which converted cyanate (CNO−) to ammonia and CO2. On the other hand, cyanase activity either was absent or was present at very low levels in the autotrophic strains grown on thiocyanate as the sole energy and N source. As a result, large amounts of cyanate were found to accumulate in the media during utilization of thiocyanate at pH 10 in batch and thiocyanate-limited continuous cultures. This is a first direct proof of a “cyanate pathway” in pure cultures of thiocyanate-degrading bacteria. Since it is relatively stable under alkaline conditions, cyanate is likely to play a role as an N buffer that keeps the alkaliphilic bacteria safe from inhibition by free ammonia, which otherwise would reach toxic levels during dissimilatory degradation of thiocyanate. PMID:11157213

Photobiological hydrogen production and carbon dioxide sequestration

NASA Astrophysics Data System (ADS)

Berberoglu, Halil

Photobiological hydrogen production is an alternative to thermochemical and electrolytic technologies with the advantage of carbon dioxide sequestration. However, it suffers from low solar to hydrogen energy conversion efficiency due to limited light transfer, mass transfer, and nutrient medium composition. The present study aims at addressing these limitations and can be divided in three parts: (1) experimental measurements of the radiation characteristics of hydrogen producing and carbon dioxide consuming microorganisms, (2) solar radiation transfer modeling and simulation in photobioreactors, and (3) parametric experiments of photobiological hydrogen production and carbon dioxide sequestration. First, solar radiation transfer in photobioreactors containing microorganisms and bubbles was modeled using the radiative transport equation (RTE) and solved using the modified method of characteristics. The study concluded that Beer-Lambert's law gives inaccurate results and anisotropic scattering must be accounted for to predict the local irradiance inside a photobioreactor. The need for accurate measurement of the complete set of radiation characteristics of microorganisms was established. Then, experimental setup and analysis methods for measuring the complete set of radiation characteristics of microorganisms have been developed and successfully validated experimentally. A database of the radiation characteristics of representative microorganisms have been created including the cyanobacteria Anabaena variabilis, the purple non-sulfur bacteria Rhodobacter sphaeroides and the green algae Chlamydomonas reinhardtii along with its three genetically engineered strains. This enabled, for the first time, quantitative assessment of the effect of genetic engineering on the radiation characteristics of microorganisms. In addition, a parametric experimental study has been performed to model the growth, CO2 consumption, and H 2 production of Anabaena variabilis as functions of irradiance and CO2 concentration. Kinetic models were successfully developed based on the Monod model and on a novel scaling analysis employing the CO2 consumption half-time as the time scale. Finally, the growth and hydrogen production of Anabaena variabilis have been compared in a flat panel photobioreactor using three different nutrient media under otherwise similar conditions. Light to hydrogen energy conversion efficiency for Allen-Arnon medium was superior by a factor of 5.5 to both BG-11 and BG-11o media. This was attributed to the presence of vanadium and larger heterocyst frequency observed in the Allen-Arnon medium.

Antioxidant and prebiotic activity of five peonidin-based anthocyanins extracted from purple sweet potato (Ipomoea batatas (L.) Lam.).

PubMed

Sun, Hanju; Zhang, Pingping; Zhu, Yongsheng; Lou, Qiuyan; He, Shudong

2018-03-22

Twelve kinds of anthocyanins from the Chinese purple sweet potato cultivar (Ipomoea batatas (L.) Lam.) were extracted and identified using LC-MS/MS, which had a high content of peonidin-based anthocyanins. Five peonidin-based anthocyanin monomers (P1, P2, P3, P4 and P5) were isolated by preparative liquid chromatography with structural analyses using an Impact II Q-TOF MS/MS. Then, the functional properties of the anthocyanin monomers, such as the antioxidant activities, proliferative effects on probiotics, and their inhibition on harmful bacteria in vitro, were investigated. The peonidin-based components in purple sweet potato anthocyanins (PSPAs) showed good properties regarding scavenging 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals and superoxide anions, and had good potential in reducing the total power activity and Fe 2+ chelating ability. While the order of the antioxidant abilities was as follows: P4 > P5 > P3 > P2 > P1 > PSPAs. Microbial cultivations showed that P1, P2, P3, P4, P5 and PSPAs could induce the proliferation of Bifidobacterium bifidum, Bifidobacterium adolescentis, Bifidobacterium infantis and Lactobacillus acidophilus, and they inhibited the growth of Staphylococcus aureus and Salmonella typhimurium, suggesting the anthocyanins might have prebiotic-like activity through the modulation of the intestinal microbiota. Our results indicate that peonidin-based anthocyanins could be further utilized in health foods and pharmaceutical developments.

From Mantle to Microbe to Mollusc: How Animal-Microbial Symbioses Influence Carbon and Sulfur Cycling in Hydrothermal Vent Flows.

NASA Astrophysics Data System (ADS)

Girguis, P. R.; Beinart, R.

2014-12-01

Symbioses between animals and chemoautotrophic bacteria dominate many hydrothermal vents. In these associations, symbiotic bacteria harness energy and "fix" carbon from the oxidation of reduced chemicals such as sulfide, methane, and hydrogen that are found in venting fluids. At vents along the Eastern Lau Spreading Center (ELSC) in the South Pacific, snails and mussels with chemoautotrophic symbionts have been shown to harness energy via the oxidation of sulfide. However, partially oxidized sulfur species such as thiosulfate and polysulfides have also been detected in abundance in their habitats. No studies to date have established whether thiosulfate or other partially oxidized sulfur compounds are used by these symbiotic associations, nor have studies constrained the potential role that symbioses might play in sulfur biogeochemical cycles at diffuse vent flows. To address these questions, we used high-pressure, flow through incubations to study three symbiotic molluscs from the ELSC - the snails Alviniconcha and Ifremeria nautilei and the mussel Bathymodiolus brevior - at conditions mimicking those in situ. Via the use of isotopically labeled inorganic carbon, shipboard mass spectrometry and voltammetric microelectrodes, we quantified the production and consumption of different sulfur compounds by each of these symbioses. We established that the uptake and oxidation of either sulfide or thiosulfate could -to varying degrees- support carbon fixation in all three species. Notably, we also observed that some symbioses excreted thiosulfate and polysulfides under sulfidic conditions, suggesting that these symbioses are a source of partially oxidized sulfur species in the environment. We further observed spatial disparity in the carbon fixation rates among the individuals in our incubations that have implications for the variability of productivity in situ.Collectively, these data reveal that thiosulfate can support net autotrophy, and may be an ecologically important energy source for vent symbioses. Furthermore, symbioses-mediated sulfur transformations may influence the ecology of the free-living community by governing the production and consumption of reduced sulfur species in this habitat.

Comparison Analysis of Coal Biodesulfurization and Coal's Pyrite Bioleaching with Acidithiobacillus ferrooxidans

PubMed Central

Hong, Fen-Fen; He, Huan; Liu, Jin-Yan; Tao, Xiu-Xiang; Zheng, Lei; Zhao, Yi-Dong

2013-01-01

Acidithiobacillus ferrooxidans (A. ferrooxidans) was applied in coal biodesulfurization and coal's pyrite bioleaching. The result showed that A. ferrooxidans had significantly promoted the biodesulfurization of coal and bioleaching of coal's pyrite. After 16 days of processing, the total sulfur removal rate of coal was 50.6%, and among them the removal of pyritic sulfur was up to 69.9%. On the contrary, after 12 days of processing, the coal's pyrite bioleaching rate was 72.0%. SEM micrographs showed that the major pyrite forms in coal were massive and veinlets. It seems that the bacteria took priority to remove the massive pyrite. The sulfur relative contents analysis from XANES showed that the elemental sulfur (28.32%) and jarosite (18.99%) were accumulated in the biotreated residual coal. However, XRD and XANES spectra of residual pyrite indicated that the sulfur components were mainly composed of pyrite (49.34%) and elemental sulfur (50.72%) but no other sulfur contents were detected. Based on the present results, we speculated that the pyrite forms in coal might affect sulfur biooxidation process. PMID:24288464

Single-cell sequencing of Thiomargarita reveals genomic flexibility for adaptation to dynamic redox conditions

DOE PAGES

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja; ...

2016-06-21

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

X-Ray Absorption Spectroscopy As a Probe of Microbial Sulfur Biochemistry: the Nature of Bacterial Sulfur Globules Revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

George, G.N.; Gnida, M.; Bazylinski, D.A.

2009-05-18

The chemical nature of the sulfur in bacterial sulfur globules has been the subject of controversy for a number of years. Sulfur K-edge X-ray absorption spectroscopy (XAS) is a powerful technique for probing the chemical forms of sulfur in situ, but two groups have used it with very different conclusions. The root of the controversy lies with the different detection strategies used by the two groups, which result in very different spectra. This paper seeks to resolve the controversy. We experimentally demonstrate that the use of transmittance detection for sulfur K-edge XAS measurements is highly prone to spectroscopic distortions andmore » that much of the published work on sulfur bacteria is very likely based on distorted data. We also demonstrate that all three detection methods used for X-ray absorption experiments yield essentially identical spectra when the measurements are carried out under conditions where no experimental distortions are expected. Finally, we turn to the original question--the chemical nature of bacterial sulfur. We examine isolated sulfur globules of Allochromatium vinosum and intact cells of a strain of magnetotactic coccus and show that XAS indicates the presence of a chemical form of sulfur resembling S{sub 8}.« less

Preparation and Antioxidant Activity of Purple Potato Wine

PubMed Central

Zhong-hua, Liu; Jie, Guo

2015-01-01

Purple potatoes were used as raw material to study the purple potato wine production process and antioxidant activity. This paper analyzed different fermentation time, fermentation temperature, yeast inoculum, initial pH, the initial sugar content on alcohol and anthocyanin contents of purple potato wine by single factor experiments and response surface methodology(RSM). The results showed that the optimum fermentation conditions of purple potato wine were as follows: fermentation temperature was 26oC, yeast inoculum was 0.15%, fermentation time was 7 d, initial pH was 3.0 and initial sugar content was 11 %. Under these conditions the alcohol and anthocyanin contents of purple potato wine could reach 10.55%/Vol and 6.42 μg/mL, respectively. The purple potato wine was purple, bright in colour, pleasant fragrance and pure taste. Prepared purple potato wine had the ability of reducing Fe3+ and scavenging superoxide anion radicals, which meant that purple potato wine had certain antioxidant activity. PMID:26998173

Importance of Extracellular Polymeric Substances from Thiobacillus ferrooxidans for Bioleaching

PubMed Central

Gehrke, Tilman; Telegdi, Judit; Thierry, Dominique; Sand, Wolfgang

1998-01-01

Leaching bacteria such as Thiobacillus ferrooxidans attach to pyrite or sulfur by means of extracellular polymeric substances (EPS) (lipopolysaccharides). The primary attachment to pyrite at pH 2 is mediated by exopolymer-complexed iron(III) ions in an electrochemical interaction with the negatively charged pyrite surface. EPS from sulfur cells possess increased hydrophobic properties and do not attach to pyrite, indicating adaptability to the substrate or substratum. PMID:9647862

Sulfur plumes off Namibia

NASA Technical Reports Server (NTRS)

2002-01-01

Sulfur plumes rising up from the bottom of the ocean floor produce colorful swirls in the waters off the coast of Namibia in southern Africa. The plumes come from the breakdown of marine plant matter by anaerobic bacteria that do not need oxygen to live. This image was acquired by the Moderate Resolution Imaging Spectroradiometer (MODIS) on the Terra satellite on April 24, 2002 Credit: Jacques Descloitres, MODIS Land Rapid Response Team, NASA/GSFC

Evaluation of haloalkaliphilic sulfur-oxidizing microorganisms with potential application in the effluent treatment of the petroleum industry.

PubMed

Olguín-Lora, P; Le Borgne, S; Castorena-Cortés, G; Roldán-Carrillo, T; Zapata-Peñasco, I; Reyes-Avila, J; Alcántara-Pérez, S

2011-02-01

Haloalkaliphilic sulfur-oxidizing mixed cultures for the treatment of alkaline-saline effluents containing sulfide were characterized and evaluated. The mixed cultures (IMP-PB, IMP-XO and IMP-TL) were obtained from Mexican alkaline soils collected in Puebla (PB), Xochimilco (XO) and Tlahuac (TL), respectively. The Ribosomal Intergenic Spacer Analysis (RISA) revealed bacteria related to Thioalkalibacterium and Thioalkalivibrio in IMP-XO and IMP-PB mixed cultures. Halomonas strains were detected in IMP-XO and IMP-TL. In addition, an uncultured Bacteroides bacterium was present in IMP-TL. Mixed cultures were evaluated at different pH and NaCl concentrations at 30°C. IMP-PB and IMP-TL expressed thiosulfate-oxidizing activity in the 7.5-10.5 pH range, whereas IMP-XO presented its maximal activity with 19.0 mg O₂ g (protein)⁻¹ min⁻¹, at pH 10.6; it was not affected by NaCl concentrations up to 1.7 M. In continuous culture, IMP-XO showed a growth rate of 15 day⁻¹, productivity of 433.4 mg(protein) l⁻¹ day⁻¹ and haloalkaliphilic sulfur-oxidizing activity was also detected up to 170 mM by means of N-methyl-diethanolamine (MDEA). Saline-alkaline soil samples are potential sources of haloalkaliphilic sulfur-oxidizing bacteria and the mixed cultures could be applied in the treatment of inorganic sulfur compounds in petroleum industry effluents under alkaline-saline conditions.

Fe-S cluster biogenesis in Gram-positive bacteria: SufU is a zinc-dependent sulfur transfer protein.

PubMed

Selbach, Bruna P; Chung, Alexander H; Scott, Aubrey D; George, Simon J; Cramer, Stephen P; Dos Santos, Patricia C

2014-01-14

The biosynthesis of Fe-S clusters in Bacillus subtilis and other Gram-positive bacteria is catalyzed by the SufCDSUB system. The first step in this pathway involves the sulfur mobilization from the free amino acid cysteine to a sulfur acceptor protein SufU via a PLP-dependent cysteine desulfurase SufS. In this reaction scheme, the formation of an enzyme S-covalent intermediate is followed by the binding of SufU. This event leads to the second half of the reaction where a deprotonated thiol of SufU promotes the nucleophilic attack onto the persulfide intermediate of SufS. Kinetic analysis combined with spectroscopic methods identified that the presence of a zinc atom tightly bound to SufU (Ka = 10(17) M(-1)) is crucial for its structural and catalytic competency. Fe-S cluster assembly experiments showed that despite the high degree of sequence and structural similarity to the ortholog enzyme IscU, the B. subtilis SufU does not act as a standard Fe-S cluster scaffold protein. The involvement of SufU as a dedicated agent of sulfur transfer, rather than as an assembly scaffold, in the biogenesis of Fe-S clusters in Gram-positive microbes indicates distinct strategies used by bacterial systems to assemble Fe-S clusters.

Discovery of a new subgroup of sulfur dioxygenases and characterization of sulfur dioxygenases in the sulfur metabolic network of Acidithiobacillus caldus

PubMed Central

Pang, Xin; Lin, Jianqiang; Liu, Xiangmei; Wang, Rui; Lin, Jianqun; Chen, Linxu

2017-01-01

Acidithiobacillus caldus is a chemolithoautotrophic sulfur-oxidizing bacterium that is widely used for bioleaching processes. Acidithiobacillus spp. are suggested to contain sulfur dioxygenases (SDOs) that facilitate sulfur oxidation. In this study, two putative sdo genes (A5904_0421 and A5904_1112) were detected in the genome of A. caldus MTH-04 by BLASTP searching with the previously identified SDO (A5904_0790). We cloned and expressed these genes, and detected the SDO activity of recombinant protein A5904_0421 by a GSH-dependent in vitro assay. Phylogenetic analysis indicated that A5904_0421and its homologous SDOs, mainly found in autotrophic bacteria, were distantly related to known SDOs and were categorized as a new subgroup of SDOs. The potential functions of genes A5904_0421 (termed sdo1) and A5904_0790 (termed sdo2) were investigated by generating three knockout mutants (Δsdo1, Δsdo2 and Δsdo1&2), two sdo overexpression strains (OE-sdo1 and OE-sdo2) and two sdo complemented strains (Δsdo1/sdo1’ and Δsdo2/sdo2’) of A. caldus MTH-04. Deletion or overexpression of the sdo genes did not obviously affect growth of the bacteria on S0, indicating that the SDOs did not play an essential role in the oxidation of extracellular elemental sulfur in A. caldus. The deletion of sdo1 resulted in complete inhibition of growth on tetrathionate, slight inhibition of growth on thiosulfate and increased GSH-dependent sulfur oxidation activity on S0. Transcriptional analysis revealed a strong correlation between sdo1 and the tetrathionate intermediate pathway. The deletion of sdo2 promoted bacterial growth on tetrathionate and thiosulfate, and overexpression of sdo2 altered gene expression patterns of sulfide:quinone oxidoreductase and rhodanese. Taken together, the results suggest that sdo1 is essential for the survival of A. caldus when tetrathionate is used as the sole energy resource, and sdo2 may also play a role in sulfur metabolism. PMID:28873420

Electrogenic sulfur oxidation in a northern saltmarsh (St. Lawrence Estuary, Canada).

PubMed

Rao, Alexandra; Risgaard-Petersen, Nils; Neumeier, Urs

2016-06-01

Measurements of porewater O2, pH, and H2S microprofiles in intact sediment cores collected in a northern saltmarsh in the St. Lawrence Estuary (Quebec, Canada) revealed the occurrence of electrogenic sulfur oxidation (e-SOx) by filamentous "cable" bacteria in submerged marsh pond sediments in the high marsh. In summer, the geochemical fingerprint of e-SOx was apparent in intact cores, while in fall, cable bacteria were detected by fluorescence in situ hybridization and the characteristic geochemical signature of e-SOx was observed only upon prolonged incubation. In exposed, unvegetated creek bank sediments sampled in the low marsh in summer, cable bacteria developed only in repacked cores of sieved (500 μm), homogenized sediments. These results suggest that e-SOx is suppressed by the activity of macrofauna in exposed, unvegetated marsh sediments. A reduced abundance of benthic invertebrates may promote e-SOx development in marsh ponds, which are dominant features of subarctic saltmarshes as in the St. Lawrence Estuary.

Sulfur and iron accumulation in three marine-archaeological shipwrecks in the Baltic Sea: The Ghost, the Crown and the Sword

NASA Astrophysics Data System (ADS)

Fors, Yvonne; Grudd, Håkan; Rindby, Anders; Jalilehvand, Farideh; Sandström, Magnus; Cato, Ingemar; Bornmalm, Lennart

2014-02-01

Sulfur and iron concentrations in wood from three 17th century shipwrecks in the Baltic Sea, the Ghost wreck, the Crown and the Sword, were obtained by X-ray fluorescence (XRF) scanning. In near anaerobic environments symbiotic microorganisms degrade waterlogged wood, reduce sulfate and promote accumulation of low-valent sulfur compounds, as previously found for the famous wrecks of the Vasa and Mary Rose. Sulfur K-edge X-ray absorption near-edge structure (XANES) analyses of Ghost wreck wood show that organic thiols and disulfides dominate, together with elemental sulfur probably generated by sulfur-oxidizing Beggiatoa bacteria. Iron sulfides were not detected, consistent with the relatively low iron concentration in the wood. In a museum climate with high atmospheric humidity oxidation processes, especially of iron sulfides formed in the presence of corroding iron, may induce post-conservation wood degradation. Subject to more general confirmation by further analyses no severe conservation concerns are expected for the Ghost wreck wood.

High growth potential and nitrogen removal performance of marine anammox bacteria in shrimp-aquaculture sediment.

PubMed

Van Duc, Luong; Song, Bongkeun; Ito, Hiroaki; Hama, Takehide; Otani, Masashi; Kawagoshi, Yasunori

2018-04-01

Anaerobic ammonium oxidation (anammox) bacteria were enriched in continuous packed-bed columns with marine sediment. One column (SB-C) was packed with only marine sediment collected from a shrimp-aquaculture pond, and another column (SB-AMX) was inoculated with marine anammox bacteria (MAB) as a control. These columns were continuously fed with natural or artificial seawater including ammonium (NH 4 + ) and nitrite (NO 2 - ). The SB-AMX showed anammox activities from the beginning and continued for over 200 days. However, the SB-C had no nitrogen removal performance for over 170 days. After adding a bicarbonate solution (KHCO 3 ) to the sediment-only packed column, anammox activity was observed within 13 days. The column exhibited a nitrogen removal efficiency (NRE) of 88% at a nitrogen loading rate (NLR) of 1.0 kg-N·m -3 ·day -1 , which was comparable to the control one. A next-generation sequencing analysis revealed the predominance of MAB related to "Candidatus Scalindua spp.". In addition, the co-occurrence of sulfur-oxidizing denitrifiers was observed, which suggests their symbiotic relationship. This study suggests the applicability of MAB for in-situ bioremediation of nitrogen-contaminated marine sediments and reveals a potential microbial interaction between anammox and sulfur-oxidizing communities responsible for nitrogen and sulfur cycling in marine aquaculture systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Carotenoid diagenesis in recent marine sediments. I. The Peru continental shelf (15/sup 0/S, 75/sup 0/W)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Repeta, D.J.; Gagosian, R.B.

1987-04-01

The authors report here the distribution of carotenoids in Peru marine surface sediments, including partial identification of 37 pigments, 33 of which have not been previously reported to occur in marine sediments. Their analysis demonstrates that zooplanktonic crustacea, diatoms, dinoflagellates, cryptomonads, purple nonsulfur photosynthetic bacteria, and unidentified species of photosynthetic bacteria are contributors to sedimentary organic matter. Fucoxanthin, fucoxanthinol, diadinoxanthin, peridinin and peridininol, the principal carotenoids of diatoms and dinoflagellates observed in sediment traps, are nearly absent from their sample, even though these phytoplankton are the primary source of organic matter. They attribute this to the presence of 5,6 epoxidesmore » in these pigments, a feature which causes rapid cleavage of the polyene and fragmentation to low molecular weight compounds.« less

Highly selective colorimetric bacteria sensing based on protein-capped nanoparticles.

PubMed

Qiu, Suyan; Lin, Zhenyu; Zhou, Yaomin; Wang, Donggen; Yuan, Lijuan; Wei, Yihua; Dai, Tingcan; Luo, Linguang; Chen, Guonan

2015-02-21

A rapid and cost-effective colorimetric sensor has been developed for the detection of bacteria (Bacillus subtilis was selected as an example). The sensor was designed to rely on lysozyme-capped AuNPs with the advantages of effective amplification and high specificity. In the sensing system, lysozyme was able to bind strongly to Bacillus subtilis, which effectively induced a color change of the solution from light purple to purplish red. The lowest concentration of Bacillus subtilis detectable by the naked eye was 4.5 × 10(3) colony-forming units (CFU) mL(-1). Similar results were discernable from UV-Vis absorption measurements. A good specificity was observed through a statistical analysis method using the SPSS software (version 17.0). This simple colorimetric sensor may therefore be a rapid and specific method for a bacterial detection assay in complex samples.

Buoyant densities of phototrophic sulfur bacteria and cyanobacteria

NASA Technical Reports Server (NTRS)

Guerrero, R.

1985-01-01

The buoyant densities of bacterial cells are greatly influenced by the accumulation of intracellular reserve material. The buoyant density of phototrophic bacteria that are planktonic is of particular interest, since these organisms must remain in the photic zone of the water column for optimal growth. Separation of cells by their buoyant density may also be of use in separating and identifying organisms from a natural population. The bacteria used were obtained from pure cultures, enrichments, or samples taken directly from the environment.

Proceedings of the International Congress (12th), Corrosion Control for Low-Cost Reliability, Held in Houston, Texas on September 19 -24, 1993. Volume 6. Electric Power Industry

DTIC Science & Technology

1993-09-24

Protection 567 Passivity of Carbon Steel in Organic Solutions in the Presence of Iron Bacteria 0. Schifler, P. Moran, and j. Kruger...under Impingement Attack 190 Anaerobic Corrosion of Steel by Phototrophic Sulfur Bacteria M. Reda and J. Alhalji...of Sulfate Reducing Bacteria in Western Canadian Oil Field Fluids K. Hashimoto, S. Kato, B. In, E. Akiyama, H. Habakazi, A. D. Westlake, I. Foght, P

On the identification of folium and orchil on illuminated manuscripts

NASA Astrophysics Data System (ADS)

Aceto, Maurizio; Calà, Elisa; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Porter, Cheryl; Gulmini, Monica

2017-01-01

The identification of the two purple dyes folium and orchil has rarely been reported in the analysis of painted artworks, especially when analysing illuminated manuscripts. This is not consistent with the fact that ancient literary sources suggested their use as substitutes for the more expensive Tyrian purple dye. By employing non-invasive spectroscopic techniques, the present work demonstrates that these dyes were actually widely used in the production of ancient manuscripts. By employing UV-visible diffuse reflectance spectrophotometry with optic fibres (FORS) and spectrofluorimetry, the abundant identification of both dyes on medieval manuscripts was performed by comparing the spectra recorded on ancient codices with those obtained on accurate replicas of dyed or painted parchment. Moreover, examples are also reported whereby the considered purple dyes were used in mixtures with other colourants. The overall information obtained here allowed us to define new boundaries for the time range in which orchil and folium dyes were used which is wider than previously thought, and to focus on their particular uses in the decoration of books.

Kinetic mechanism of the dimeric ATP sulfurylase from plants

PubMed Central

Ravilious, Geoffrey E.; Herrmann, Jonathan; Goo Lee, Soon; Westfall, Corey S.; Jez, Joseph M.

2013-01-01

In plants, sulfur must be obtained from the environment and assimilated into usable forms for metabolism. ATP sulfurylase catalyses the thermodynamically unfavourable formation of a mixed phosphosulfate anhydride in APS (adenosine 5′-phosphosulfate) from ATP and sulfate as the first committed step of sulfur assimilation in plants. In contrast to the multi-functional, allosterically regulated ATP sulfurylases from bacteria, fungi and mammals, the plant enzyme functions as a mono-functional, non-allosteric homodimer. Owing to these differences, here we examine the kinetic mechanism of soybean ATP sulfurylase [GmATPS1 (Glycine max (soybean) ATP sulfurylase isoform 1)]. For the forward reaction (APS synthesis), initial velocity methods indicate a single-displacement mechanism. Dead-end inhibition studies with chlorate showed competitive inhibition versus sulfate and non-competitive inhibition versus APS. Initial velocity studies of the reverse reaction (ATP synthesis) demonstrate a sequential mechanism with global fitting analysis suggesting an ordered binding of substrates. ITC (isothermal titration calorimetry) showed tight binding of APS to GmATPS1. In contrast, binding of PPi (pyrophosphate) to GmATPS1 was not detected, although titration of the E•APS complex with PPi in the absence of magnesium displayed ternary complex formation. These results suggest a kinetic mechanism in which ATP and APS are the first substrates bound in the forward and reverse reactions, respectively. PMID:23789618

Bacterial Bolsheviks: PS II and the Evolution of the Oxygenic Revolution

NASA Astrophysics Data System (ADS)

Kopp, R. E.; Kirschvink, J. L.; Newman, D. K.; Nash, C. Z.; Hilburn, I. A.

2003-12-01

After the rise of life itself, the most radical transformation of Earth's biogeochemical cycles was the transition from an anoxic to an oxic world. Though various studies have suggested O2 made its first bulk appearance in the atmosphere some time between 3.8 and 2.1 Ga, virtually all analyses agree the production of large quantities of free O2 was triggered by the evolution of oxygenic photosynthesis. We suggest the oldest strong geological evidence for O2 is the 2.22 Ga Kalahari Mn member of the Hotazel BIF (1), as in the oceans only free O2 can oxidize soluble Mn(II) into insoluble Mn(IV). Some have argued, however, that oxygenic cyanobacteria had originated by 2.7 Ga. The ˜500 Myr "gap" has often been interpreted as the timescale for gradual evolutionary improvement of the O2-generating system. Biochemical and genomic analyses of photosynthetic bacteria indicate that photosystems I and II, which operate together in cyanobacteria, had a long history of parallel development. Green sulfur bacteria and heliobacteria use PS-II, while green non-sulfur and purple bacteria use PS-I; none can use H2O as an electron donor. Recent genetic analyses show lateral gene transfer was rampant among photosynthetic lineages (2). Moreover, extant cyanobacteria shut down PS-II in the presence of an alternative electron donor like H2S. This suggests PS-I and PS-II came together with their functions intact. Hence, most `debugging' of the two systems predates their merger in the ancestor of modern cyanobacteria. The time interval between the lateral transfer events and the evolution of oxygenic photosynthesis could thus have been geologically short. We suggest the ˜500 Myr "gap" may result from misinterpretations. The presence of oxygenic photosynthesis is uncertain before the deposition of the Hotazel formation, in the aftermath of the Makganyene glaciation (1). A simple model of nutrient and reductant fluxes argues that, once triggered, the oxygenation of a reducing surface environment warmed by a CH4 greenhouse (3) should occur fairly rapidly, within ˜ 10 My. The trigger requires both the evolution of cyanobacteria and sufficiently high nutrient (mainly P) fluxes to allow O2 production to overwhelm reductant fluxes. P flux into the oceans in glaciated worlds correlates with increased continental weathering during glacial intervals (4). Thus, were cyanobacteria present during the Huronian glaciations, which predate 2.22 Ga (5), these glaciations should have triggered the oxygenation event. Instead, the oxygenation event seems to correlate with the Makganyene glaciation, at 2.22 Ga (6). The appearance of red beds in the Upper Timeball Hill formation directly underlying the Makganyene diamictite supports this interpretation. As would be expected from a glaciation associated with the destruction of a CH4 greenhouse, paleomagnetic data indicate the Makganyene glaciation was a global Snowball event (7). Cyanobacteria appear to have evolved in the short interval between the Huronian glaciations and the Makganyene glaciation. The lengthy delay between the earliest life on Earth and the appearance of cyanobacteria suggests that the oxygenic revolution was a fairly low probability event; planets with oxygenic biospheres may be quite rare. 1. J. L. Kirschvink et al., PNAS 97, 1400-1405 (2000). 2. J. Raymond et al., Science 298, 1616-1620 (2002). 3. A. A. Pavlov et al., JGR 105, 11981-11990 (2000). 4. K. B. F”llmi, Geology 23, 503-506 (1995). 5. S. R. Noble, P. C. Lightfoot, Can. J. Earth Sci. 29, 1424-1429 (1992). 6. D. H. Cornell et al., Precamb. Res. 79, 101-123 (1996). 7. D. A. Evans et al., Nature 386, 262-266 (1997).

Insights into the relation between adhesion force and chalcopyrite-bioleaching by Acidithiobacillus ferrooxidans.

PubMed

Zhu, Jianyu; Wang, Qianfen; Zhou, Shuang; Li, Qian; Gan, Min; Jiang, Hao; Qin, Wenqing; Liu, Xueduan; Hu, Yuehua; Qiu, Guanzhou

2015-02-01

This paper presents a study on the relation between bacterial adhesion force and bioleaching rate of chalcopyrite, which sheds light on the influence of interfacial interaction on bioleaching behavior. In our research, Acidithiobacillus ferrooxidans (A. ferrooxidans) were adapted to grow with FeSO4 · 7H2O, element sulfur or chalcopyrite. Then, surface properties of Acidithiobacillus ferrooxidans and chalcopyrite were analyzed by contact angle, zeta potential and Fourier transform infrared spectroscopy (FTIR). Adhesion force between bacteria and chalcopyrite was measured by atomic force microscopy (AFM). Attachment and bioleaching behaviors were also monitored. The results showed that A. ferrooxidans adapted with chalcopyrite exhibited the strongest adhesion force to chalcopyrite and the highest bioleaching rate. Culture adapted with sulfur bacteria took second place and FeSO4 · 7H2O-adapted bacteria were the lowest. Bioleaching rate and bacterial attachment capacity were positively related to bacterial adhesion force, which is affected by the nature of energy source. According to this work, the attachment of bacteria to chalcopyrite surface is one of the most important aspects that influence the bioleaching process of chalcopyrite. Copyright © 2014 Elsevier B.V. All rights reserved.

Enhancement of growth and yield of tomato by Rhodopseudomonas sp. under greenhouse conditions.

PubMed

Lee, Kang-Hyeong; Koh, Rae-Hyun; Song, Hong-Gyu

2008-12-01

A greenhouse test was carried out to examine the effects on tomato growth of application of purple non-sulfur bacterium Rhodopseudomonas sp. which had enhanced germination and growth of tomato seed under axenic conditions. The shoot length of tomato plant inoculated by Rhodopseudomonas sp. KL9 increased by 34.6% compared to that of control in 8 weeks of cultivation. During the same period, this strain increased 120.6 and 78.6% of dry weight of shoot and root of tomato plants, respectively. The formation ratio of tomato fruit from flower was also raised by inoculation of KL9. In addition, Rhodopseudomonas sp. KL9 treatment enhanced the fresh weight and lycopene content in the harvested tomato fruits by 98.3 and 48.3%, respectively compared to those of the uninoculated control. When the effect on the indigenous bacterial community and fate of the inoculated Rhodopseudomonas sp. KL9 were monitored by denaturing gradient gel electrophoresis analysis, its application did not affect the native bacterial community in tomato rhizosphere soil, but should be repeated to maintain its population size. This bacterial capability may be applied as an environment-friendly biofertilizer to cultivation of high quality tomato and other crops including lycopene-containing vegetables and fruits.

Enhanced elementary sulfur recovery in integrated sulfate-reducing, sulfur-producing rector under micro-aerobic condition.

PubMed

Xu, Xi-jun; Chen, Chuan; Wang, Ai-jie; Fang, Ning; Yuan, Ye; Ren, Nan-qi; Lee, Duu-jong

2012-07-01

Biological treatment of sulfate-laden wastewater consists of two separate reactors to reduce sulfate to sulfide by sulfate-reducing bacteria (SRB) and to oxidize sulfide to sulfur (S(0)) by sulfide oxidation bacteria (SOB). To have SRB+SOB in a single reactor faced difficulty of low S(0) conversion. This study for the first time revealed that dissolved oxygen (DO) level can be used to manipulate SRB+SOB reactions in a single reactor. This work demonstrated successful operation of an integrated SRB+SOB reactor under micro-aerobic condition. At DO = 0.10-0.12 mg l(-1), since the activities of SOB were enhanced by limited oxygen, the removal efficiency for sulfate reached 81.5% and the recovery of S(0) peaked at 71.8%, higher than those reported in literature. At increased DO, chemical oxidation of sulfide with molecular oxygen competed with SOB so conversion of S(0) started to decline. At DO>0.30 mg l(-1) activities of SRB were inhibited, leading to failure of the SRB+SOB reactor. Copyright © 2012 Elsevier Ltd. All rights reserved.

Identification of a fourth family of lycopene cyclases in photosynthetic bacteria

PubMed Central

Maresca, Julia A.; Graham, Joel E.; Wu, Martin; Eisen, Jonathan A.; Bryant, Donald A.

2007-01-01

A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium tepidum, was identified in a complementation assay with a lycopene-producing strain of Escherichia coli. Orthologs of cruA are found in all available green sulfur bacterial genomes and in all cyanobacterial genomes that lack genes encoding CrtL- or CrtY-type lycopene cyclases. The cyanobacterium Synechococcus sp. PCC 7002 has two homologs of CruA, denoted CruA and CruP, and both were shown to have lycopene cyclase activity. Although all characterized lycopene cyclases in plants are CrtL-type proteins, genes orthologous to cruP also occur in plant genomes. The CruA- and CruP-type carotenoid cyclases are members of the FixC dehydrogenase superfamily and are distantly related to CrtL- and CrtY-type lycopene cyclases. Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria. PMID:17606904

Identification of a fourth family of lycopene cyclases in photosynthetic bacteria.

PubMed

Maresca, Julia A; Graham, Joel E; Wu, Martin; Eisen, Jonathan A; Bryant, Donald A

2007-07-10

A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium tepidum, was identified in a complementation assay with a lycopene-producing strain of Escherichia coli. Orthologs of cruA are found in all available green sulfur bacterial genomes and in all cyanobacterial genomes that lack genes encoding CrtL- or CrtY-type lycopene cyclases. The cyanobacterium Synechococcus sp. PCC 7002 has two homologs of CruA, denoted CruA and CruP, and both were shown to have lycopene cyclase activity. Although all characterized lycopene cyclases in plants are CrtL-type proteins, genes orthologous to cruP also occur in plant genomes. The CruA- and CruP-type carotenoid cyclases are members of the FixC dehydrogenase superfamily and are distantly related to CrtL- and CrtY-type lycopene cyclases. Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria.

The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

PubMed Central

Scott, Kathleen M; Sievert, Stefan M; Abril, Fereniki N; Ball, Lois A; Barrett, Chantell J; Blake, Rodrigo A; Boller, Amanda J; Chain, Patrick S. G; Clark, Justine A; Davis, Carisa R; Detter, Chris; Do, Kimberly F; Dobrinski, Kimberly P; Faza, Brandon I; Fitzpatrick, Kelly A; Freyermuth, Sharyn K; Harmer, Tara L; Hauser, Loren J; Hügler, Michael; Kerfeld, Cheryl A; Klotz, Martin G; Kong, William W; Land, Miriam; Lapidus, Alla; Larimer, Frank W; Longo, Dana L; Lucas, Susan; Malfatti, Stephanie A; Massey, Steven E; Martin, Darlene D; McCuddin, Zoe; Meyer, Folker; Moore, Jessica L; Ocampo, Luis H; Paul, John H; Paulsen, Ian T; Reep, Douglas K; Ren, Qinghu; Ross, Rachel L; Sato, Priscila Y; Thomas, Phaedra; Tinkham, Lance E; Zeruth, Gary T

2006-01-01

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome. PMID:17105352

Assessing acute toxicity of effluent from a textile industry and nearby river waters using sulfur-oxidizing bacteria in continuous mode.

PubMed

Gurung, Anup; Hassan, Sedky H A; Oh, Sang-Eun

2011-10-01

Bioassays are becoming an important tool for assessing the toxicity of complex mixtures of substances in aquatic environments in which Daphnia magna is routinely used as a test organism. Bioassays outweigh physicochemical analyses and are valuable in the decision-making process pertaining to the final discharge of effluents from wastewater treatment plants as they measure the total effect of the discharge which is ecologically relevant. In this study, the aquatic toxicity of a textile plant effluent and river water downstream from the plant were evaluated with sulfur-oxidizing bacterial biosensors in continuous mode. Collected samples were analysed for different physicochemical parameters and 1,4-dioxane was detected in the effluent. The effluent contained a relatively high chemical oxygen demand of 60 mg L(-1), which exceeded the limit set by the Korean government for industrial effluent discharges. Results showed that both the effluent and river waters were toxic to sulfur-oxidizing bacteria. These results show the importance of incorporating bioassays to detect toxicity in wastewater effluents for the sustainable management of water resources.

Lysogenic bacteriophage isolated from acidophilium

DOEpatents

Ward, Thomas W.; Bruhn, Debby F.; Bulmer, Deborah K.

1992-01-01

A bacteriophage identified as .phi.Ac1 capable of infecting acidophilic heterotropic bacteria (such as Acidiphilium sp.) and processes for genetically engineering acidophilic bacteria for biomining or sulfur removal from coal are disclosed. The bacteriophage is capable of growth in cells existing at pH at or below 3.0. Lytic forms of the phage introduced into areas experiencing acid drainage kill the bacteria causing such drainage. Lysogenic forms of the phase having genes for selective removal of metallic or nonmetallic elements can be introduced into acidophilic bacteria to effect removal of the desired element form ore or coal.

Purple Pelisse: A specialty fingerling potato with purple skin and flesh and medium specific gravity

USDA-ARS?s Scientific Manuscript database

Purple Pelisse is a specialty fingerling potato with purple skin and dark purple flesh. It has medium maturity and sets a large number of smooth, small, fingerling-shaped tubers. The tubers have medium specific gravity and high levels of antioxidants. This potato variety is mainly intended for the f...

Perturbation of gut bacteria induces a coordinated cellular immune response in the purple sea urchin larva.

PubMed

Ch Ho, Eric; Buckley, Katherine M; Schrankel, Catherine S; Schuh, Nicholas W; Hibino, Taku; Solek, Cynthia M; Bae, Koeun; Wang, Guizhi; Rast, Jonathan P

2016-10-01

The purple sea urchin (Strongylocentrotus purpuratus) genome sequence contains a complex repertoire of genes encoding innate immune recognition proteins and homologs of important vertebrate immune regulatory factors. To characterize how this immune system is deployed within an experimentally tractable, intact animal, we investigate the immune capability of the larval stage. Sea urchin embryos and larvae are morphologically simple and transparent, providing an organism-wide model to view immune response at cellular resolution. Here we present evidence for immune function in five mesenchymal cell types based on morphology, behavior and gene expression. Two cell types are phagocytic; the others interact at sites of microbial detection or injury. We characterize immune-associated gene markers for three cell types, including a perforin-like molecule, a scavenger receptor, a complement-like thioester-containing protein and the echinoderm-specific immune response factor 185/333. We elicit larval immune responses by (1) bacterial injection into the blastocoel and (2) seawater exposure to the marine bacterium Vibrio diazotrophicus to perturb immune state in the gut. Exposure at the epithelium induces a strong response in which pigment cells (one type of immune cell) migrate from the ectoderm to interact with the gut epithelium. Bacteria that accumulate in the gut later invade the blastocoel, where they are cleared by phagocytic and granular immune cells. The complexity of this coordinated, dynamic inflammatory program within the simple larval morphology provides a system in which to characterize processes that direct both aspects of the echinoderm-specific immune response as well as those that are shared with other deuterostomes, including vertebrates.

Sulfur Nanoparticles Synthesis and Characterization from H2S Gas, Using Novel Biodegradable Iron Chelates in W/O Microemulsion

NASA Astrophysics Data System (ADS)

Deshpande, Aniruddha S.; Khomane, Ramdas B.; Vaidya, Bhalchandra K.; Joshi, Renuka M.; Harle, Arti S.; Kulkarni, Bhaskar D.

2008-06-01

Sulfur nanoparticles were synthesized from hazardous H2S gas using novel biodegradable iron chelates in w/o microemulsion system. Fe3+ malic acid chelate (0.05 M aqueous solution) was studied in w/o microemulsion containing cyclohexane, Triton X-100 and n-hexanol as oil phase, surfactant, co-surfactant, respectively, for catalytic oxidation of H2S gas at ambient conditions of temperature, pressure, and neutral pH. The structural features of sulfur nanoparticles have been characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), energy dispersive spectroscopy (EDS), diffused reflectance infra-red Fourier transform technique, and BET surface area measurements. XRD analysis indicates the presence of α-sulfur. TEM analysis shows that the morphology of sulfur nanoparticles synthesized in w/o microemulsion system is nearly uniform in size (average particle size 10 nm) and narrow particle size distribution (in range of 5 15 nm) as compared to that in aqueous surfactant systems. The EDS analysis indicated high purity of sulfur (>99%). Moreover, sulfur nanoparticles synthesized in w/o microemulsion system exhibit higher antimicrobial activity (against bacteria, yeast, and fungi) than that of colloidal sulfur.

Sulfur Nanoparticles Synthesis and Characterization from H2S Gas, Using Novel Biodegradable Iron Chelates in W/O Microemulsion

PubMed Central

2008-01-01

Sulfur nanoparticles were synthesized from hazardous H2S gas using novel biodegradable iron chelates in w/o microemulsion system. Fe3+–malic acid chelate (0.05 M aqueous solution) was studied in w/o microemulsion containing cyclohexane, Triton X-100 andn-hexanol as oil phase, surfactant, co-surfactant, respectively, for catalytic oxidation of H2S gas at ambient conditions of temperature, pressure, and neutral pH. The structural features of sulfur nanoparticles have been characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), energy dispersive spectroscopy (EDS), diffused reflectance infra-red Fourier transform technique, and BET surface area measurements. XRD analysis indicates the presence of α-sulfur. TEM analysis shows that the morphology of sulfur nanoparticles synthesized in w/o microemulsion system is nearly uniform in size (average particle size 10 nm) and narrow particle size distribution (in range of 5–15 nm) as compared to that in aqueous surfactant systems. The EDS analysis indicated high purity of sulfur (>99%). Moreover, sulfur nanoparticles synthesized in w/o microemulsion system exhibit higher antimicrobial activity (against bacteria, yeast, and fungi) than that of colloidal sulfur.

Thermophilic Carbon-Sulfur-Bond-Targeted Biodesulfurization

PubMed Central

Konishi, J.; Ishii, Y.; Onaka, T.; Okumura, K.; Suzuki, M.

1997-01-01

Petroleum contains many heterocyclic organosulfur compounds refractory to conventional hydrodesulfurization carried out with chemical catalysts. Among these, dibenzothiophene (DBT) and DBTs bearing alkyl substitutions are representative compounds. Two bacterial strains, which have been identified as Paenibacillus strains and which are capable of efficiently cleaving carbon-sulfur (C--S) bonds in DBT at high temperatures, have been isolated for the first time. Upon attacking DBT and its various methylated derivatives at temperatures up to 60(deg)C, both growing and resting cells of these bacteria can release sulfur atoms as sulfate ions and leave the monohydroxylated hydrocarbon moieties intact. Moreover, when either of these paenibacilli was incubated at 50(deg)C with light gas oil previously processed through hydrodesulfurization, the total sulfur content in the oil phase clearly decreased. PMID:16535672

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiao, Y.; Navid, A.

Rising energy demands and the imperative to reduce carbon dioxide (CO 2) emissions are driving research on biofuels development. Hydrogen gas (H 2) is one of the most promising biofuels and is seen as a future energy carrier by virtue of the fact that 1) it is renewable, 2) does not evolve the “greenhouse gas” CO 2 in combustion, 3) liberates large amounts of energy per unit weight in combustion (having about 3 times the energy content of gasoline), and 4) is easily converted to electricity by fuel cells. Among the various bioenergy strategies, environmental groups and others say thatmore » the concept of the direct manufacture of alternative fuels, such as H 2, by photosynthetic organisms is the only biofuel alternative without significant negative criticism [1]. Biological H 2 production by photosynthetic microorganisms requires the use of a simple solar reactor such as a transparent closed box, with low energy requirements, and is considered as an attractive system to develop as a biocatalyst for H 2 production [2]. Various purple bacteria including Rhodopseudomonas palustris, can utilize organic substrates as electron donors to produce H 2 at the expense of solar energy. Because of the elimination of energy cost used for H 2O oxidation and the prevention of the production of O 2 that inhibits the H 2-producing enzymes, the efficiency of light energy conversion to H 2 by anoxygenic photosynthetic bacteria is in principle much higher than that by green algae or cyanobacteria, and is regarded as one of the most promising cultures for biological H 2 production [3]. Here implemented a simple and relatively straightforward strategy for hydrogen production by photosynthetic microorganisms using sunlight, sulfur- or iron-based inorganic substrates, and CO 2 as the feedstock. Carefully selected microorganisms with bioengineered beneficial traits act as the biocatalysts of the process designed to both enhance the system efficiency of CO 2 fixation and the net hydrogen production rate. Additionally we applied metabolic engineering approaches guided by computational modeling for the chosen model microorganisms to enable efficient hydrogen production.« less

New Proteins Involved in Sulfur Trafficking in the Cytoplasm of Allochromatium vinosum*

PubMed Central

Stockdreher, Yvonne; Sturm, Marga; Josten, Michaele; Sahl, Hans-Georg; Dobler, Nadine; Zigann, Renate; Dahl, Christiane

2014-01-01

The formation of periplasmic sulfur globules is an intermediate step during the oxidation of reduced sulfur compounds in various sulfur-oxidizing microorganisms. The mechanism of how this sulfur is activated and crosses the cytoplasmic membrane for further oxidation to sulfite by the dissimilatory reductase DsrAB is incompletely understood, but it has been well documented that the pathway involves sulfur trafficking mediated by sulfur-carrying proteins. So far sulfur transfer from DsrEFH to DsrC has been established. Persulfurated DsrC very probably serves as a direct substrate for DsrAB. Here, we introduce further important players in oxidative sulfur metabolism; the proteins Rhd_2599, TusA, and DsrE2 are strictly conserved in the Chromatiaceae, Chlorobiaceae, and Acidithiobacillaceae families of sulfur-oxidizing bacteria and are linked to genes encoding complexes involved in sulfur oxidation (Dsr or Hdr) in the latter two. Here we show via relative quantitative real-time PCR and microarray analysis an increase of mRNA levels under sulfur-oxidizing conditions for rhd_2599, tusA, and dsrE2 in Allochromatium vinosum. Transcriptomic patterns for the three genes match those of major genes for the sulfur-oxidizing machinery rather than those involved in biosynthesis of sulfur-containing biomolecules. TusA appears to be one of the major proteins in A. vinosum. A rhd_2599-tusA-dsrE2-deficient mutant strain, although not viable in liquid culture, was clearly sulfur oxidation negative upon growth on solid media containing sulfide. Rhd_2599, TusA, and DsrE2 bind sulfur atoms via conserved cysteine residues, and experimental evidence is provided for the transfer of sulfur between these proteins as well as to DsrEFH and DsrC. PMID:24648525

Assessment of the stoichiometry and efficiency of CO2 fixation coupled to reduced sulfur oxidation

PubMed Central

Klatt, Judith M.; Polerecky, Lubos

2015-01-01

Chemolithoautotrophic sulfur oxidizing bacteria (SOB) couple the oxidation of reduced sulfur compounds to the production of biomass. Their role in the cycling of carbon, sulfur, oxygen, and nitrogen is, however, difficult to quantify due to the complexity of sulfur oxidation pathways. We describe a generic theoretical framework for linking the stoichiometry and energy conservation efficiency of autotrophic sulfur oxidation while accounting for the partitioning of the reduced sulfur pool between the energy generating and energy conserving steps as well as between the main possible products (sulfate vs. zero-valent sulfur). Using this framework, we show that the energy conservation efficiency varies widely among SOB with no apparent relationship to their phylogeny. Aerobic SOB equipped with reverse dissimilatory sulfite reductase tend to have higher efficiency than those relying on the complete Sox pathway, whereas for anaerobic SOB the presence of membrane-bound, as opposed to periplasmic, nitrate reductase systems appears to be linked to higher efficiency. We employ the framework to also show how limited rate measurements can be used to estimate the primary productivity of SOB without the knowledge of the sulfate-to-zero-valent-sulfur production ratio. Finally, we discuss how the framework can help researchers gain new insights into the activity of SOB and their niches. PMID:26052315

Microbial Communities Associated with Phosphorite-bearing Sediments

NASA Astrophysics Data System (ADS)

Zoss, R.; Bailey, J.; Flood, B.; Jones, D. S.

2016-12-01

Phosphorus is a limiting nutrient in the environment and is an important component of many biological molecules. Calcium phosphate mineral deposits known as phosphorites, are also the primary source of P for agriculture. Understanding phosphorite formation may improve management of P resources. However, the processes that mediate calcium phosphate mineral precipitation in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating giant sulfur bacteria (GSB). These bacteria may concentrate phosphate in sediment pore waters - creating supersaturated conditions with respect to apatite. However, the relationship between microbes and phosphogenesis is not fully resolved. To further study this relationship, we examined microbial communities from two sources: sediment cores recovered from the shelf of the Benguela region, and DNA extracted from washed phosphorites recovered from those same sediments. We used itag and clone library sequencing of the 16S rRNA gene to examine the microbial communities and their relationship with the environment. We found that many of our sediments shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfur-reducing bacteria and sulfur-oxidizing bacteria were abundant in our datasets. Phylotypes that are known to carry out nitrification and/or anammox (anaerobic ammonia oxidation) were also well-represented. Our phosphorite extraction, however, contained a distinct microbial community from those observed in the modern sediments. We observed both an enrichment of certain common microbial classes and a complete absence of others. These results could represent an ancient microbial assemblage that was present when the apatite precipitated. While these taxa may or may not have contributed to apatite precipitation, several groups represented in the phosphorite dataset have the genetic potential, as determined through the analysis of published genomes, to synthesize, and perhaps accumulate, polyphosphate.

Seasonal occurrence of anoxygenic photosynthesis in Tillari and Selaulim reservoirs, Western India

NASA Astrophysics Data System (ADS)

Kurian, S.; Roy, R.; Repeta, D. J.; Gauns, M.; Shenoy, D. M.; Suresh, T.; Sarkar, A.; Narvenkar, G.; Johnson, C. G.; Naqvi, S. W. A.

2012-07-01

Phytoplankton and bacterial pigment compositions were determined by high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) in two freshwater reservoirs (Tillari Dam and Selaulim Dam), which are located at the foothills of the Western Ghats in India. These reservoirs experience anoxia in the hypolimnion during summer. Water samples were collected from both reservoirs during anoxic periods while one of them (Tillari Reservoir) was also sampled in winter, when convective mixing results in well-oxygenated conditions throughout the water column. During the period of anoxia (summer), bacteriochlorophyll (BChl) e isomers and isorenieratene, characteristic of brown sulfur bacteria, were dominant in the anoxic (sulfidic) layer of the Tillari Reservoir under low light intensities. The winter observations showed the dominance of small cells of Chlorophyll b-containing green algae and cyanobacteria, with minor presence of fucoxanthin-containing diatoms and peridinin-containing dinoflagellates. Using total BChl e concentration observed in June, the standing stock of brown sulfur bacteria carbon in the anoxic compartment of Tillari Reservoir was estimated to be 2.27 gC m-2, which is much higher than the similar estimate for carbon derived from oxygenic photosynthesis (0.82 gC m-2. The Selaulim Reservoir also displayed similar characteristics with the presence of BChl e isomers and isorenieratene in the anoxic hypolimnion during summer. Although sulfidic conditions prevailed in the water column below the thermocline, the occurrence of photo-autotrophic bacteria was restricted only to mid-depths (maximal concentration of BChl e isomers was detected at 0.2% of the surface incident light). This shows that the vertical distribution of photo-autotrophic sulfur bacteria is primarily controlled by light penetration in the water column where the presence of H2S provides a suitable biogeochemical environment for them to flourish.

Spatial variability in photosynthetic and heterotrophic activity drives localized δ13C org fluctuations and carbonate precipitation in hypersaline microbial mats.

PubMed

Houghton, J; Fike, D; Druschel, G; Orphan, V; Hoehler, T M; Des Marais, D J

2014-11-01

Modern laminated photosynthetic microbial mats are ideal environments to study how microbial activity creates and modifies carbon and sulfur isotopic signatures prior to lithification. Laminated microbial mats from a hypersaline lagoon (Guerrero Negro, Baja California, Mexico) maintained in a flume in a greenhouse at NASA Ames Research Center were sampled for δ(13) C of organic material and carbonate to assess the impact of carbon fixation (e.g., photosynthesis) and decomposition (e.g., bacterial respiration) on δ(13) C signatures. In the photic zone, the δ(13) C org signature records a complex relationship between the activities of cyanobacteria under variable conditions of CO2 limitation with a significant contribution from green sulfur bacteria using the reductive TCA cycle for carbon fixation. Carbonate is present in some layers of the mat, associated with high concentrations of bacteriochlorophyll e (characteristic of green sulfur bacteria) and exhibits δ(13) C signatures similar to DIC in the overlying water column (-2.0‰), with small but variable decreases consistent with localized heterotrophic activity from sulfate-reducing bacteria (SRB). Model results indicate respiration rates in the upper 12 mm of the mat alter in situ pH and HCO3- concentrations to create both phototrophic CO2 limitation and carbonate supersaturation, leading to local precipitation of carbonate minerals. The measured activity of SRB with depth suggests they variably contribute to decomposition in the mat dependent on organic substrate concentrations. Millimeter-scale variability in the δ(13) C org signature beneath the photic zone in the mat is a result of shifting dominance between cyanobacteria and green sulfur bacteria with the aggregate signature overprinted by heterotrophic reworking by SRB and methanogens. These observations highlight the impact of sedimentary microbial processes on δ(13) C org signatures; these processes need to be considered when attempting to relate observed isotopic signatures in ancient sedimentary strata to conditions in the overlying water column at the time of deposition and associated inferences about carbon cycling. © 2014 John Wiley & Sons Ltd.

Iridescence in the neck feathers of domestic pigeons

NASA Astrophysics Data System (ADS)

Yin, Haiwei; Shi, Lei; Sha, Jing; Li, Yizhou; Qin, Youhua; Dong, Biqin; Meyer, Serge; Liu, Xiaohan; Zhao, Li; Zi, Jian

2006-11-01

We conducted structural characterizations, reflection measurements, and theoretical simulations on the iridescent green and purple neck feathers of domestic pigeons (Columba livia domestica). We found that both green and purple barbules are composed of an outer keratin cortex layer surrounding a medullary layer. The thickness of the keratin cortex layer shows a distinct difference between green and purple barbules. Green barbules vary colors from green to purple with the observing angle changed from normal to oblique, while purple barbules from purple to green in an opposite way. Both the experimental and theoretical results suggest that structural colors in green and purple neck feathers should originate from the interference in the top keratin cortex layer, while the structure beyond acts as a poor mirror.

Solid oxide fuel cell process and apparatus

DOEpatents

Cooper, Matthew Ellis [Morgantown, WV; Bayless, David J [Athens, OH; Trembly, Jason P [Durham, NC

2011-11-15

Conveying gas containing sulfur through a sulfur tolerant planar solid oxide fuel cell (PSOFC) stack for sulfur scrubbing, followed by conveying the gas through a non-sulfur tolerant PSOFC stack. The sulfur tolerant PSOFC stack utilizes anode materials, such as LSV, that selectively convert H.sub.2S present in the fuel stream to other non-poisoning sulfur compounds. The remaining balance of gases remaining in the completely or near H.sub.2S-free exhaust fuel stream is then used as the fuel for the conventional PSOFC stack that is downstream of the sulfur-tolerant PSOFC. A broad range of fuels such as gasified coal, natural gas and reformed hydrocarbons are used to produce electricity.

Indirect Redox Transformations of Iron, Copper, and Chromium Catalyzed by Extremely Acidophilic Bacteria

PubMed Central

Johnson, D. Barrie; Hedrich, Sabrina; Pakostova, Eva

2017-01-01

Experiments were carried out to examine redox transformations of copper and chromium by acidophilic bacteria (Acidithiobacillus, Leptospirillum, and Acidiphilium), and also of iron (III) reduction by Acidithiobacillus spp. under aerobic conditions. Reduction of iron (III) was found with all five species of Acidithiobacillus tested, grown aerobically on elemental sulfur. Cultures maintained at pH 1.0 for protracted periods displayed increasing propensity for aerobic iron (III) reduction, which was observed with cell-free culture liquors as well as those containing bacteria. At. caldus grown on hydrogen also reduced iron (III) under aerobic conditions, confirming that the unknown metabolite(s) responsible for iron (III) reduction were not (exclusively) sulfur intermediates. Reduction of copper (II) by aerobic cultures of sulfur-grown Acidithiobacillus spp. showed similar trends to iron (III) reduction in being more pronounced as culture pH declined, and occurring in both the presence and absence of cells. Cultures of Acidithiobacillus grown anaerobically on hydrogen only reduced copper (II) when iron (III) (which was also reduced) was also included; identical results were found with Acidiphilium cryptum grown micro-aerobically on glucose. Harvested biomass of hydrogen-grown At. ferridurans oxidized iron (II) but not copper (I), and copper (I) was only oxidized by growing cultures of Acidithiobacillus spp. when iron (II) was also included. The data confirmed that oxidation and reduction of copper were both mediated by acidophilic bacteria indirectly, via iron (II) and iron (III). No oxidation of chromium (III) by acidophilic bacteria was observed even when, in the case of Leptospirillum spp., the redox potential of oxidized cultures exceeded +900 mV. Cultures of At. ferridurans and A. cryptum reduced chromium (VI), though only when iron (III) was also present, confirming an indirect mechanism and contradicting an earlier report of direct chromium reduction by A. cryptum. Measurements of redox potentials of iron, copper and chromium couples in acidic, sulfate-containing liquors showed that these differed from situations where metals are not complexed by inorganic ligands, and supported the current observations of indirect copper oxido-reduction and chromium reduction mediated by acidophilic bacteria. The implications of these results for both industrial applications of acidophiles and for exobiology are discussed. PMID:28239375

A life detection problem in a High Arctic microbial community

NASA Astrophysics Data System (ADS)

Rogers, J. D.; Perreault, N. N.; Niederberger, T. D.; Lichten, C.; Whyte, L. G.; Nadeau, J. L.

2010-03-01

Fluorescent labeling of bacterial cell walls, DNA, and metabolic processes demonstrates high (potentially single molecule) sensitivity, is non-invasive, and in some cases can differentiate strains and species. Robust microscopes such as the custom instruments presented here can provide good image quality in the field and are potentially suitable for flight. However, ambiguous or false-positive results with bacterial stains can occur and can create difficulties in interpretation even on Earth. We present a "real" life detection problem in a sample of biofilms taken from the Canadian High Arctic. The samples consisted of numerous small sulfur-oxidizing bacteria and larger structures resembling fungi or diatoms. The identity of these latter structures remained ambiguous until electron microscopy and X-ray spectroscopy were performed, indicating that they were unusual sulfur minerals probably precipitated by the bacterial communities. While such mineral structures may possibly serve as biosignatures after the cells have disappeared, it is important that they not be mistaken for cells themselves. It is also possible that unusual mineral structures will be performed under extraterrestrial conditions, so great care is needed to differentiate cell structures from minerals.

Towards the Integration of Dark- and Photo-Fermentative Waste Treatment. 4. Repeated Batch Sequential Dark- and Photofermentation using Starch as Substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laurinavichene, T. V.; Belokopytov, B. F.; Laurinavichius, K. S.

In this study we demonstrated the technical feasibility of a prolonged, sequential two-stage integrated process under a repeated batch mode of starch fermentation. In this durable scheme, the photobioreactor with purple bacteria in the second stage was fed directly with dark culture from the first stage without centrifugation, filtration, or sterilization (not demonstrated previously). After preliminary optimization, both the dark- and the photo-stages were performed under repeated batch modes with different process parameters. Continuous H{sub 2} production in this system was observed at a H{sub 2} yield of up to 1.4 and 3.9 mole mole{sup -1} hexose during the dark-more » and photo-stage, respectively (for a total of 5.3 mole mole{sup -1} hexose), and rates of 0.9 and 0.5 L L{sup -1} d{sup -1}, respectively. Prolonged repeated batch H{sub 2} production was maintained for up to 90 days in each stage and was rather stable under non-aseptic conditions. Potential for improvements in these results are discussed.« less

Expression of recombinant sea urchin cellulase SnEG54 using mammalian cell lines.

PubMed

Okumura, Fumihiko; Kameda, Hiroyuki; Ojima, Takao; Hatakeyama, Shigetsugu

2010-05-07

We previously identified the cellulase SnEG54 from Japanese purple sea urchin Strongylocentrotus nudus, the molecular mass of which is about 54kDa on SDS-PAGE. It is difficult to express and purify a recombinant cellulase protein using bacteria such as Escherichia coli or yeast. In this study, we generated mammalian expression vectors encoding SnEG54 to transiently express SnEG54 in mammalian cells. Both SnEG54 expressed in mammalian cells and SnEG54 released into the culture supernatant showed hydrolytic activity toward carboxymethyl cellulose. By using a retroviral expression system, we also established a mammalian cell line that constitutively produces SnEG54. Unexpectedly, SnEG54 released into the culture medium was not stable, and the peak time showing the highest concentration was approximately 1-2days after seeding into fresh culture media. These findings suggest that non-mammalian sea urchin cellulase can be generated in human cell lines but that recombinant SnEG54 is unstable in culture medium due to an unidentified mechanism. Copyright (c) 2010 Elsevier Inc. All rights reserved.

The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale.

PubMed

Włodarczyk, Agnieszka; Lirski, Maciej; Fogtman, Anna; Koblowska, Marta; Bidziński, Grzegorz; Matlakowska, Renata

2018-01-01

Black shales are one of the largest reservoirs of fossil organic carbon and inorganic reduced sulfur on Earth. It is assumed that microorganisms play an important role in the transformations of these sedimentary rocks and contribute to the return of organic carbon and inorganic sulfur to the global geochemical cycles. An outcrop of deep subterrestrial ~256-million-year-old Kupferschiefer black shale was studied to define the metabolic processes of the deep biosphere important in transformations of organic carbon and inorganic reduced sulfur compounds. This outcrop was created during mining activity 12 years ago and since then it has been exposed to the activity of oxygen and microorganisms. The microbial processes were described based on metagenome and metaproteome studies as well as on the geochemistry of the rock. The microorganisms inhabiting the subterrestrial black shale were dominated by bacterial genera such as Pseudomonas, Limnobacter, Yonghaparkia, Thiobacillus, Bradyrhizobium , and Sulfuricaulis . This study on black shale was the first to detect archaea and fungi, represented by Nitrososphaera and Aspergillus genera, respectively. The enzymatic oxidation of fossil aliphatic and aromatic hydrocarbons was mediated mostly by chemoorganotrophic bacteria, but also by archaea and fungi. The dissimilative enzymatic oxidation of primary reduced sulfur compounds was performed by chemolithotrophic bacteria. The geochemical consequences of microbial activity were the oxidation and dehydrogenation of kerogen, as well as oxidation of sulfide minerals.

Biological conversion of anglesite (PbSO(4)) and lead waste from spent car batteries to galena (PbS).

PubMed

Weijma, Jan; De Hoop, Klaas; Bosma, Wobby; Dijkman, Henk

2002-01-01

Lead paste, a solid mixture containing PbSO(4), PbO(2), PbO/Pb(OH)(2) precipitate, and elemental Pb, is one of the main waste fractions from spent car batteries. Biological sulfidation represents a new process for recovery of lead from this waste. In this process the lead salts in lead paste are converted to galena (PbS) by sulfate-reducing bacteria. This paper investigates a continuous process for sulfidation of anglesite (PbSO(4)), the main constituent of lead paste, and lead paste, consisting of a laboratory-scale gas-lift bioreactor to which a slurry of anglesite or lead paste was supplied. Sulfate or elemental sulfur was added as an additional sulfur source. Hydrogen gas served as an electron donor for the biological reduction of sulfate and elemental sulfur to sulfide by sulfate- and sulfur-reducing bacteria. Anglesite was almost completely converted to galena at a loading rate of 19 kg of PbSO(4) m(-)(3) day(-)(1), producing a sludge of which the crystalline lead phases consisted of >98% PbS (galena) and 1-2% elemental Pb. With lead paste, stable sulfidation rates of up to 17 kg of lead paste m(-)(3) day(-)(1) were demonstrated, producing a sludge of which the crystalline lead phases consisted of an estimated >96% PbS, 1-2% elemental Pb, and 1-2% PbO(2).

Effect of gas-liquid flow pattern and microbial diversity analysis of a pilot-scale biotrickling filter for anoxic biogas desulfurization.

PubMed

Almenglo, Fernando; Bezerra, Tercia; Lafuente, Javier; Gabriel, David; Ramírez, Martín; Cantero, Domingo

2016-08-01

Hydrogen sulfide removal from biogas was studied under anoxic conditions in a pilot-scale biotrickling filter operated under counter- and co-current gas-liquid flow patterns. The best performance was found under counter-current conditions (maximum elimination capacity of 140 gS m(-3) h(-1)). Nevertheless, switching conditions between co- and counter-current flow lead to a favorable redistribution of biomass and elemental sulfur along the bed height. Moreover, elemental sulfur was oxidized to sulfate when the feeding biogas was disconnected and the supply of nitrate (electron acceptor) was maintained. Removal of elemental sulfur was important to prevent clogging in the packed bed and, thereby, to increase the lifespan of the packed bed between maintenance episodes. The larger elemental sulfur removal rate during shutdowns was 59.1 gS m(-3) h(-1). Tag-encoded FLX amplicon pyrosequencing was used to study the diversity of bacteria under co-current flow pattern with liquid recirculation and counter-current mode with a single-pass flow of the liquid phase. The main desulfurizing bacteria were Sedimenticola while significant role of heterotrophic, opportunistic species was envisaged. Remarkable differences between communities were found when a single-pass flow of industrial water was fed to the biotrickling filter. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of carbon-to-sulfur (C/S) ratio and nitrate (N) dosage on Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorus Removal (DS-EBPR)

PubMed Central

Yu, Mei; Lu, Hui; Wu, Di; Zhao, Qing; Meng, Fangang; Wang, Yudan; Hao, Xiaodi; Chen, Guang-Hao

2016-01-01

In this study, the Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorous Removal (DS-EBPR) with 20 mg P/L/d of the volumetric P removal rate was successfully achieved in a Sequencing Batch Reactor (SBR). The effects of carbon-to-sulfur (C/S) mass ratio and nitrate (N) dosage were investigated through two batch tests to reveal the role of wastewater compositions in DS-EBPR performance. The optimal specific P release and uptake rates (0.4 and 2.4 mg P/g VSS/h, respectively) were achieved at C/S/P/N mass ratio of 150/200/20/20, and poly-S is supplied as a potential electron and energy storage. The nitrate dosage in a range of 10–50 mg N/L had no significant influence on P uptake rates (2.1 ~ 2.4 mg P/g VSS/h), but significantly affected the storage of inclusion poly-S, the poly-S oxidation rate was increased about 16% while dosing nitrate from 20 to 30 mg N/L. It implies that nitrate is denitrified in the P uptake phase, and excess nitrate is further consumed by poly-S. Moreover, the microbial analysis showed that the functional bacteria should mostly belong to denitrifying bacteria or Unclassified genera. PMID:26983801

Acne -- self-care

MedlinePlus

... It may help to use a wash with salicylic acid or benzoyl if your skin is oily and ... products may contain benzoyl peroxide, sulfur, resorcinol, or salicylic acid. They work by killing bacteria, drying up skin ...

Terminal steps of bacteriochlorophyll a phytol formation in purple photosynthetic bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shioi, Y.; Sasa, T.

1984-04-01

Four chemically different bacteriochlorophylls (Bchls) a esterified with geranylgeraniol, dihydrogeranyl-geraniol, tetrahydrogeraniol, and phytol have been detected by high-pressure liquid chromatography in cell extracts from Rhodopseudomonas sphaeroides and Chromatium vinosum. Bchl a containing phytol is the principal component, and the other three Bchls a comprise about 4% of the total Bchls a in stationary-phase cells of R. sphaeroides and C. vinosum. The high levels of the minor pigments occur in the beginning of Bchl a phytol formation, indicating that they are not degradation products, but intermediates of Bchl a phytol formation.

Permeation of limonene through disposable nitrile gloves using a dextrous robot hand

PubMed Central

Banaee, Sean; S Que Hee, Shane

2017-01-01

Objectives: The purpose of this study was to investigate the permeation of the low-volatile solvent limonene through different disposable, unlined, unsupported, nitrile exam whole gloves (blue, purple, sterling, and lavender, from Kimberly-Clark). Methods: This study utilized a moving and static dextrous robot hand as part of a novel dynamic permeation system that allowed sampling at specific times. Quantitation of limonene in samples was based on capillary gas chromatography-mass spectrometry and the internal standard method (4-bromophenol). Results: The average post-permeation thicknesses (before reconditioning) for all gloves for both the moving and static hand were more than 10% of the pre-permeation ones (P≤0.05), although this was not so on reconditioning. The standardized breakthrough times and steady-state permeation periods were similar for the blue, purple, and sterling gloves. Both methods had similar sensitivity. The lavender glove showed a higher permeation rate (0.490±0.031 μg/cm2/min) for the moving robotic hand compared to the non-moving hand (P≤0.05), this being ascribed to a thickness threshold. Conclusions: Permeation parameters for the static and dynamic robot hand models indicate that both methods have similar sensitivity in detecting the analyte during permeation and the blue, purple, and sterling gloves behave similarly during the permeation process whether moving or non-moving. PMID:28111415

Carbonate Biogenic Structures in Storrs Lake, Bahamas

NASA Technical Reports Server (NTRS)

Byrne, Monica; Morris, Penny A.; Wentworth, Susan J.; Brigmon, Robin L.; McKay, David S.

2001-01-01

Storr's Lake, an inland hypersaline lake on San Salvador Island, Bahamas, contains calcium carbonate-rich lithified mats of filamentous microorganisms, diatoms, associated photosynthetic and chemotrophic bacteria, and trapped sediment. In addition, 16S rRNA analysis indicates the presence of five sulfur-reducing genera of bacteria. These microbes are potential modern-day analogs to some ancient stromatolitic structures. The goals of this study are to identify unique compositional and biogenic features, possibly correlating some of these with some of the sulfate-reducing bacteria. Additional information is contained in the original extended abstract.

Sulfur oxidation genes in diverse deep-sea viruses.

PubMed

Anantharaman, Karthik; Duhaime, Melissa B; Breier, John A; Wendt, Kathleen A; Toner, Brandy M; Dick, Gregory J

2014-05-16

Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary effects of viruses on marine phototrophs are well recognized, little is known about their impact on ubiquitous marine lithotrophs. Here, we report 18 genome sequences of double-stranded DNA viruses that putatively infect widespread sulfur-oxidizing bacteria. Fifteen of these viral genomes contain auxiliary metabolic genes for the α and γ subunits of reverse dissimilatory sulfite reductase (rdsr). This enzyme oxidizes elemental sulfur, which is abundant in the hydrothermal plumes studied here. Our findings implicate viruses as a key agent in the sulfur cycle and as a reservoir of genetic diversity for bacterial enzymes that underpin chemosynthesis in the deep oceans. Copyright © 2014, American Association for the Advancement of Science.

An isotopic biogeochemical study of the Green River oil shale

NASA Technical Reports Server (NTRS)

Collister, J. W.; Summons, R. E.; Lichtfouse, E.; Hayes, J. M.

1992-01-01

Thirty-five different samples from three different sulfur cycles were examined in this stratigraphically oriented study of the Shell 22x-l well (U.S.G.S. C177 core) in the Piceance Basin, Colorado. Carbon isotopic compositions of constituents of Green River bitumens indicate mixing of three main components: products of primary photoautotrophs and their immediate consumers (delta approximately -30% vs PDB), products of methanotrophic bacteria (delta approximately -85%), and products of unknown bacteria (delta approximately -40%). For individual compounds synthesized by primary producers, delta-values ranged from -28 to -32%. 13C contents of individual primary products (beta-carotane, steranes, acyclic isoprenoids, tricyclic triterpenoids) were not closely correlated, suggesting diverse origins for these materials. 13C contents of numerous hopanoids were inversely related to sulfur abundance, indicating that they derived both from methanotrophs and from other bacteria, with abundances of methanotrophs depressed when sulfur was plentiful in the paleoenvironment. gamma-Cerane coeluted with 3 beta(CH3),17 alpha(H),21 beta(H)-hopane, but delta-values could be determined after deconvolution. gamma-Cerane (delta approximately -25%) probably derives from a eukaryotic heterotroph grazing on primary materials, the latter compound (delta approximately -90%) must derive from methanotrophic organisms. 13C contents of n-alkanes in bitumen differed markedly from those of paraffins generated pyrolytically. Isotopic and quantitative relationships suggest that alkanes released by pyrolysis derived from a resistant biopolymer of eukaryotic origin and that this was a dominant constituent of total organic carbon.

Removal of H2S in down-flow GAC biofiltration using sulfide oxidizing bacteria from concentrated latex wastewater.

PubMed

Rattanapan, Cheerawit; Boonsawang, Piyarat; Kantachote, Duangporn

2009-01-01

A biofiltration system with sulfur oxidizing bacteria immobilized on granular activated carbon (GAC) as packing materials had a good potential when used to eliminate H(2)S. The sulfur oxidizing bacteria were stimulated from concentrated latex wastewater with sulfur supplement under aerobic condition. Afterward, it was immobilized on GAC to test the performance of cell-immobilized GAC biofilter. In this study, the effect of inlet H(2)S concentration, H(2)S gas flow rate, air gas flow rate and long-term operation on the H(2)S removal efficiency was investigated. In addition, the comparative performance of sulfide oxidizing bacterium immobilized on GAC (biofilter A) and GAC without cell immobilization (biofilter B) systems was studied. It was found that the efficiency of the H(2)S removal was more than 98% even at high concentrations (200-4000 ppm) and the maximum elimination capacity was about 125 g H(2)S/m(3)of GAC/h in the biofilter A. However, the H(2)S flow rate of 15-35 l/h into both biofilters had little influence on the efficiency of H(2)S removal. Moreover, an air flow rate of 5.86 l/h gave complete removal of H(2)S (100%) in biofilter A. During the long-term operation, the complete H(2)S removal was achieved after 3-days operation in biofilter A and remained stable up to 60-days.

Woodchip-sulfur based heterotrophic and autotrophic denitrification (WSHAD) process for nitrate contaminated water remediation.

PubMed

Li, Rui; Feng, Chuanping; Hu, Weiwu; Xi, Beidou; Chen, Nan; Zhao, Baowei; Liu, Ying; Hao, Chunbo; Pu, Jiaoyang

2016-02-01

Nitrate contaminated water can be effectively treated by simultaneous heterotrophic and autotrophic denitrification (HAD). In the present study, woodchips and elemental sulfur were used as co-electron donors for HAD. It was found that ammonium salts could enhance the denitrifying activity of the Thiobacillus bacteria, which utilize the ammonium that is produced by the dissimilatory nitrate reduction to ammonium (DNRA) in the woodchip-sulfur based heterotrophic and autotrophic denitrification (WSHAD) process. The denitrification performance of the WSHAD process (reaction constants range from 0.05485 h(-1) to 0.06637 h(-1)) is better than that of sulfur-based autotrophic denitrification (reaction constants range from 0.01029 h(-1) to 0.01379 h(-1)), and the optimized ratio of woodchips to sulfur is 1:1 (w/w). No sulfate accumulation is observed in the WSHAD process and the alkalinity generated in the heterotrophic denitrification can compensate for alkalinity consumption by the sulfur-based autotrophic denitrification. The symbiotic relationship between the autotrophic and the heterotrophic denitrification processes play a vital role in the mixotrophic environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sulfur-Oxidizing Bacteria in Soap Lake (Washington State), a Meromictic, Haloalkaline Lake with an Unprecedented High Sulfide Content▿

PubMed Central

Sorokin, Dimitry Y.; Foti, Mirjam; Pinkart, Holly C.; Muyzer, Gerard

2007-01-01

Culture-dependent and -independent techniques were used to study the diversity of chemolithoautotrophic sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake containing an unprecedentedly high sulfide concentration in the anoxic monimolimnion. Both approaches revealed the dominance of bacteria belonging to the genus Thioalkalimicrobium, which are common inhabitants of soda lakes. A dense population of Thioalkalimicrobium (up to 107 cells/ml) was found at the chemocline, which is characterized by a steep oxygen-sulfide gradient. Twelve Thioalkalimicrobium strains exhibiting three different phenotypes were isolated in pure culture from various locations in Soap Lake. The isolates fell into two groups according to 16S rRNA gene sequence analysis. One of the groups was closely related to T. cyclicum, which was isolated from Mono Lake (California), a transiently meromictic, haloalkaline lake. The second group, consisting of four isolates, was phylogenetically and phenotypically distinct from known Thioalkalimicrobium species and unique to Soap Lake. It represented a new species, for which we suggest the name Thioalkalimicrobium microaerophilum sp. nov. PMID:17114324

Insights into the single cell draft genome of "Candidatus Achromatium palustre".

PubMed

Salman, Verena; Berben, Tom; Bowers, Robert M; Woyke, Tanja; Teske, Andreas; Angert, Esther R

2016-01-01

"Candidatus Achromatium palustre" was recently described as the first marine representative of the Achromatium spp. in the Thiotrichaceae - a sister lineage to the Chromatiaceae in the Gammaproteobacteria. Achromatium spp. belong to the group of large sulfur bacteria as they can grow to nearly 100 μm in size and store elemental sulfur (S(0)) intracellularly. As a unique feature, Achromatium spp. can accumulate colloidal calcite (CaCO3) inclusions in great amounts. Currently, both process and function of calcite accumulation in bacteria is unknown, and all Achromatium spp. are uncultured. Recently, three single-cell draft genomes of Achromatium spp. from a brackish mineral spring were published, and here we present the first draft genome of a single "Candidatus Achromatium palustre" cell collected in the sediments of the Sippewissett Salt Marsh, Cape Cod, MA. Our draft dataset consists of 3.6 Mbp, has a G + C content of 38.1 % and is nearly complete (83 %). The next closest relative to the Achromatium spp. genomes is Thiorhodovibrio sp. 907 of the family Chromatiaceae, containing phototrophic sulfide-oxidizing bacteria.

Enhanced fatty acid production in engineered chemolithoautotrophic bacteria using reduced sulfur compounds as energy sources

DOE PAGES

Beller, Harry R.; Zhou, Peng; Jewell, Talia N. M.; ...

2016-07-05

Chemolithoautotrophic bacteria that oxidize reduced sulfur compounds, such as H 2 S, while fixing CO 2 are an untapped source of renewable bioproducts from sulfide-laden waste, such as municipal wastewater. In this study, we report engineering of the chemolithoautotrophic bacterium Thiobacillus denitrificans to produce up to 52-fold more fatty acids than the wild-type strain when grown with thiosulfate and CO 2 . A modified thioesterase gene from E. coli ('tesA) was integrated into the T. denitrificans chromosome under the control of P kan or one of two native T. denitrificans promoters. The relative strength of the two native promoters asmore » assessed by fatty acid production in engineered strains was very similar to that assessed by expression of the cognate genes in the wild-type strain. This proof-of-principle study suggests that engineering sulfide-oxidizing chemolithoautotrophic bacteria to overproduce fatty acid-derived products merits consideration as a technology that could simultaneously produce renewable fuels/chemicals as well as cost-effectively remediate sulfide-contaminated wastewater.« less

Insights into the single cell draft genome of “ Candidatus Achromatium palustre”

DOE PAGES

Salman, Verena; Berben, Tom; Bowers, Robert M.; ...

2016-03-23

" Candidatus Achromatium palustre" was recently described as the first marine representative of the Achromatium spp. in the Thiotrichaceae - a sister lineage to the Chromatiaceae in the Gammaproteobacteria. Achromatium spp. belong to the group of large sulfur bacteria as they can grow to nearly 100 mu m in size and store elemental sulfur (S-0) intracellularly. As a unique feature, Achromatium spp. can accumulate colloidal calcite (CaCO 3) inclusions in great amounts. Currently, both process and function of calcite accumulation in bacteria is unknown, and all Achromatium spp. are uncultured. Recently, three single-cell draft genomes of Achromatium spp. from amore » brackish mineral spring were published, and here we present the first draft genome of a single " Candidatus Achromatium palustre" cell collected in the sediments of the Sippewissett Salt Marsh, Cape Cod, MA. Our draft dataset consists of 3.6 Mbp, has a G + C content of 38.1 % and is nearly complete (83 %). In conclusion, the next closest relative to the Achromatium spp. genomes is Thiorhodovibrio sp. 907 of the family Chromatiaceae, containing phototrophic sulfide-oxidizing bacteria.« less

Sulfur Isotropic Studies of Archean Slate and Graywacke from Northern Minnesota: Evidence for the Existence of Sulfate Reducing Bacteria

NASA Technical Reports Server (NTRS)

Ripley, E. M.; Nicol, D. L.

1979-01-01

Sulfur isotopic studies of pyrite from metasediments in the 2.6 b.y. old Deer Lake greenstone sequence, Minnesota, were conducted in order to evaluate the possible importance of sulfate reducing bacteria in sulfide formation. Pyrite occurs as ovules up to 2 cm in diameter within graphitic slates, and as fine disseminations in metagraywacke units. SEM studies indicate the pyrite is framboidal in morphology. Delta notation values of pyrite from the Deer Lake sediments range from -2.3 to 11.1 0/00, with a peak at approximately +2 o/oo. Isotopic data is consistent with either high temperature inorganic reduction of circulating seawater sulfate, or low temperature bacterial reduction. However, the lack of sulfide bands or massive occurrences in the sediments, the restriction of pyrite mineralization to the sediments, and the absence of evidence for hot spring activity suggest that a diagenetic origin of pyrite is more feasible. Sulfide in such an environment would be produced principally by the action of sulfate reducing bacteria.

Effects of plant downtime on the microbial community composition in the highly saline brine of a geothermal plant in the North German Basin.

PubMed

Westphal, Anke; Lerm, Stephanie; Miethling-Graff, Rona; Seibt, Andrea; Wolfgramm, Markus; Würdemann, Hilke

2016-04-01

The microbial biocenosis in highly saline fluids produced from the cold well of a deep geothermal heat store located in the North German Basin was characterized during regular plant operation and immediately after plant downtime phases. Genetic fingerprinting revealed the dominance of sulfate-reducing bacteria (SRB) and fermentative Halanaerobiaceae during regular plant operation, whereas after shutdown phases, sequences of sulfur-oxidizing bacteria (SOB) were also detected. The detection of SOB indicated oxygen ingress into the well during the downtime phase. High 16S ribosomal RNA (rRNA) and dsrA gene copy numbers at the beginning of the restart process showed an enrichment of bacteria, SRB, and SOB during stagnant conditions consistent with higher concentrations of dissolved organic carbon (DOC), sulfate, and hydrogen sulfide in the produced fluids. The interaction of SRB and SOB during plant downtimes might have enhanced the corrosion processes occurring in the well. It was shown that scale content of fluids was significantly increased after stagnant phases. Moreover, the sulfur isotopic signature of the mineral scales indicated microbial influence on scale formation.

Bioassays of quorum sensing compounds using Agrobacterium tumefaciens and Chromobacterium violaceum.

PubMed

Chu, Weihua; Vattem, Dhiraj A; Maitin, Vatsala; Barnes, Mary B; McLean, Robert J C

2011-01-01

In most bacteria, a global level of regulation exists involving intercellular communication via the production and response to cell density-dependent signal molecules. This cell density-dependent regulation has been termed quorum sensing (QS). QS is a global regulator, which has been associated with a number of important features in bacteria including virulence regulation and biofilm formation. Consequently, there is considerable interest in understanding, detecting, and inhibiting QS. Acyl homoserine lactones (acyl HSLs) are used as extracellular QS signals by a variety of Gram-negative bacteria. Chromobacterium violaceum, a Gram-negative bacterium commonly found in soil and water, produces the characteristic purple pigment violacein, the production of which is regulated by acyl HSL-mediated QS. Based on this readily observed pigmentation phenotype, C. violaceum strains can be used to detect various aspects of acyl HSL-mediated QS activity. In another commonly used bioassay organism, Agrobacterium tumefaciens, QS can be detected by the use of a reporter gene such as lacZ. Here, we describe several commonly used approaches incorporating C. violaceum and A. tumefaciens that can be used to detect acyl HSLs and QS inhibition.

Geochemical and biological influences on the distribution of bacteriohopanepolyol biomarkers in hydrothermal springs

NASA Astrophysics Data System (ADS)

Boyer, G. M.; Woods, J.; Schubotz, F.; Shock, E.; Boyd, E. S.; Summons, R. E.

2013-12-01

Bacteriohopanepolyols (BHPs) and their geohopanoid derivatives comprise a structurally-diverse and ubiquitous family of lipid biomarkers. It is known that certain structural motifs present in BHPs, such as methylations or composite sugars, are indicative of certain bacterial taxonomic groups or particular metabolisms, but the link between geochemistry and the structural diversity of BHPs remains poorly understood. In this study, BHPs were extracted from 18 sediment or microbial mat samples collected along the outflow channels or source pools of six geochemically diverse hot springs in Yellowstone National Park, USA and Fludir, Iceland. The abundance and distribution of over 30 structurally diverse BHPs were determined by liquid chromatography mass spectrometry and correlated to aqueous and solid phase geochemical measurements and 16S rDNA pyrosequencing data collected in parallel from the same sample locations. In general, BHP abundance is correlated more strongly to dissolved oxygen concentrations (Pearson R = 0.87) than to pH, temperature, or conductivity. This is also the case for bacteriohopanetetrol (R = 0.81) and especially its 2-methyl counterpart (R = 0.90), a BHP commonly associated with the presence of cyanobacteria and purple non-sulfur bacteria [1]. Sulfide appears to be negatively associated with BHP abundance, with over 90% of BHP mass found in sites where total sulfide concentrations are below 50 μg/L, which may be due to either the activity of sulfide oxidizing populations that function to maintain low sulfide concentrations [2] or the sensitivity of oxygenic phototrophs to sulfide [3,4]. The abundance of bulk solid-phase carbon associated with the sediment or mat samples correlates to overall BHP concentrations (R = 0.87) and the within-site percent abundance of bacteriohopanetetrol-cyclitol ether (R = 0.90). Intriguingly, bulk solid-phase nitrogen concentration seems to be related to the percent abundance of nitrogen-bearing BHPs, suggesting that as more nitrogen becomes available, bacteria incorporate it into a greater proportion of their BHPs. However, this relationship appears to be highly influenced by pH, with acidic sites having a greater percentage of nitrogen-bearing BHPs than near-neutral or alkaline sites. Finally, the number of BHP structures detected is positively correlated with the diversity of bacterial 16S rDNA genes (R2 = 0.62, logarithmic fit), suggesting that BHP structural diversity is a good proxy for estimating bacterial taxonomic diversity. [1] H. M. Talbot et al., Org. Geochem. 39, 232-263 (2008). [2] S. D'Imperio et al., Appl. Environ. Microbiol. 74, 5802-5808 (2008). [3] R. W. Castenholz, Microb. Ecol. 3, 79-105 (1977). [4] E. S. Boyd et al., Front. Microbiol. 3: 221 (2012).

Zero-sulfur diesel fuel from non-petroleum resources : the key to reducing U.S. oil imports.

DOT National Transportation Integrated Search

2012-09-01

Zero-sulfur diesel fuel of the highest quality, the fuel used in this project, can be made by Fischer-Tropsch (FT) synthesis from many non-petroleum resources, including natural gas, which is increasingly abundant in the United States. Zero-sulfur FT...

An investigation of the efficacy of biological additives for the suppression of pyritic sulphur during simulated froth flotation of coal.

PubMed

Stainthorpe, A C

1989-02-05

The biological molecule responsible for the suppression of pyritic sulfur in fine coal simulated froth flotation treated with bacteria was identified. Protein was found to be the most effective agent in pyrite suppression of the three cell components (protein, lipid, and carbohydrate) assayed. Coal recovery and ash removal of the flotation process were only slightly reduced by this treatment. Other protein-containing materials were evaluated for their ability to suppress pyrite flotation. Whey was found to be the most cost-effective flotation additive of those assayed. The sulfur content of the whey-treated float was reduced by 84.0% in a synthetically prepared fractionated coal (10.7% sulfur), by a raw whey dosage of 20 microL/g coal. The inorganic sulfur component of a natural high sulfur coal fraction (10.9%) was completely depressed by this whey addition. The effect of particle size and pulp density upon the process were investigated.

Archaea S-layer nanotube from a "black smoker" in complex with cyclo-octasulfur (S8 ) rings.

PubMed

McDougall, Matthew; Francisco, Olga; Harder-Viddal, Candice; Roshko, Roy; Meier, Markus; Stetefeld, Jörg

2017-12-01

Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion. Comparisons with earlier MD studies of the free energy of hydration as a function of water occupancy in the same cavity of archaeal tetrabrachion show that the sulfur ring is energetically favored over water. © 2017 Wiley Periodicals, Inc.

Sulfur, ultraviolet radiation, and the early evolution of life

NASA Technical Reports Server (NTRS)

Kasting, J. F.; Zahnle, K. J.; Pinto, J. P.; Young, A. T.

1989-01-01

The present biosphere is shielded from harmful solar near ultraviolet (UV) radiation by atmospheric ozone. It is suggested that elemental sulfur vapor could have played a similar role in an anoxic, ozone-free, primitive atmosphere. Sulfur vapor would have been produced photochemically from volcanogenic SO2 and H2S. It is composed of ring molecules, primarily S8, that absorb strongly throughout the near UV, yet are expected to be relatively stable against photolysis and chemical attack. It is also insoluble in water and would thus have been immune to rainout or surface deposition over the oceans. Since the concentration of S8 in the primitive atmosphere would have been limited by its saturation vapor pressure, surface temperatures of 45 C or higher, corresponding to carbon dioxide partial pressures exceeding 2 bars, are required to sustain an effective UV screen. A warm, sulfur-rich, primitive atmosphere is consistent with inferences drawn from molecular phylogeny, which suggest that some of the earliest organisms were thermophilic bacteria that metabolized elemental sulfur.

JPRS Report. Science & Technology: Japan

DTIC Science & Technology

1987-07-16

methane. So, it has been proved that seawater containing methane and sulfur, which oozed out at this point from underground, grew bacteria, a food ...activity was measured by dispersing glass powder at the seabed and the speed of extinction due to food poisoning was also measured by leaving dead...solar light is very small due to the scarcity of food . However, a special ecosystem nourished with bacteria, which eat methane and inorganic compounds

Volatile sulfur compounds produced by probiotic bacteria in the presence of cysteine or methionine.

PubMed

Sreekumar, R; Al-Attabi, Z; Deeth, H C; Turner, M S

2009-06-01

To investigate the abilities of various probiotic bacteria to produce volatile sulfur compounds (VSCs) relevant to food flavour and aroma. Probiotic strains (Lactobacillus acidophilus NCFM, Lactobacillus plantarum 299v, Lactobacillus rhamnosus GG, Lactobacillus reuteri ATCC55730 and L. reuteri BR11), Lactobacillus delbrueckii ATCC4797, L. plantarum ATCC14917 and Lactococcus lactis MG1363 were incubated with either cysteine or methionine. Volatile compounds were captured, identified and quantified using a sensitive solid-phase microextraction (SPME) technique combined with gas chromatography coupled to a pulsed flame photometric detector (SPME/GC/PFPD). Several VSCs were identified including H(2)S, methanethiol, dimethyldisulfide and dimethyltrisulfide. The VSC profiles varied substantially for different strains of L. plantarum and L. reuteri and it was found that L. reuteri ATCC55730 and L. lactis MG1363 produced the lowest levels of VSCs (P < 0.05). Levels of VSCs generated by bacteria were found to be equivalent to, or higher than, that found in commercial cheeses. Several probiotic strains are able to generate considerable levels of VSCs and substantial variations in VSC generating potential exists between different strains from the same species. This study demonstrates that probiotic bacteria are able to efficiently generate important flavour and aroma compounds and therefore has implications for the development of probiotic containing foods.

Role of an elliptical structure in photosynthetic energy transfer: Collaboration between quantum entanglement and thermal fluctuation

PubMed Central

Oka, Hisaki

2016-01-01

Recent experiments have revealed that the light-harvesting complex 1 (LH1) in purple photosynthetic bacteria has an elliptical structure. Generally, symmetry lowering in a structure leads to a decrease in quantum effects (quantum coherence and entanglement), which have recently been considered to play a role in photosynthetic energy transfer, and hence, elliptical structure seems to work against efficient photosynthetic energy transfer. Here we analyse the effect of an elliptical structure on energy transfer in a purple photosynthetic bacterium and reveal that the elliptical distortion rather enhances energy transfer from peripheral LH2 to LH1 at room temperature. Numerical results show that quantum entanglement between LH1 and LH2 is formed over a wider range of high energy levels than would have been the case with circular LH1. Light energy absorbed by LH2 is thermally pumped via thermal fluctuation and is effectively transferred to LH1 through the entangled states at room temperature rather than at low temperature. This result indicates the possibility that photosynthetic systems adopt an elliptical structure to effectively utilise both quantum entanglement and thermal fluctuation at physiological temperature. PMID:27173144

Role of an elliptical structure in photosynthetic energy transfer: Collaboration between quantum entanglement and thermal fluctuation

NASA Astrophysics Data System (ADS)

Oka, Hisaki

2016-05-01

Recent experiments have revealed that the light-harvesting complex 1 (LH1) in purple photosynthetic bacteria has an elliptical structure. Generally, symmetry lowering in a structure leads to a decrease in quantum effects (quantum coherence and entanglement), which have recently been considered to play a role in photosynthetic energy transfer, and hence, elliptical structure seems to work against efficient photosynthetic energy transfer. Here we analyse the effect of an elliptical structure on energy transfer in a purple photosynthetic bacterium and reveal that the elliptical distortion rather enhances energy transfer from peripheral LH2 to LH1 at room temperature. Numerical results show that quantum entanglement between LH1 and LH2 is formed over a wider range of high energy levels than would have been the case with circular LH1. Light energy absorbed by LH2 is thermally pumped via thermal fluctuation and is effectively transferred to LH1 through the entangled states at room temperature rather than at low temperature. This result indicates the possibility that photosynthetic systems adopt an elliptical structure to effectively utilise both quantum entanglement and thermal fluctuation at physiological temperature.

Characteristics of purple nonsulfur bacteria grown under Stevia residue extractions.

PubMed

Xu, J; Feng, Y; Wang, Y; Lin, X

2013-11-01

As a consequence of the large-scale cultivation of Stevia plants, releases of plant residues, the byproduct after sweetener extraction, to the environment are inevitable. Stevia residue and its effluent after batching up contain large amounts of organic matters with small molecular weight, which therefore are a potential pollution source. Meanwhile, they are favourite substrates for micro-organism growths. This investigation was aimed to utilize the simulated effluent of Stevia residue to enrich the representative purple nonsulfur bacterium (PNSB), Rhodopseudomonas palustris (Rps. palustris), which has important economic values. The growth profile and quality of Rps. palustris were characterized by spectrophotometry, compared to those grown in common PNSB mineral synthetic medium. Our results revealed that the simulated effluent of Stevia residue not only stimulated Rps. palustris growth to a greater extent, but also increased its physiologically active cytochrome concentrations and excreted indole-3-acetic acid (IAA) content. This variation in phenotype of Rps. palustris could result from the shift in its genotype, further revealed by the repetitive sequence-based PCR (rep-PCR) fingerprinting analysis. Our results showed that the effluent of Stevia residue was a promising substrate for microbial growth. © 2013 The Society for Applied Microbiology.

Role of an elliptical structure in photosynthetic energy transfer: Collaboration between quantum entanglement and thermal fluctuation.

PubMed

Oka, Hisaki

2016-05-13

Recent experiments have revealed that the light-harvesting complex 1 (LH1) in purple photosynthetic bacteria has an elliptical structure. Generally, symmetry lowering in a structure leads to a decrease in quantum effects (quantum coherence and entanglement), which have recently been considered to play a role in photosynthetic energy transfer, and hence, elliptical structure seems to work against efficient photosynthetic energy transfer. Here we analyse the effect of an elliptical structure on energy transfer in a purple photosynthetic bacterium and reveal that the elliptical distortion rather enhances energy transfer from peripheral LH2 to LH1 at room temperature. Numerical results show that quantum entanglement between LH1 and LH2 is formed over a wider range of high energy levels than would have been the case with circular LH1. Light energy absorbed by LH2 is thermally pumped via thermal fluctuation and is effectively transferred to LH1 through the entangled states at room temperature rather than at low temperature. This result indicates the possibility that photosynthetic systems adopt an elliptical structure to effectively utilise both quantum entanglement and thermal fluctuation at physiological temperature.

Distribution of rhodopin and spirilloxanthin between LH1 and LH2 complexes when incorporating carotenoid mixture into the membrane of purple sulfur bacterium Allochromatium minutissimum in vitro.

PubMed

Bolshakov, M A; Ashikhmin, A A; Makhneva, Z K; Moskalenko, A A

2016-11-01

Carotenoid mixture enriched by rhodopin and spirilloxanthin was incorporated in LH2 and LH1 complexes from Allochromatium (Alc.) minutissimum in vitro. The maximum incorporating level was ~95%. Rhodopin (56.4%) and spirilloxanthin (13.8%) were incorporated into the LH1 complex, in contrast to the control complex, which contained primarily spirilloxanthin (66.8%). After incorporating, the LH2 complex contained rhodopin (66.7%) and didehydrorhodopin (14.6%), which was close to their content in the control (67.4 and 20.5%, respectively). Thus, it was shown that carotenoids from the total pool are not selectively incorporated into LH2 and LH1 complexes in vitro in the proportion corresponding to the carotenoid content in the complexes in vivo.

Analytical investigations on the Coronation Gospels manuscript

NASA Astrophysics Data System (ADS)

Aceto, Maurizio; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Crivello, Fabrizio; Griesser, Martina; Kirchweger, Franz; Uhlir, Katharina; Puyo, Patricia Roger

2017-01-01

The Coronation Gospels or Krönungsevangeliar is a manuscript kept in Vienna at the Kunsthistorisches Museum Wien, datable to the end of VIII century A.D. and produced at Charlemagne court. It is an example of a purple codex, i.e. its parchment is coloured in purple. It has to be considered as one of the most important medieval codices, according to its use to take oath in the coronation ceremony of kings and emperors of the Holy Roman Empire up to 1792. In order to gather information of the manufacture of the manuscript and its present conservation state, a diagnostic investigation campaign has been carried out in situ with totally non-invasive techniques. X-ray Fluorescence Spectrometry (XRF), UV-visible diffuse reflectance spectrophotometry with optical fibres (FORS), spectrofluorimetry, optical microscopy and multispectral analysis have been applied in order to identify the colourants used in the decoration of the manuscript, with the main concern to the dye used to impart the purple hue to the parchment. The information collected was useful in order to address some of the questions raised by art historians concerning its history.

On the identification of folium and orchil on illuminated manuscripts.

PubMed

Aceto, Maurizio; Calà, Elisa; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Porter, Cheryl; Gulmini, Monica

2017-01-15

The identification of the two purple dyes folium and orchil has rarely been reported in the analysis of painted artworks, especially when analysing illuminated manuscripts. This is not consistent with the fact that ancient literary sources suggested their use as substitutes for the more expensive Tyrian purple dye. By employing non-invasive spectroscopic techniques, the present work demonstrates that these dyes were actually widely used in the production of ancient manuscripts. By employing UV-visible diffuse reflectance spectrophotometry with optic fibres (FORS) and spectrofluorimetry, the abundant identification of both dyes on medieval manuscripts was performed by comparing the spectra recorded on ancient codices with those obtained on accurate replicas of dyed or painted parchment. Moreover, examples are also reported whereby the considered purple dyes were used in mixtures with other colourants. The overall information obtained here allowed us to define new boundaries for the time range in which orchil and folium dyes were used which is wider than previously thought, and to focus on their particular uses in the decoration of books. Copyright © 2016 Elsevier B.V. All rights reserved.

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity.

PubMed

Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

2018-01-01

Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile genetic potential to adapt to the unique environmental conditions.

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity

PubMed Central

Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A.; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

2018-01-01

Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile genetic potential to adapt to the unique environmental conditions. PMID:29527196

Clades of Photosynthetic Bacteria Belonging to the Genus Rhodopseudomonas Show Marked Diversity in Light-Harvesting Antenna Complex Gene Composition and Expression

DOE PAGES

Fixen, Kathryn R.; Oda, Yasuhiro; Harwood, Caroline S.; ...

2015-12-22

Many photosynthetic bacteria have peripheral light-harvesting (LH) antenna complexes that increase the efficiency of light energy capture. The purple nonsulfur photosynthetic bacteriumRhodopseudomonas palustrisproduces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complexes). There are multiplepucBAoperons that encode the α and β peptides that make up these complexes. But, low-resolution structures, amino acid similarities between the complexes, and a lack of transcription analysis have made it difficult to determine the contributions of differentpucBAoperons to the composition and function of different LH complexes. It was also unclear how much diversity of LHmore » complexes exists inR. palustrisand affiliated strains. To address this, we undertook an integrative genomics approach using 20 sequenced strains. Gene content analysis revealed that even closely related strains have differences in theirpucBAgene content. Transcriptome analyses of the strains grown under high light and low light revealed that the patterns of expression of thepucBAoperons varied among strains grown under the same conditions. We also found that one set of LH2 complex proteins compensated for the lack of an LH4 complex under low light intensities but not under extremely low light intensities, indicating that there is functional redundancy between some of the LH complexes under certain light intensities. The variation observed in LH gene composition and expression inRhodopseudomonasstrains likely reflects how they have evolved to adapt to light conditions in specific soil and water microenvironments. ImportanceRhodopseudomonas palustrisis a phototrophic purple nonsulfur bacterium that adapts its photosystem to allow growth at a range of light intensities. It does this by adjusting the amount and composition of peripheral light-harvesting (LH) antenna complexes that it synthesizes.Rhodopseudomonasstrains are notable for containing numerous sets of light-harvesting genes. We determined the diversity of LH complexes and their transcript levels during growth under high and low light intensities in 20 sequenced genomes of strains related to the speciesRhodopseudomonas palustris. Finally, the data obtained are a resource for investigators with interests as wide-ranging as the biophysics of photosynthesis, the ecology of phototrophic bacteria, and the use of photosynthetic bacteria for biotechnology applications.« less

Clades of Photosynthetic Bacteria Belonging to the Genus Rhodopseudomonas Show Marked Diversity in Light-Harvesting Antenna Complex Gene Composition and Expression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fixen, Kathryn R.; Oda, Yasuhiro; Harwood, Caroline S.

Many photosynthetic bacteria have peripheral light-harvesting (LH) antenna complexes that increase the efficiency of light energy capture. The purple nonsulfur photosynthetic bacteriumRhodopseudomonas palustrisproduces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complexes). There are multiplepucBAoperons that encode the α and β peptides that make up these complexes. But, low-resolution structures, amino acid similarities between the complexes, and a lack of transcription analysis have made it difficult to determine the contributions of differentpucBAoperons to the composition and function of different LH complexes. It was also unclear how much diversity of LHmore » complexes exists inR. palustrisand affiliated strains. To address this, we undertook an integrative genomics approach using 20 sequenced strains. Gene content analysis revealed that even closely related strains have differences in theirpucBAgene content. Transcriptome analyses of the strains grown under high light and low light revealed that the patterns of expression of thepucBAoperons varied among strains grown under the same conditions. We also found that one set of LH2 complex proteins compensated for the lack of an LH4 complex under low light intensities but not under extremely low light intensities, indicating that there is functional redundancy between some of the LH complexes under certain light intensities. The variation observed in LH gene composition and expression inRhodopseudomonasstrains likely reflects how they have evolved to adapt to light conditions in specific soil and water microenvironments. ImportanceRhodopseudomonas palustrisis a phototrophic purple nonsulfur bacterium that adapts its photosystem to allow growth at a range of light intensities. It does this by adjusting the amount and composition of peripheral light-harvesting (LH) antenna complexes that it synthesizes.Rhodopseudomonasstrains are notable for containing numerous sets of light-harvesting genes. We determined the diversity of LH complexes and their transcript levels during growth under high and low light intensities in 20 sequenced genomes of strains related to the speciesRhodopseudomonas palustris. Finally, the data obtained are a resource for investigators with interests as wide-ranging as the biophysics of photosynthesis, the ecology of phototrophic bacteria, and the use of photosynthetic bacteria for biotechnology applications.« less

Domestic wastewater treatment with purple phototrophic bacteria using a novel continuous photo anaerobic membrane bioreactor.

PubMed

Hülsen, Tim; Barry, Edward M; Lu, Yang; Puyol, Daniel; Keller, Jürg; Batstone, Damien J

2016-09-01

A key future challenge of domestic wastewater treatment is nutrient recovery while still achieving acceptable discharge limits. Nutrient partitioning using purple phototrophic bacteria (PPB) has the potential to biologically concentrate nutrients through growth. This study evaluates the use of PPB in a continuous photo-anaerobic membrane bioreactor (PAnMBR) for simultaneous organics and nutrient removal from domestic wastewater. This process could continuously treat domestic wastewater to discharge limits (<50 mgCOD L(-1), 5 mgN L(-1), 1.0 mgP L(-1)). Approximately 6.4 ± 1.3 gNH4-N and 1.1 ± 0.2 gPO4-P for every 100 gSCOD were removed at a hydraulic retention time of 8-24 h and volumetric loading rates of 0.8-2.5 COD kg m(3) d(-1). Thus, a minimum of 200 mg L(-1) of ethanol (to provide soluble COD) was required to achieve these discharge limits. Microbial community through sequencing indicated dominance of >60% of PPB, though the PPB community was highly variable. The outcomes from the current work demonstrate the potential of PPB for continuous domestic (and possibly industrial) wastewater treatment and nutrient recovery. Technical challenges include the in situ COD supply in a continuous reactor system, as well as efficient light delivery. Addition of external (agricultural or fossil) derived organics is not financially nor environmentally justified, and carbon needs to be sourced internally from the biomass itself to enable this technology. Reduced energy consumption for lighting is technically feasible, and needs to be addressed as a key objective in scaleup. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Construction and Characterization of B850-Only LH2 Energy Transfer System in Purple Bacteria].

PubMed

Li, Kai; Zhao, Chun-gui; Yue, Hui-ying; Yang, Su-ping; Qu, Yin-bo; Jiao, Nian-zhi

2015-04-01

To seek microscopic molecular mechanism of energy transfer and complex reconstitution in the photosynthesis, the conditions for construction of B850-only peripheral light-harvesting complex (LH2) and their properties were investigated using absorption, fluorescence spectroscopy, molecular sieve chromatography, ultrafiltration and sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) from the purple bacteria. The results indicated that bacteriochlorophylls (BChl) of B800 incubated in 10 mmo · L(-1) Tris-HCl (pH 8.0) buffer are selectively released from their binding sites of LH2 of Rhodobacter azotoformans (A-LH2) by 0.08% (W/V) SDS. B850-only A-LH2 was constructed after removing free BChl mixing with 10% methyl alcohol by ultrafiltration. B850 BChl was released after A-LH2 was incubated for 240 min in dark at room temperature (RT). While BChl of B800 incubated in pH 1.9 buffer were selectively released from their binding sites of LH2 of Rhodopseudomonas palustris (P-LH2). The authors acquired two components using molecular sieve chromatography. Free BChl of one component was not removed and self-assembled to P-LH2. The other removed free BChl and B850-only P-LH2 was constructed. B850 unchanged after P-LH2 was incubated. P-LH2 α and β subunits have different molecular weights, but those of A-LH2 are in the contrary. It is concluded that B850-only P-LH2 is more stable than A-LH2. The enigmatic split of the B800 absorption band was not observed in these LH2, but we acquired two kinds of B800-released LH2 from Rhodopseudomonas palustris. The authors' results may provide a new light to separate homogeneous Apoprotein LH2.

Photoprotection in a purple phototrophic bacterium mediated by oxygen-dependent alteration of carotenoid excited-state properties

PubMed Central

Šlouf, Václav; Chábera, Pavel; Olsen, John D.; Martin, Elizabeth C.; Qian, Pu; Hunter, C. Neil; Polívka, Tomáš

2012-01-01

Carotenoids are known to offer protection against the potentially damaging combination of light and oxygen encountered by purple phototrophic bacteria, but the efficiency of such protection depends on the type of carotenoid. Rhodobacter sphaeroides synthesizes spheroidene as the main carotenoid under anaerobic conditions whereas, in the presence of oxygen, the enzyme spheroidene monooxygenase catalyses the incorporation of a keto group forming spheroidenone. We performed ultrafast transient absorption spectroscopy on membranes containing reaction center-light-harvesting 1-PufX (RC-LH1-PufX) complexes and showed that when oxygen is present the incorporation of the keto group into spheroidene, forming spheroidenone, reconfigures the energy transfer pathway in the LH1, but not the LH2, antenna. The spheroidene/spheroidenone transition acts as a molecular switch that is suggested to twist spheroidenone into an s-trans configuration increasing its conjugation length and lowering the energy of the lowest triplet state so it can act as an effective quencher of singlet oxygen. The other consequence of converting carotenoids in RC-LH1-PufX complexes is that S2/S1/triplet pathways for spheroidene is replaced with a new pathway for spheroidenone involving an activated intramolecular charge-transfer (ICT) state. This strategy for RC-LH1-PufX-spheroidenone complexes maintains the light-harvesting cross-section of the antenna by opening an active, ultrafast S1/ICT channel for energy transfer to LH1 Bchls while optimizing the triplet energy for singlet oxygen quenching. We propose that spheroidene/spheroidenone switching represents a simple and effective photoprotective mechanism of likely importance for phototrophic bacteria that encounter light and oxygen. PMID:22586075

Emission lineshapes of the B850 band of light-harvesting 2 (LH2) complex in purple bacteria: a second order time-nonlocal quantum master equation approach.

PubMed

Kumar, Praveen; Jang, Seogjoo

2013-04-07

The emission lineshape of the B850 band in the light harvesting complex 2 of purple bacteria is calculated by extending the approach of 2nd order time-nonlocal quantum master equation [S. Jang and R. J. Silbey, J. Chem. Phys. 118, 9312 (2003)]. The initial condition for the emission process corresponds to the stationary excited state density where exciton states are entangled with the bath modes in equilibrium. This exciton-bath coupling, which is not diagonal in either site excitation or exciton basis, results in a new inhomogeneous term that is absent in the expression for the absorption lineshape. Careful treatment of all the 2nd order terms are made, and explicit expressions are derived for both full 2nd order lineshape expression and the one based on secular approximation that neglects off-diagonal components in the exciton basis. Numerical results are presented for a few representative cases of disorder and temperature. Comparison of emission line shape with the absorption line shape is also made. It is shown that the inhomogeneous term coming from the entanglement of the system and bath degrees of freedom makes significant contributions to the lineshape. It is also found that the perturbative nature of the theory can result in negative portion of lineshape in some situations, which can be removed significantly by inclusion of the inhomogeneous term and completely by using the secular approximation. Comparison of the emission and absorption lineshapes at different temperatures demonstrates the role of thermal population of different exciton states and exciton-phonon couplings.

Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

PubMed

Sturgis, James N; Niederman, Robert A

2008-01-01

Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

Pigment organization and their interactions in reaction centers of photosystem II: optical spectroscopy at 6 K of reaction centers with modified pheophytin composition.

PubMed

Germano, M; Shkuropatov, A Y; Permentier, H; de Wijn, R; Hoff, A J; Shuvalov, V A; van Gorkom, H J

2001-09-25

Photosystem II reaction centers (RC) with selectively exchanged pheophytin (Pheo) molecules as described in [Germano, M., Shkuropatov, A. Ya., Permentier, H., Khatypov, R. A., Shuvalov, V. A., Hoff, A. J., and van Gorkom, H. J. (2000) Photosynth. Res. 64, 189-198] were studied by low-temperature absorption, linear and circular dichroism, and triplet-minus-singlet absorption-difference spectroscopy. The ratio of extinction coefficients epsilon(Pheo)/epsilon(Chl) for Q(Y) absorption in the RC is approximately 0.40 at 6 K and approximately 0.45 at room temperature. The presence of 2 beta-carotenes, one parallel and one perpendicular to the membrane plane, is confirmed. Absorption at 670 nm is due to the perpendicular Q(Y) transitions of the two peripheral chlorophylls (Chl) and not to either Pheo. The "core" pigments, two Pheo and four Chl absorb in the 676-685 nm range. Delocalized excited states as predicted by the "multimer model" are seen in the active branch. The inactive Pheo and the nearby Chl, however, mainly contribute localized transitions at 676 and 680 nm, respectively, although large CD changes indicate that exciton interactions are present on both branches. Replacement of the active Pheo prevents triplet formation, causes an LD increase at 676 and 681 nm, a blue-shift of 680 nm absorbance, and a bleach of the 685 nm exciton band. The triplet state is mainly localized on the Chl corresponding to B(A) in purple bacteria. Both Pheo Q(Y) transitions are oriented out of the membrane plane. Their Q(X) transitions are parallel to that plane, so that the Pheos in PSII are structurally similar to their homologues in purple bacteria.

Aphrodisiac Activity of the Aqueous Crude Extract of Purple Corn ( Zea mays) in Male Rats.

PubMed

Carro-Juárez, Miguel; Rodríguez-Santiago, Magdalena G; Franco, Miguel Angel; Hueletl-Soto, María Eugenia

2017-10-01

In the present study, the aphrodisiac properties of the purple corn ( Zea mays) in male rats were analyzed. The aqueous crude extract of purple corn (at 25, 50, and 75 mg/kg) was administered to ( a) copulating male rats and ( b) anesthetized and spinal cord transected male rats. Behavioral parameters of copulatory behavior and parameters of the genital motor pattern of ejaculation previous to its inhibition, under the influence of the purple corn extract, are described. Administration of the aqueous crude extract of purple corn significantly facilitates the arousal and execution of male rat sexual behavior without significant influences on the ambulatory behavior. In addition, purple corn extract elicit a significant increase in the number of discharges of the ejaculatory motor patterns and in the total number of genital motor patterns evoked in spinal rats. The present findings show that the aqueous crude extract of purple corn possesses aphrodisiac activity.

Aphrodisiac Activity of the Aqueous Crude Extract of Purple Corn (Zea mays) in Male Rats

PubMed Central

Carro-Juárez, Miguel; Rodríguez-Santiago, Magdalena G.; Franco, Miguel Angel; Hueletl-Soto, María Eugenia

2017-01-01

In the present study, the aphrodisiac properties of the purple corn (Zea mays) in male rats were analyzed. The aqueous crude extract of purple corn (at 25, 50, and 75 mg/kg) was administered to (a) copulating male rats and (b) anesthetized and spinal cord transected male rats. Behavioral parameters of copulatory behavior and parameters of the genital motor pattern of ejaculation previous to its inhibition, under the influence of the purple corn extract, are described. Administration of the aqueous crude extract of purple corn significantly facilitates the arousal and execution of male rat sexual behavior without significant influences on the ambulatory behavior. In addition, purple corn extract elicit a significant increase in the number of discharges of the ejaculatory motor patterns and in the total number of genital motor patterns evoked in spinal rats. The present findings show that the aqueous crude extract of purple corn possesses aphrodisiac activity. PMID:28508664

Growth of Acidithiobacillus Ferrooxidans ATCC 23270 in Thiosulfate Under Oxygen-Limiting Conditions Generates Extracellular Sulfur Globules by Means of a Secreted Tetrathionate Hydrolase

PubMed Central

Beard, Simón; Paradela, Alberto; Albar, Juan P.; Jerez, Carlos A.

2011-01-01

Production of sulfur globules during sulfide or thiosulfate oxidation is a characteristic feature of some sulfur bacteria. Although their generation has been reported in Acidithiobacillus ferrooxidans, its mechanism of formation and deposition, as well as the physiological significance of these globules during sulfur compounds oxidation, are currently unknown. Under oxygen-sufficient conditions (OSC), A. ferrooxidans oxidizes thiosulfate to tetrathionate, which accumulates in the culture medium. Tetrathionate is then oxidized by a tetrathionate hydrolase (TTH) generating thiosulfate, elemental sulfur, and sulfate as final products. We report here a massive production of extracellular conspicuous sulfur globules in thiosulfate-grown A. ferrooxidans cultures shifted to oxygen-limiting conditions (OLC). Concomitantly with sulfur globule deposition, the extracellular concentration of tetrathionate greatly diminished and sulfite accumulated in the culture supernatant. A. ferrooxidans cellular TTH activity was negligible in OLC-incubated cells, indicating that this enzymatic activity was not responsible for tetrathionate disappearance. On the other hand, supernatants from both OSC- and OLC-incubated cells showed extracellular TTH activity, which most likely accounted for tetrathionate consumption in the culture medium. The extracellular TTH activity described here: (i) gives experimental support to the TTH-driven model for hydrophilic sulfur globule generation, (ii) explains the extracellular location of A. ferrooxidans sulfur deposits, and (iii) strongly suggests that the generation of sulfur globules in A. ferrooxidans corresponds to an early step during its adaptation to an anaerobic lifestyle. PMID:21833324

Comparative analysis of Beggiatoa from hypersaline and marine environments.

PubMed

de Albuquerque, Julia Peixoto; Keim, Carolina Neumann; Lins, Ulysses

2010-07-01

The main criterion to classify a microorganism as belonging to the genus Beggiatoa is its morphology. All multicellular, colorless, gliding bacterial filaments containing sulfur globules described so far belong to this genus. At the ultrastructural level, they show also a very complex cell envelope structure. Here we describe uncultured vacuolated and non-vacuolated bacteria from two different environments showing all characteristics necessary to assign a bacterium to the genus Beggiatoa. We also intended to investigate whether narrow and vacuolate Beggiatoa do differ morphologically as much as they do phylogenetically. Both large, vacuolated trichomes and narrow filaments devoid of vacuoles were observed. We confirmed the identity of the narrow filaments by 16S rRNA phylogenetic analysis. The diameters of the trichomes ranged from 2.4 to 34 microm, and their lengths ranged from 10 microm to over 30 mm. Narrow trichomes moved by gliding at 3.0 microm/s; large filaments moved at 1.5 microm/s. Periplasmic sulfur inclusions were observed in both types of filaments, whereas phosphorus-rich bodies were found only in narrow trichomes. On the other hand, nitrate vacuoles were observed only in large trichomes. Ultra-thin section transmission electron microscopy showed differences between the cell ultrastructure of narrow (non-vacuolated) and large (vacuolated) Beggiatoa. We observed that cell envelopes from narrow Beggiatoa consist of five layers, whereas cell envelopes from large trichomes contain four layers. Copyright 2010 Elsevier Ltd. All rights reserved.

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin

PubMed Central

Sharrar, Allison M.; Flood, Beverly E.; Bailey, Jake V.; Jones, Daniel S.; Biddanda, Bopaiah A.; Ruberg, Steven A.; Marcus, Daniel N.; Dick, Gregory J.

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea. PMID:28533768

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.

PubMed

Sharrar, Allison M; Flood, Beverly E; Bailey, Jake V; Jones, Daniel S; Biddanda, Bopaiah A; Ruberg, Steven A; Marcus, Daniel N; Dick, Gregory J

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H 2 -based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H 2 oxidation via Ni-Fe hydrogenases, and the use of O 2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction ( sat, apr , and dsr ) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate-reducing bacteria, and archaea.

Use of Whole-Cell Bioassays for Screening Quorum Signaling, Quorum Interference, and Biofilm Dispersion.

PubMed

Thornhill, Starla G; McLean, Robert J C

2018-01-01

In most bacteria, a global level of regulation, termed quorum sensing (QS), exists involving intercellular communication via the production and response to cell density-dependent signal molecules. QS has been associated with a number of important features in bacteria including virulence regulation and biofilm formation. Consequently, there is considerable interest in understanding, detecting, and inhibiting QS. N-acylated homoserine lactones (AHLs) are used as extracellular QS signals by a variety of Gram-negative bacteria. Chromobacterium violaceum, commonly found in soil and water, produces the characteristic purple pigment violacein, regulated by AHL-mediated QS. Based on this readily observed pigmentation phenotype, C. violaceum strains can be used to detect various aspects of AHL-mediated QS activity. In another commonly used bioassay organism, Agrobacterium tumefaciens, QS can be detected by the use of a reporter gene such as lacZ. Here, we describe several commonly used approaches incorporating C. violaceum and A. tumefaciens that can be used to detect AHL and QS inhibitors. Due to the inherent low susceptibility of biofilm bacteria to antimicrobial agents, biofilm dispersion, whereby bacteria reenter the planktonic community, is another increasingly important area of research. At least one signal, distinct from traditional QS, has been identified and there are a variety of other environmental factors that also trigger dispersion. We describe a microtiter-based experimental strategy whereby potential biofilm dispersion compounds can be screened.

A putative functional MYB transcription factor induced by low temperature regulates anthocyanin biosynthesis in purple kale (Brassica Oleracea var. acephala f. tricolor).

PubMed

Zhang, Bin; Hu, Zongli; Zhang, Yanjie; Li, Yali; Zhou, Shuang; Chen, Guoping

2012-02-01

The purple kale (Brassica Oleracea var. acephala f. tricolor) is a mutation in kales, giving the mutant phenotype of brilliant purple color in the interior. Total anthocyanin analysis showed that the amount of anthocyanins in the purple kale was up to 1.73 mg g(-1) while no anthocyanin was detected in the white kale. To elucidate the molecular mechanism of the anthocyanin biosynthesis in the purple kale, we analyzed the expression of structural genes and some transcription factors associated with anthocyanin biosynthesis in the purple cultivar "Red Dove" and the white cultivar "White Dove". The result showed that nearly all the anthocyanin biosynthetic genes showed higher expression levels in the purple cultivar than in the white cultivar, especially for DFR and ANS, they were barely detected in the white cultivar. Interestingly, the fact that a R2R3 MYB transcription factor named BoPAP1 was extremely up-regulated in the purple kale and induced by low temperature attracted our attention. Further sequence analysis showed that BoPAP1 shared high similarity with AtPAP1 and BoMYB1. In addition, the anthocyanin accumulation in the purple kale is strongly induced by the low temperature stress. The total anthocyanin contents in the purple kale under low temperature were about 50-fold higher than the plants grown in the greenhouse. The expression of anthocyanin biosynthetic genes C4H, F3H, DFR, ANS and UFGT were all enhanced under the low temperature. These evidences strongly suggest that BoPAP1 may play an important role in activating the anthocyanin structural genes for the abundant anthocyanin accumulation in the purple kale.

Assembly of purple membranes on polyelectrolyte films.

PubMed

Saab, Marie-belle; Estephan, Elias; Cloitre, Thierry; Legros, René; Cuisinier, Frédéric J G; Zimányi, László; Gergely, Csilla

2009-05-05

The membrane protein bacteriorhodopsin in its native membrane bound form (purple membrane) was adsorbed and incorporated into polyelectrolyte multilayered films, and adsorption was in situ monitored by optical waveguide light-mode spectroscopy. The formation of a single layer or a double layer of purple membranes was observed when adsorbed on negatively or positively charged surfaces, respectively. The purple membrane patches adsorbed on the polyelectrolyte multilayers were also evidenced by atomic force microscopy images. The driving forces of the adsorption process were evaluated by varying the ionic strength of the solution as well as the purple membrane concentration. At high purple membrane concentration, interpenetrating polyelectrolyte loops might provide new binding sites for the adsorption of a second layer of purple membranes, whereas at lower concentrations only a single layer is formed. Negative surfaces do not promote a second protein layer adsorption. Driving forces other than just electrostatic ones, such as hydrophobic forces, should play a role in the polyelectrolyte/purple membrane layering. The subtle interplay of all these factors determines the formation of the polyelectrolyte/purple membrane matrix with a presumably high degree of orientation for the incorporated purple membranes, with their cytoplasmic, or extracellular side toward the bulk on negatively or positively charged polyelectrolyte, respectively. The structural stability of bacteriorhodopsin during adsorption onto the surface and incorporation into the polyelectrolyte multilayers was investigated by Fourier transform infrared spectroscopy in attenuated total reflection mode. Adsorption and incorporation of purple membranes within polyelectrolyte multilayers does not disturb the conformational majority of membrane-embedded alpha-helix structures of the protein, but may slightly alter the structure of the extramembraneous segments or their interaction with the environment. This high stability is different from the lower stability of the predominantly beta-sheet structures of numerous globular proteins when adsorbed onto surfaces.

Impact of Violacein-Producing Bacteria on Survival and Feeding of Bacterivorous Nanoflagellates

PubMed Central

Matz, Carsten; Deines, Peter; Boenigk, Jens; Arndt, Hartmut; Eberl, Leo; Kjelleberg, Staffan; Jürgens, Klaus

2004-01-01

We studied the role of bacterial secondary metabolites in the context of grazing protection against protozoans. A model system was used to examine the impact of violacein-producing bacteria on feeding rates, growth, and survival of three common bacterivorous nanoflagellates. Freshwater isolates of Janthinobacterium lividum and Chromobacterium violaceum produced the purple pigment violacein and exhibited acute toxicity to the nanoflagellates tested. High-resolution video microscopy revealed that these bacteria were ingested by the flagellates at high rates. The uptake of less than three bacteria resulted in rapid flagellate cell death after about 20 min and cell lysis within 1 to 2 h. In selectivity experiments with nontoxic Pseudomonas putida MM1, flagellates did not discriminate against pigmented strains. Purified violacein from cell extracts of C. violaceum showed high toxicity to nanoflagellates. In addition, antiprotozoal activity was found to positively correlate with the violacein content of the bacterial strains. Pigment synthesis in C. violaceum is regulated by an N-acylhomoserine lactone (AHL)-dependent quorum-sensing system. An AHL-deficient, nonpigmented mutant provided high flagellate growth rates, while the addition of the natural C. violaceum AHL could restore toxicity. Moreover, it was shown that the presence of violacein-producing bacteria in an otherwise nontoxic bacterial diet considerably inhibited flagellate population growth. Our results suggest that violacein-producing bacteria possess a highly effective survival mechanism which may exemplify the potential of some bacterial secondary metabolites to undermine protozoan grazing pressure and population dynamics. PMID:15006783

Impact of violacein-producing bacteria on survival and feeding of bacterivorous nanoflagellates.

PubMed

Matz, Carsten; Deines, Peter; Boenigk, Jens; Arndt, Hartmut; Eberl, Leo; Kjelleberg, Staffan; Jürgens, Klaus

2004-03-01

We studied the role of bacterial secondary metabolites in the context of grazing protection against protozoans. A model system was used to examine the impact of violacein-producing bacteria on feeding rates, growth, and survival of three common bacterivorous nanoflagellates. Freshwater isolates of Janthinobacterium lividum and Chromobacterium violaceum produced the purple pigment violacein and exhibited acute toxicity to the nanoflagellates tested. High-resolution video microscopy revealed that these bacteria were ingested by the flagellates at high rates. The uptake of less than three bacteria resulted in rapid flagellate cell death after about 20 min and cell lysis within 1 to 2 h. In selectivity experiments with nontoxic Pseudomonas putida MM1, flagellates did not discriminate against pigmented strains. Purified violacein from cell extracts of C. violaceum showed high toxicity to nanoflagellates. In addition, antiprotozoal activity was found to positively correlate with the violacein content of the bacterial strains. Pigment synthesis in C. violaceum is regulated by an N-acylhomoserine lactone (AHL)-dependent quorum-sensing system. An AHL-deficient, nonpigmented mutant provided high flagellate growth rates, while the addition of the natural C. violaceum AHL could restore toxicity. Moreover, it was shown that the presence of violacein-producing bacteria in an otherwise nontoxic bacterial diet considerably inhibited flagellate population growth. Our results suggest that violacein-producing bacteria possess a highly effective survival mechanism which may exemplify the potential of some bacterial secondary metabolites to undermine protozoan grazing pressure and population dynamics.

Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides

NASA Astrophysics Data System (ADS)

Zirak, P.; Penzkofer, A.; Hegemann, P.; Mathes, T.

2007-05-01

The photo-cycle dynamics of the H44R mutant of the BLUF domain of the transcriptional anti-repressor protein AppA (AppA-H44R) from the non-sulfur anoxyphototropic purple bacterium Rhodobacter sphaeroides is studied in order to gain information on the involvement of His44 in the photo-cyclic mechanism of the AppA BLUF domain and to add information to the involved processes. The amino acid residue histidine at position 44 is replaced by arginine. A 12 nm red-shifted signalling state is formed upon blue-light excitation, while in wild-type AppA (AppA-wt) the red-shift is 16 nm. The recovery to the receptor dark state is approximately a factor of 2.5 faster ( τrec ≈ 6.5 min) than the recovery of the wild-type counterpart. Extended light exposure of the mutant causes photo-degradation of flavin (mainly free flavin conversion to lumichrome and re-equilibration between free and non-covalently bound flavin) and protein aggregation (showing up as light scattering). No photo-degradation was observed for AppA-wt. The quantum efficiency of signalling-state formation determined by intensity dependent absorption measurements is found to be ϕs ≈ 0.3 (for AppA-wt: ϕs ≈ 0.24). A two-component single-exponential fluorescence relaxation was observed, which is interpreted as fast fluorescence quenching to an equilibrium value by photo-induced electron transfer followed by slower fluorescence decay due to charge recombination. Based on the experimental findings, an extended photo-cycle model for BLUF domains is proposed.

Small-scale, hydrogen-oxidizing-denitrifying bioreactor for treatment of nitrate-contaminated drinking water.

PubMed

Smith, Richard L; Buckwalter, Seanne P; Repert, Deborah A; Miller, Daniel N

2005-05-01

Nitrate removal by hydrogen-coupled denitrification was examined using flow-through, packed-bed bioreactors to develop a small-scale, cost effective system for treating nitrate-contaminated drinking-water supplies. Nitrate removal was accomplished using a Rhodocyclus sp., strain HOD 5, isolated from a sole-source drinking-water aquifer. The autotrophic capacity of the purple non-sulfur photosynthetic bacterium made it particularly adept for this purpose. Initial tests used a commercial bioreactor filled with glass beads and countercurrent, non-sterile flow of an autotrophic, air-saturated, growth medium and hydrogen gas. Complete removal of 2 mM nitrate was achieved for more than 300 days of operation at a 2-h retention time. A low-cost hydrogen generator/bioreactor system was then constructed from readily available materials as a water treatment approach using the Rhodocyclus strain. After initial tests with the growth medium, the constructed system was tested using nitrate-amended drinking water obtained from fractured granite and sandstone aquifers, with moderate and low TDS loads, respectively. Incomplete nitrate removal was evident in both water types, with high-nitrite concentrations in the bioreactor output, due to a pH increase, which inhibited nitrite reduction. This was rectified by including carbon dioxide in the hydrogen stream. Additionally, complete nitrate removal was accomplished with wastewater-impacted surface water, with a concurrent decrease in dissolved organic carbon. The results of this study using three chemically distinct water supplies demonstrate that hydrogen-coupled denitrification can serve as the basis for small-scale remediation and that pilot-scale testing might be the next logical step.

Small-scale, hydrogen-oxidizing-denitrifying bioreactor for treatment of nitrate-contaminated drinking water

USGS Publications Warehouse

Smith, R.L.; Buckwalter, S.P.; Repert, D.A.; Miller, D.N.

2005-01-01

Nitrate removal by hydrogen-coupled denitrification was examined using flow-through, packed-bed bioreactors to develop a small-scale, cost effective system for treating nitrate-contaminated drinking-water supplies. Nitrate removal was accomplished using a Rhodocyclus sp., strain HOD 5, isolated from a sole-source drinking-water aquifer. The autotrophic capacity of the purple non-sulfur photosynthetic bacterium made it particularly adept for this purpose. Initial tests used a commercial bioreactor filled with glass beads and countercurrent, non-sterile flow of an autotrophic, air-saturated, growth medium and hydrogen gas. Complete removal of 2 mM nitrate was achieved for more than 300 days of operation at a 2-h retention time. A low-cost hydrogen generator/bioreactor system was then constructed from readily available materials as a water treatment approach using the Rhodocyclus strain. After initial tests with the growth medium, the constructed system was tested using nitrate-amended drinking water obtained from fractured granite and sandstone aquifers, with moderate and low TDS loads, respectively. Incomplete nitrate removal was evident in both water types, with high-nitrite concentrations in the bioreactor output, due to a pH increase, which inhibited nitrite reduction. This was rectified by including carbon dioxide in the hydrogen stream. Additionally, complete nitrate removal was accomplished with wastewater-impacted surface water, with a concurrent decrease in dissolved organic carbon. The results of this study using three chemically distinct water supplies demonstrate that hydrogen-coupled denitrification can serve as the basis for small-scale remediation and that pilot-scale testing might be the next logical step.

Biogeochemistry of a submerged groundwater seep ecosystem in Lake Huron near karst region of Alpena, MI

NASA Astrophysics Data System (ADS)

Kinsman-Costello, L. E.; Dick, G.; Sheik, C.; Burton, G. A.; Sheldon, N. D.

2015-12-01

Submerged groundwater seeps in Lake Huron establish ecosystems with distinctive geochemical conditions. In the Middle Island Sinkhole (MIS), a 23-m deep seep, groundwater seepage establishes low O2 (< 4 mg L-1), high sulfate (6 mM) conditions, in which a purple cyanobacteria-dominated mat thrives. The mat is capable of anoxygenic photosynthesis, oxygenic photosynthesis, and chemosynthesis. Within the top 3 cm of the mat-water interface, hydrogen sulfide concentrations increase to 1-7 mM. Little is known about the structure and function of microbes within organic-rich, high-sulfide sediments beneath the mat. Using pore water and sediment geochemical characterization along with microbial community analysis, we elucidated relationships between microbial community structure and ecosystem function along vertical gradients. In sediment pore waters, biologically reactive solutes (SO42-, NH4+, PO43-, and CH4) displayed steep vertical gradients, reflecting biological and geochemical functioning. In contrast, more conservative ions (Ca+2, Mg+2, Na+, and Cl-), did not change significantly with depth in MIS sediments, indicating groundwater influence in the sediment profile. MIS sediments contained more organic matter than typical Lake Huron sediments, and were generally higher in nutrients, metals, and sulfur (acid volatile sulfide). Using the Illumina MiSeq platform we detected 14,127 unique operational taxonomic units across sediment and surface mat samples. Microbial community composition in the MIS was distinctly different from non-groundwater affected areas at similar depth nearby in Lake Huron (ANOSIM, R= 0.74, p=0.002). MIS sediment communities were more diverse that MIS surface mat communities and changed with depth into sediments. MIS sediment community composition was related to several geochemical variables, including organic matter and multiple indicators of phosphorus availability. Elucidating the structure and function of microbial consortia in MIS, a highly unique and environmentally vulnerable ecosystem, provides a rare opportunity to understand relationships between microbial species and their environment and may provide insights into the evolution of life under ancient low-oxygen, high-sulfur conditions.

Lipoic Acid as a Possible Pharmacological Source of Hydrogen Sulfide/Sulfane Sulfur.

PubMed

Bilska-Wilkosz, Anna; Iciek, Małgorzata; Kowalczyk-Pachel, Danuta; Górny, Magdalena; Sokołowska-Jeżewicz, Maria; Włodek, Lidia

2017-03-02

The aim of the present study was to verify whether lipoic acid (LA) itself is a source of H₂S and sulfane sulfur. It was investigated in vitro non-enzymatically and enzymatically (in the presence of rat tissue homogenate). The results indicate that both H₂S and sulfane sulfur are formed from LA non-enzymatically in the presence of environmental light. These results suggest that H₂S is the first product of non-enzymatic light-dependent decomposition of LA that is, probably, next oxidized to sulfane sulfur-containing compound(s). The study performed in the presence of rat liver and kidney homogenate revealed an increase of H₂S level in samples containing LA and its reduced form dihydrolipoic acid (DHLA). It was accompanied by a decrease in sulfane sulfur level. It seems that, in these conditions, DHLA acts as a reducing agent that releases H₂S from an endogenous pool of sulfane sulfur compounds present in tissues. Simultaneously, it means that exogenous LA cannot be a direct donor of H₂S/sulfane sulfur in animal tissues. The present study is an initial approach to the question whether LA itself is a donor of H₂S/sulfane sulfur.

Mapping axillary microbiota responsible for body odours using a culture-independent approach.

PubMed

Troccaz, Myriam; Gaïa, Nadia; Beccucci, Sabine; Schrenzel, Jacques; Cayeux, Isabelle; Starkenmann, Christian; Lazarevic, Vladimir

2015-01-01

Human axillary odour is commonly attributed to the bacterial degradation of precursors in sweat secretions. To assess the role of bacterial communities in the formation of body odours, we used a culture-independent approach to study axillary skin microbiota and correlated these data with olfactory analysis. Twenty-four Caucasian male and female volunteers and four assessors showed that the underarms of non-antiperspirant (non-AP) users have significantly higher global sweat odour intensities and harboured on average about 50 times more bacteria than those of AP users. Global sweat odour and odour descriptors sulfury-cat urine and acid-spicy generally increased from the morning to the afternoon sessions. Among non-AP users, male underarm odours were judged higher in intensity with higher fatty and acid-spicy odours and higher bacterial loads. Although the content of odour precursors in underarm secretions varied widely among individuals, males had a higher acid: sulfur precursor ratio than females did. No direct correlations were found between measured precursor concentration and sweat odours. High-throughput sequencing targeting the 16S rRNA genes of underarm bacteria collected from 11 non-AP users (six females and five males) confirmed the strong dominance of the phyla Firmicutes and Actinobacteria, with 96% of sequences assigned to the genera Staphylococcus, Corynebacterium and Propionibacterium. The proportion of several bacterial taxa showed significant variation between males and females. The genera Anaerococcus and Peptoniphilus and the operational taxonomic units (OTUs) from Staphylococcus haemolyticus and the genus Corynebacterium were more represented in males than in females. The genera Corynebacterium and Propionibacterium were correlated and anti-correlated, respectively, with body odours. Within the genus Staphylococcus, different OTUs were either positively or negatively correlated with axillary odour. The relative abundance of five OTUs (three assigned to S. hominis and one each to Corynebacterium tuberculostearicum and Anaerococcus) were positively correlated with at least one underarm olfactory descriptor. Positive and negative correlations between bacterial taxa found at the phylum, genus and OTU levels suggest the existence of mutualism and competition among skin bacteria. Such interactions, and the types and quantities of underarm bacteria, affect the formation of body odours. These findings open the possibility of developing new solutions for odour control.

Experimental production of indicators for microbial sulfur metabolism in the Chelyabinsk LL5 chondrite: meteorites as standards for biomarker detection on Mars

NASA Astrophysics Data System (ADS)

Tait, A. W.; Wilson, S. A.; Tomkins, A. G.; Gagen, E. J.; Southam, G.

2016-12-01

One hurdle to finding evidence for life beyond Earth is being able to identify its chemical, textural and isotopic fingerprints. This is a challenge in environments that can mask biomarker discovery and/or where geochemical and mineralogical limits are still being established. An ideal solution would be to use standards with known chemical and isotopic compositions to reduce/remove any ambiguity of detection. We propose that chondritic meteorites are ideal standards. Chondrites have narrow ranges in mineralogical, chemical and isotopic compositions, including δ34S values. As such, they could preserve biomarkers of theorized sulfur-based metabolisms on Mars. Here, we demonstrate that bacteria can alter the chemistry of chondrites in a detectable and recognisable manner. We exposed polished fragments of the Chelyabinsk LL5 chondrite to an inoculum of the sulfur/iron oxidising bacterium, Acidithiobacillus ferrooxidans. Cell counts and aqueous sulfate concentrations were recorded over the course of a month. Meteorite samples were taken after one, two and four week exposures for FEG-SEM and FIB-SEM imaging, XRD phase analysis, and stable isotope (δ34S) geochemistry. Our electron microscopy work shows that bacteria and associated extracellular polymeric substances coat grains of troilite (FeS) and FeNi alloys. Decreasing aqueous sulfate concentrations, compared to increasing sulfate in abiotic controls, suggests that A. ferrooxidans may have been assimilating the sulfur released by oxidation of troilite. Also, low abundances of secondary minerals that are capable of recording biological fractionation of stable sulfur and/or iron isotopes were also produced: rozenite, gypsum, goethite, lepidocrocite, and jarosite, and may explain the reduction in soluble sulfur. Our FIB-SEM results show that nutrients (e.g., carbon, sulfur and nitrogen) become concentrated in layers at the surfaces of troilite and FeNi alloys within 1 week of incubation. These nutrient-rich regions are encased and preserved beneath mm-scale efflorescences of Fe-oxyhydroxide minerals, essentially fossilizing them. Meteorites that have landed on the surface of Mars are therefore favourable targets for future sample return missions, because they can record unambiguous evidence of a putative biosphere in multiple ways.

Sulfate-reducing bacteria lower sulfur-mediated pitting corrosion under conditions of oxygen ingress.

PubMed

Johnston, Shawna L; Voordouw, Gerrit

2012-08-21

The effect of oxygen ingress into sour water containing dissolved sulfide on the production of sulfur and polysulfide (S-PS) and associated iron corrosion was investigated. Biotic (active SRB present), abiotic (autoclaved SRB present), and chemical (no bacteria present) conditions were compared. Under biotic conditions formation of S-PS was only seen at a high ratio of oxygen to sulfide (R(OS)) of 1 to 2.4. General corrosion rates increased 10-fold to 0.10 mm/yr under these conditions. Under abiotic and chemical conditions S-PS formation increased over the entire range of R(OS) with general corrosion rates reaching 0.06 mm/yr. Although general corrosion rates were thus highest under biotic conditions, biotically corroded coupons showed much less pitting corrosion. Maximum pit depth increased to 40-80 μm with increasing R(OS) for coupons incubated for 1 month under abiotic or chemical conditions but not for biotically incubated coupons (10 μm). This appeared to be related to the properties and size of the sulfur formed, which was hydrophobic and in excess of 10 μm under chemical or abiotic conditions and hydrophilic and 0.5 to 1 μm under biotic conditions. Hence, perhaps contrary to expectation, SRB lowered pitting corrosion rates under conditions of oxygen ingress due to their ability to respire oxygen and produce a less aggressive form of sulfur. Microbial control, which is usually required in sour systems, may be counterproductive under these conditions.

Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

PubMed Central

Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

2008-01-01

The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

Purple drank prevalence and characteristics of misusers of codeine cough syrup mixtures.

PubMed

Agnich, Laura E; Stogner, John M; Miller, Bryan Lee; Marcum, Catherine D

2013-09-01

A mixture of codeine cough syrup with alcohol and/or a soft drink known as "purple drank" has gained media attention in recent years as a drug associated with professional athletes and southern rap music. The existing research on purple drank consumption has primarily utilized samples of African Americans residing in the Houston, Texas area. This is the first scholarly study of purple drank use outside of the Houston, Texas area among a general population of young adults, and indicates that purple drank use is not limited to African American males. The findings depict higher odds of the use of purple drank among other racial and ethnic groups, males, and homosexual, bisexual, and transgender college students from urban areas. Published by Elsevier Ltd.

Using biological and physico-chemical test methods to assess the role of concrete mixture design in resistance to microbially induced corrosion

NASA Astrophysics Data System (ADS)

House, Mitchell Wayne

Concrete is the most widely used material for construction of wastewater collection, storage, and treatment infrastructure. The chemical and physical characteristics of hydrated portland cement make it susceptible to degradation under highly acidic conditions. As a result, some concrete wastewater infrastructure may be susceptible to a multi-stage degradation process known as microbially induced corrosion, or MIC. MIC begins with the production of aqueous hydrogen sulfide (H2S(aq)) by anaerobic sulfate reducing bacteria present below the waterline. H2S(aq) partitions to the gas phase where it is oxidized to sulfuric acid by the aerobic sulfur oxidizing bacteria Thiobacillus that resides on concrete surfaces above the waterline. Sulfuric acid then attacks the cement paste portion of the concrete matrix through decalcification of calcium hydroxide and calcium silica hydrate coupled with the formation of expansive corrosion products. The attack proceeds inward resulting in reduced service life and potential failure of the concrete structure. There are several challenges associated with assessing a concrete's susceptibility to MIC. First, no standard laboratory tests exist to assess concrete resistance to MIC. Straightforward reproduction of MIC in the laboratory is complicated by the use of microorganisms and hydrogen sulfide gas. Physico-chemical tests simulating MIC by immersing concrete specimens in sulfuric acid offer a convenient alternative, but do not accurately capture the damage mechanisms associated with biological corrosion. Comparison of results between research studies is difficult due to discrepancies that can arise in experimental methods even if current ASTM standards are followed. This thesis presents two experimental methods to evaluate concrete resistance to MIC: one biological and one physico-chemical. Efforts are made to address the critical aspects of each testing method currently absent in the literature. The first method presented is a new test to evaluate performance of concrete specimens under conditions designed to accelerate MIC. Concrete specimens representing 12 mixture designs were inoculated with 5 species of Thiobacillus bacteria and placed in a biological growth chamber designed to encourage bacterial growth and sulfuric acid production by optimizing temperature, delivering necessary nutrients, and providing hydrogen sulfide gas. Results indicate that using supplementary cementitious materials, limestone aggregates, and sulfate resistant cement can improve resistance to MIC. It is interesting to note that this study showed that unlike many other durability problems the role of water to cement ratio was unclear. The second method presented is a sulfuric acid immersion study designed to evaluate the resistance of 12 concrete mixture designs to 5 concentrations of sulfuric acid. Experimental protocols (like those in ASTM) previously considered trivial were found to have a dramatic effect on experimental results. It was found that using supplementary cementitious materials, limestone coarse aggregate, and sulfate resistant cement can increase concrete resistance to moderate sulfuric acid concentrations. The primary damage mechanism was observed to change depending on sulfuric acid concentration. Rapid deterioration of specimens exposed to aggressive sulfuric acid solutions indicates that degradation of concrete under the most severe MIC conditions (i.e., a pH < 1.0) cannot be prevented by strictly manipulating concrete mixture proportions. A holistic approach is needed for these situations that considers environmental conditions as well.

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701 T) and emended description of the genus Thermanaerovibrio

DOE PAGES

Palaniappan, Krishna; Meier-Kolthoff, Jan P.; Teshima, Hazuki; ...

2013-10-16

Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of itsmore » morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883 T, the type strain of T. acidaminovorans, stain Z-9701 T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701 T) and emended description of the genus Thermanaerovibrio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palaniappan, Krishna; Meier-Kolthoff, Jan P.; Teshima, Hazuki

Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of itsmore » morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883 T, the type strain of T. acidaminovorans, stain Z-9701 T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio

PubMed Central

Palaniappan, Krishna; Meier-Kolthoff, Jan P.; Teshima, Hazuki; Nolan, Matt; Lapidus, Alla; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Rohde, Manfred; Mayilraj, Shanmugam; Spring, Stefan; Detter, John C.; Göker, Markus; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Woyke, Tanja

2013-01-01

Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883T, the type strain of T. acidaminovorans, stain Z-9701T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:24501645

Participation of S. Typhimurium cysJIH Operon in the H2S-mediated Ciprofloxacin Resistance in Presence of Sulfate as Sulfur Source

PubMed Central

Álvarez, Ricardo; Frávega, Jorge; Rodas, Paula I.; Fuentes, Juan A.; Paredes-Sabja, Daniel; Calderón, Iván L.; Gil, Fernando

2015-01-01

H2S production has been proposed as a mechanism to explain bacterial resistance to antibiotics. In this work, we present evidence for the role of the cysJIH operon in resistance to ciprofloxacin mediated by H2S production with different sulfate as the only sulfur source. We found that the products of the cysJIH operon are involved in ciprofloxacin resistance by increasing both, the levels of H2S and reduced thiols apparently counteracting antimicrobial-induced reactive oxygen species (ROS). This protective effect was observed only when bacteria were cultured in the presence of sulfate, but not with cysteine, as the sole sulfur source.

Evaluation of biological hydrogen sulfide oxidation coupled with two-stage upflow filtration for groundwater treatment.

PubMed

Levine, Audrey D; Raymer, Blake J; Jahn, Johna

2004-01-01

Hydrogen sulfide in groundwater can be oxidized by aerobic bacteria to form elemental sulfur and biomass. While this treatment approach is effective for conversion of hydrogen sulfide, it is important to have adequate control of the biomass exiting the biological treatment system to prevent release of elemental sulfur into the distribution system. Pilot scale tests were conducted on a Florida groundwater to evaluate the use of two-stage upflow filtration downstream of biological sulfur oxidation. The combined biological and filtration process was capable of excellent removal of hydrogen sulfide and associated turbidity. Additional benefits of this treatment approach include elimination of odor generation, reduction of chlorine demand, and improved stability of the finished water.

Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake

PubMed Central

Yau, Sheree; Lauro, Federico M; Williams, Timothy J; DeMaere, Matthew Z; Brown, Mark V; Rich, John; Gibson, John AE; Cavicchioli, Ricardo

2013-01-01

Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria, and indicate the use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant, indicating that DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment. PMID:23619305

Production and Consumption of Hydrogen in Hot Spring Microbial Mats Dominated by a Filamentous Anoxygenic Photosynthetic Bacterium

PubMed Central

Otaki, Hiroyo; Everroad, R. Craig; Matsuura, Katsumi; Haruta, Shin

2012-01-01

Microbial mats containing the filamentous anoxygenic photosynthetic bacterium Chloroflexus aggregans develop at Nakabusa hot spring in Japan. Under anaerobic conditions in these mats, interspecies interaction between sulfate-reducing bacteria as sulfide producers and C. aggregans as a sulfide consumer has been proposed to constitute a sulfur cycle; however, the electron donor utilized for microbial sulfide production at Nakabusa remains to be identified. In order to determine this electron donor and its source, ex situ experimental incubation of mats was explored. In the presence of molybdate, which inhibits biological sulfate reduction, hydrogen gas was released from mat samples, indicating that this hydrogen is normally consumed as an electron donor by sulfate-reducing bacteria. Hydrogen production decreased under illumination, indicating that C. aggregans also functions as a hydrogen consumer. Small amounts of hydrogen may have also been consumed for sulfur reduction. Clone library analysis of 16S rRNA genes amplified from the mats indicated the existence of several species of hydrogen-producing fermentative bacteria. Among them, the most dominant fermenter, Fervidobacterium sp., was successfully isolated. This isolate produced hydrogen through the fermentation of organic carbon. Dispersion of microbial cells in the mats resulted in hydrogen production without the addition of molybdate, suggesting that simultaneous production and consumption of hydrogen in the mats requires dense packing of cells. We propose a cyclic electron flow within the microbial mats, i.e., electron flow occurs through three elements: S (elemental sulfur, sulfide, sulfate), C (carbon dioxide, organic carbon) and H (di-hydrogen, protons). PMID:22446313

Presence of Nitrate-Accumulating Sulfur Bacteria and Their Influence on Nitrogen Cycling in a Shallow Coastal Marine Sediment

PubMed Central

Sayama, Mikio

2001-01-01

Nitrate flux between sediment and water, nitrate concentration profile at the sediment-water interface, and in situ sediment denitrification activity were measured seasonally at the innermost part of Tokyo Bay, Japan. For the determination of sediment nitrate concentration, undisturbed sediment cores were sectioned into 5-mm depth intervals and each segment was stored frozen at −30°C. The nitrate concentration was determined for the supernatants after centrifuging the frozen and thawed sediments. Nitrate in the uppermost sediment showed a remarkable seasonal change, and its seasonal maximum of up to 400 μM was found in October. The directions of the diffusive nitrate fluxes predicted from the interfacial concentration gradients were out of the sediment throughout the year. In contrast, the directions of the total nitrate fluxes measured by the whole-core incubation were into the sediment at all seasons. This contradiction between directions indicates that a large part of the nitrate pool extracted from the frozen surface sediments is not a pore water constituent, and preliminary examinations demonstrated that the nitrate was contained in the intracellular vacuoles of filamentous sulfur bacteria dwelling on or in the surface sediment. Based on the comparison between in situ sediment denitrification activity and total nitrate flux, it is suggested that intracellular nitrate cannot be directly utilized by sediment denitrification, and the probable fate of the intracellular nitrate is hypothesized to be dissimilatory reduction to ammonium. The presence of nitrate-accumulating sulfur bacteria therefore may lower nature's self-purification capacity (denitrification) and exacerbate eutrophication in shallow coastal marine environments. PMID:11472923

Visualization of Imbalances in Sulfur Assimilation and Synthesis of Sulfur-Containing Amino Acids at the Single-Cell Level

PubMed Central

Hoffmann, Kristina; Grünberger, Alexander; Lausberg, Frank; Bott, Michael

2013-01-01

We describe genetically encoded sensors which transmit elevated cytosolic concentrations of O-acetyl serine (OAS) and O-acetyl homoserine (OAH)—intermediates of l-cysteine and l-methionine synthesis—into an optical output. The sensor pSenOAS3 elicits 7.5-fold-increased fluorescence in cultures of a Corynebacterium glutamicum strain that excrete l-cysteine. Determination of the cytosolic OAS concentration revealed an increase to 0.13 mM, whereas the concentration in the reference strain was below the detection limit, indicating that incorporation of assimilatory sulfur is limited in the strain studied. In another strain, overexpression of metX encoding homoserine acetyltransferase resulted in an 8-fold increase in culture fluorescence at a cytosolic OAH concentration of 0.76 mM. We also assayed for consequences of extracellular sulfur supply and observed a graded fluorescence increase at decreasing sulfur concentrations below 400 μM. Overall, this demonstrates the usefulness of the sensors for monitoring intracellular sulfur availability. The sensors also enable monitoring at the single-cell level, and since related and close homologs of the transcription factor used in the constructed sensors are widespread among bacteria, this technology offers a new possibility of assaying in vivo for sulfur limitation and of doing this at the single-cell level. PMID:23995919

Visualization of imbalances in sulfur assimilation and synthesis of sulfur-containing amino acids at the single-cell level.

PubMed

Hoffmann, Kristina; Grünberger, Alexander; Lausberg, Frank; Bott, Michael; Eggeling, Lothar

2013-11-01

We describe genetically encoded sensors which transmit elevated cytosolic concentrations of O-acetyl serine (OAS) and O-acetyl homoserine (OAH)-intermediates of l-cysteine and l-methionine synthesis-into an optical output. The sensor pSenOAS3 elicits 7.5-fold-increased fluorescence in cultures of a Corynebacterium glutamicum strain that excrete l-cysteine. Determination of the cytosolic OAS concentration revealed an increase to 0.13 mM, whereas the concentration in the reference strain was below the detection limit, indicating that incorporation of assimilatory sulfur is limited in the strain studied. In another strain, overexpression of metX encoding homoserine acetyltransferase resulted in an 8-fold increase in culture fluorescence at a cytosolic OAH concentration of 0.76 mM. We also assayed for consequences of extracellular sulfur supply and observed a graded fluorescence increase at decreasing sulfur concentrations below 400 μM. Overall, this demonstrates the usefulness of the sensors for monitoring intracellular sulfur availability. The sensors also enable monitoring at the single-cell level, and since related and close homologs of the transcription factor used in the constructed sensors are widespread among bacteria, this technology offers a new possibility of assaying in vivo for sulfur limitation and of doing this at the single-cell level.

Influence of the sulfur species reactivity on biofilm conformation during pyrite colonization by Acidithiobacillus thiooxidans.

PubMed

Lara, René H; García-Meza, J Viridiana; Cruz, Roel; Valdez-Pérez, Donato; González, Ignacio

2012-08-01

Massive pyrite (FeS₂) electrodes were potentiostatically modified by means of variable oxidation pulse to induce formation of diverse surface sulfur species (S(n)²⁻, S⁰). The evolution of reactivity of the resulting surfaces considers transition from passive (e.g., Fe(1-x )S₂) to active sulfur species (e.g., Fe(1-x )S(2-y ), S⁰). Selected modified pyrite surfaces were incubated with cells of sulfur-oxidizing Acidithiobacillus thiooxidans for 24 h in a specific culture medium (pH 2). Abiotic control experiments were also performed to compare chemical and biological oxidation. After incubation, the attached cells density and their exopolysaccharides were analyzed by confocal laser scanning microscopy (CLMS) and atomic force microscopy (AFM) on bio-oxidized surfaces; additionally, S(n)²⁻/S⁰ speciation was carried out on bio-oxidized and abiotic pyrite surfaces using Raman spectroscopy. Our results indicate an important correlation between the evolution of S(n)²⁻/S⁰ surface species ratio and biofilm formation. Hence, pyrite surfaces with mainly passive-sulfur species were less colonized by A. thiooxidans as compared to surfaces with active sulfur species. These results provide knowledge that may contribute to establishing interfacial conditions that enhance or delay metal sulfide (MS) dissolution, as a function of the biofilm formed by sulfur-oxidizing bacteria.

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Production of purple sweet potato (Ipomoea batatas L.) juice having high anthocyanin content and antioxidant activity

NASA Astrophysics Data System (ADS)

Dwiyanti, G.; Siswaningsih, W.; Febrianti, A.

2018-05-01

The purpose of the study was to retrieve procedure of production of purple sweet potato (Ipomoea batatas L.) juice with the best total anthocyanin and antioxidant activity. Purple sweet potato was processed into purple sweet potato juice through a process of heating with temperature variations of 700C, 800C, and 900C and various duration of heating, which are 5 mins, 10 mins, and 15 mins. The total anthocyanin was determined by using pH differential method. The antioxidant activity was determined by using DPPH (2,2-Diphenyl-l-picrylhydrazyl) method. Total anthocyanin of purple sweet potato juice declined in the range between 215.08 mg/L - 101.86 mg/L. The antioxidant activity of purple sweet potato juice declined in the range between 90.63% - 67.79%. Antioxidant activity and total anthocyanin purple sweet potato juice decreases with increasing temperature and duration of heating. The best characteristics found in purple sweet potato juice were made with warming temperatures of 800C. The product with the highest antioxidant activity, total anthocyanins, and good durability was prepared at 800C heating temperature for 5 mins.

Augmenting Sulfur Metabolism and Herbivore Defense in Arabidopsis by Bacterial Volatile Signaling.

PubMed

Aziz, Mina; Nadipalli, Ranjith K; Xie, Xitao; Sun, Yan; Surowiec, Kazimierz; Zhang, Jin-Lin; Paré, Paul W

2016-01-01

Sulfur is an element necessary for the life cycle of higher plants. Its assimilation and reduction into essential biomolecules are pivotal factors determining a plant's growth and vigor as well as resistance to environmental stress. While certain soil microbes can enhance ion solubility via chelating agents or oxidation, microbial regulation of plant-sulfur assimilation has not been reported. With an increasing understanding that soil microbes can activate growth and stress tolerance in plants via chemical signaling, the question arises as to whether such beneficial bacteria also regulate sulfur assimilation. Here we report a previously unidentified mechanism by which the growth-promoting rhizobacterium Bacillus amyloliquefaciens (GB03) transcriptionally activates genes responsible for sulfur assimilation, increasing sulfur uptake and accumulation in Arabidopsis. Transcripts encoding for sulfur-rich aliphatic and indolic glucosinolates are also GB03 induced. As a result, GB03-exposed plants with elevated glucosinolates exhibit greater protection against the generalist herbivore, Spodoptera exigua (beet armyworm, BAW). In contrast, a previously characterized glucosinolate mutant compromised in the production of both aliphatic and indolic glucosinolates is also compromised in terms of GB03-induced protection against insect herbivory. As with in vitro studies, soil-grown plants show enhanced glucosinolate accumulation and protection against BAW feeding with GB03 exposure. These results demonstrate the potential of microbes to enhance plant sulfur assimilation and emphasize the sophisticated integration of microbial signaling in plant defense.

Bioactive compounds in pigmented rice bran inhibit growth of human cancer cells

USDA-ARS?s Scientific Manuscript database

Rice bran contains both lipophilic and hydrophilic antioxidants. Our previous studies have shown that pigmented rice cultivars contained several-fold higher total phenolic concentrations and antioxidant capacities than non-pigmented cultivars. We investigated three rice brans (purple, red and light-...

Viscoelastic characteristics and phytochemical properties of purple-rice drinks following ultrahigh pressure and pasteurization

NASA Astrophysics Data System (ADS)

Worametrachanon, Srivilai; Apichartsrangkoon, Arunee

2014-10-01

This study investigated how pressure (500, 600 MPa/20 min) altered the viscoelastic characteristics and phytochemical properties of germinated and non-germinated purple-rice drinks in comparison with pasteurization. Accordingly, color parameters, storage and loss moduli, anthocyanin content, γ-oryzanol, γ-aminobutyric acid (GABA), total phenolic compounds and 2,2-diphenyl-1-picrylthydrazyl (DPPH) capacity of the processed drinks were determined. The finding showed that germinated and pressurized rice drink had lower Browning Index than the non-germinated and pasteurized rice drink. The plots of storage and loss moduli for processed rice drinks indicated that time of pressurization had greater impact on gel structural modification than the level of pressure used. The phytochemicals, including total phenolics, and DPPH capacity in pressurized rice drinks retained higher quantity than those in pasteurized drink, despite less treatment effects on anthocyanin. On the contrary, both γ-oryzanol and GABA were found in high amounts in germinated rice drink with little variation among processing effects.

Path induced coherent energy transfer in light-harvesting complexes in purple bacteria

NASA Astrophysics Data System (ADS)

Sun, Kewei; Ye, Jun; Zhao, Yang

2014-09-01

Features of path dependent energy transfer in a dual-ring light-harvesting (LH2) complexes (B850) system have been examined in detail systematically. The Frenkel-Dirac time dependent variational method with the Davydov D1 Ansatz is employed with detailed evolution of polaron dynamics in real space readily obtained. It is found that the phase of the transmission amplitude through the LH2 complexes plays an important role in constructing the coherent excitonic energy transfer. It is also found that the symmetry breaking caused by the dimerization of bacteriochlorophylls and coherence or correlation between two rings will be conducive in enhancing the exciton transfer efficiency.

EFFECT OF BACTERIAL SULFATE REDUCTION ON IRON-CORROSION SCALES

EPA Science Inventory

Iron-sulfur geochemistry is important in many natural and engineered environments including drinking water systems. In the anaerobic environment beneath scales of corroding iron drinking water distribution system pipes, sulfate reducing bacteria (SRB) produce sulfide from natura...

Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

USGS Publications Warehouse

Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

1996-01-01

A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

Altamira cave Paleolithic paintings harbor partly unknown bacterial communities.

PubMed

Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

2002-05-21

Since it has been reported that microorganisms can affect painting pigments, Paleolithic painting microbiology deserves attention. The present study is the first report on the bacterial colonization of the valuable Paleolithic paintings in the famous Altamira cave (Spain). One sample taken from a painting area in the Polychromes Hall was analyzed culture-independently. This was the first time microbiologists were allowed to take sample material directly from Altamira paintings. Identification methods included PCR amplification of 16S rRNA genes (16S rDNA) and community fingerprinting by denaturing gradient gel electrophoresis (DGGE). The applied approach gave insight into a great bacterial taxonomic diversity, and allowed the detection of unexpected and unknown bacteria with potential effects on the conservation of the painting. Regarding the number of 29 visible DGGE bands in the community fingerprint, the numbers of analyzed clones described about 72% of the phylogenetic diversity present in the sample. Thirty-eight percent of the sequences analyzed were phylogenetically most closely related to cultivated bacteria, while the majority (62%) were most closely related to environmental 16S rDNA clones. Bacteria identified in Altamira were related with sequence similarities between 84.8 and 99.4% to members of the cosmopolitan Proteobacteria (52.3%), to members of the Acidobacterium division (23.8%), Cytophaga/Flexibacter/Bacteroides phylum (9.5%), green non-sulfur bacteria (4.8%), Planctomycetales (4.8%) and Actinobacteria (4.8%). The high number of clones most closely related to environmental 16S rDNA clones showed the broad spectrum of unknown and yet to be cultivated bacteria in Altamira cave.

Lipid biomarker production and preservation in acidic ecosystems: Relevance to early Earth and Mars

NASA Astrophysics Data System (ADS)

Jahnke, L. L.; Parenteau, M. N.; Harris, R.; Bristow, T.; Farmer, J. D.; Des Marais, D. J.

2013-12-01

Compared to relatively benign carbonate buffered marine environments, terrestrial Archean and Paleoproterozoic life was forced to cope with a broader range of pH values. In particular, acidic terrestrial ecosystems arose from the oxidation of reduced species in hydrothermal settings and crustal reservoirs of metal sulfides, creating acid sulfate conditions. While oxidation of reduced species is facilitated by reactions with molecular oxygen, acidic conditions also arose in Archean hydrothermal systems before the rise of oxygen (Van Kranendonk, 2006), expanding the range of time over which acidophiles could have existed on the early Earth. Acidic terrestrial habitats would have included acidic hydrothermal springs, acid sulfate soils, and possibly lakes and streams lacking substantial buffering capacity with sources of acidity in their catchments. Although acidic hot springs are considered extreme environments on Earth, robust and diverse microbial communities thrive in these habitats. Such acidophiles are found across all three domains of life and include both phototrophic and chemotrophic members. In this presentation, we examine hopanes and sterols that are characteristic of microbial communities living in acidic hydrothermal environments. Moreover we discuss taphonomic processes governing the capture and preservation of these biosignatures in acid environments. In particular, we discuss the production and early preservation of hopanoids and sterols in the following geological/mineralogical settings: 1) rapid entombment of microbes and organic matter by predominantly fine-grained silica; 2) rapid burial of organic matter by clay-rich, silica poor sediments; 3) and the survival of organics in iron oxide and sulfate rich sediments. We discovered and isolated an acid-tolerant purple non-sulfur anoxygenic phototroph from Lassen Volcanic National Park that synthesizes 3methyl-bacteriohopanepolyols. These compounds were previously thought to be exclusively made by methanotrophic and acetic acid bacteria. We also documented the production of unique patterns of abundance of C27, C28, and C29 sterols by the early diverging red and green algae Cyanidiales and Chlorella in the acidic outflow channel of Nymph Creek in Yellowstone National Park. Hydrothermal processes associated with volcanism are common features of ancient habitable environments on Earth and have been inferred for ancient Mars as well. Understanding the preservation of organics in modern acidic hydrothermal settings thus helps inform the detection of these compounds in the ancient sedimentary record on Earth, and perhaps Mars. Van Kranendonk MJ (2006) . Earth-Science Reviews 74, 197-240

Biology of Symbioses between Marine Invertebrates and Intracellular Bacteria

DTIC Science & Technology

1991-01-21

bisphosphate carboxylase ( RubisCO ) from symbiotic bacteria of various origins, b) To continue methods development for 16S rRNA sequencing from symbionts in...frozen and badly preserved specimens, and c) To use these new techniques to sequence 16s DNA from a variety of symbionts a) RubisCO We have cloned the...gene coding for RubisCO from the sulfur oxidixing symbiont of the gastropod Alvinochoncha hessleri. Nucleotide sequence analysis of the cloned fragment

Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology.

PubMed

Rudolph, C; Wanner, G; Huber, R

2001-05-01

We report the identification of novel archaea living in close association with bacteria in the cold (approximately 10 degrees C) sulfurous marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. These microorganisms form a characteristic, macroscopically visible structure, morphologically comparable to a string of pearls. Tiny, whitish globules (the pearls; diameter, about 0.5 to 3.0 mm) are connected to each other by thin, white-colored threads. Fluorescent in situ hybridization (FISH) studies have revealed that the outer part of the pearls is mainly composed of bacteria, with a filamentous bacterium predominating. Internally, archaeal cocci are the predominant microorganisms, with up to 10(7) cells estimated to be present in a single pearl. The archaea appear to be embedded in a polymer of unknown chemical composition. According to FISH and 16S rRNA gene sequence analysis, the archaea are affiliated with the euryarchaeal kingdom. The new euryarchaeal sequence represents a deep phylogenetic branch within the 16S rRNA tree and does not show extensive similarity to any cultivated archaea or to 16S rRNA gene sequences from environmental samples.

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota

PubMed Central

Waddell, Evan J.; Elliott, Terran J.; Sani, Rajesh K.; Vahrenkamp, Jefferey M.; Roggenthen, William M.; Anderson, Cynthia M.; Bang, Sookie S.

2013-01-01

Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil–like sample. Geochemical analyses indicated that both samples were high in sulfur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota typically identified from marine environments, and one OTU to a potentially novel phylum that falls sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and grouped most closely to an ammonia–oxidizing, carbon–fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that were often identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulfur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community with unique phylotypes identified within each sample. PMID:20662386

Microbiological and Geochemical Characterization of Fluvially Deposited Sulfidic Mine Tailings

PubMed Central

Wielinga, Bruce; Lucy, Juliette K.; Moore, Johnnie N.; Seastone, October F.; Gannon, James E.

1999-01-01

The fluvial deposition of mine tailings generated from historic mining operations near Butte, Montana, has resulted in substantial surface and shallow groundwater contamination along Silver Bow Creek. Biogeochemical processes in the sediment and underlying hyporheic zone were studied in an attempt to characterize interactions consequential to heavy-metal contamination of shallow groundwater. Sediment cores were extracted and fractionated based on sediment stratification. Subsamples of each fraction were assayed for culturable heterotrophic microbiota, specific microbial guilds involved in metal redox transformations, and both aqueous- and solid-phase geochemistry. Populations of cultivable Fe(III)-reducing bacteria were most prominent in the anoxic, circumneutral pH regions associated with a ferricrete layer or in an oxic zone high in organic carbon and soluble iron. Sulfur- and iron-oxidizing bacteria were distributed in discrete zones throughout the tailings and were often recovered from sections at and below the anoxic groundwater interface. Sulfate-reducing bacteria were also widely distributed in the cores and often occurred in zones overlapping iron and sulfur oxidizers. Sulfate-reducing bacteria were consistently recovered from oxic zones that contained high concentrations of metals in the oxidizable fraction. Altogether, these results suggest a highly varied and complex microbial ecology within a very heterogeneous geochemical environment. Such physical and biological heterogeneity has often been overlooked when remediation strategies for metal contaminated environments are formulated. PMID:10103249

Bacterial and chemical oxidation of pyritic mine tailings at low temperatures

NASA Astrophysics Data System (ADS)

Elberling, Bo; Schippers, Axel; Sand, Wolfgang

2000-02-01

Microbial and chemical sulfide oxidation activity and oxygen consumption was investigated in the active layer of pyritic mine tailings at Nanisivik Mine, located in a permafrost area on Baffin Island in northern Canada. Samples of tailings were collected up to a depth of 60 cm in mid-August 1998 at 4 sites, for which the metabolic activity of sulfur- and iron-oxidizing leaching bacteria besides the chemical pyrite oxidation activity were measured on 39 tailings samples and 7 samples from a natural pyritic site by calorimetry. The tailings of varying age and water content were deposited under alkaline conditions. In situ oxygen uptake rates were measured at the tailings surface every third day, prior to sampling. In addition, cell counts of iron(II), sulfur, and thiosulfate oxidizing, lithotrophic bacteria and chemoorganotrophic microorganisms were determined quantitatively by the most-probable-number technique or by agar-plating. Results show consistent pyrite oxidation rates based on in situ oxygen uptake rates, and laboratory heat output measurements. Litho- and organotrophic bacteria were found in the tailings. Calorimetric measurements revealed that the present bacterial activity is responsible for approximately one third of the ongoing oxidation. Although leaching bacteria have previously been found in the Arctic, this study is the first to prove the significance of bacterial activity in the overall pollution resulting from tailings deposited in the Arctic.

Mimicking microbial interactions under nitrate-reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio.

PubMed

Arshad, Arslan; Dalcin Martins, Paula; Frank, Jeroen; Jetten, Mike S M; Op den Camp, Huub J M; Welte, Cornelia U

2017-12-01

Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These elemental cycles are interconnected by the activity of different guilds in sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca. Kuenenia stuttgartiensis. Fifty-three percent of methane oxidation was catalyzed by archaea affiliated to Ca. Methanoperedens and 47% by Ca. Methylomirabilis bacteria. Sulfide oxidation was mainly shared between two proteobacterial groups. Interestingly, competition for nitrate did not lead to exclusion of one particular group. Metagenomic analysis showed that the most abundant taxonomic group was distantly related to Thermodesulfovibrio sp. (87-89% 16S rRNA gene identity, 52-54% average amino acid identity), representing a new family within the Nitrospirae phylum. A high quality draft genome of the new species was recovered, and analysis showed high metabolic versatility. Related microbial groups are found in diverse environments with sulfur, nitrogen and methane cycling, indicating that these novel Nitrospirae bacteria might contribute to biogeochemical cycling in natural habitats. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Long-distance electron transfer by cable bacteria in aquifer sediments

PubMed Central

Müller, Hubert; Bosch, Julian; Griebler, Christian; Damgaard, Lars Riis; Nielsen, Lars Peter; Lueders, Tillmann; Meckenstock, Rainer U

2016-01-01

The biodegradation of organic pollutants in aquifers is often restricted to the fringes of contaminant plumes where steep countergradients of electron donors and acceptors are separated by limited dispersive mixing. However, long-distance electron transfer (LDET) by filamentous ‘cable bacteria' has recently been discovered in marine sediments to couple spatially separated redox half reactions over centimeter scales. Here we provide primary evidence that such sulfur-oxidizing cable bacteria can also be found at oxic–anoxic interfaces in aquifer sediments, where they provide a means for the direct recycling of sulfate by electron transfer over 1–2-cm distance. Sediments were taken from a hydrocarbon-contaminated aquifer, amended with iron sulfide and saturated with water, leaving the sediment surface exposed to air. Steep geochemical gradients developed in the upper 3 cm, showing a spatial separation of oxygen and sulfide by 9 mm together with a pH profile characteristic for sulfur oxidation by LDET. Bacterial filaments, which were highly abundant in the suboxic zone, were identified by sequencing of 16S rRNA genes and fluorescence in situ hybridization (FISH) as cable bacteria belonging to the Desulfobulbaceae. The detection of similar Desulfobulbaceae at the oxic–anoxic interface of fresh sediment cores taken at a contaminated aquifer suggests that LDET may indeed be active at the capillary fringe in situ. PMID:27058505

Purple corn color inhibition of prostate carcinogenesis by targeting cell growth pathways.

PubMed

Long, Ne; Suzuki, Shugo; Sato, Shinya; Naiki-Ito, Aya; Sakatani, Keisuke; Shirai, Tomoyuki; Takahashi, Satoru

2013-03-01

Purple corn color is a widely used food colorant that was reported to have attenuating effects on hypertension, diabetes, and to have anti-cancer effects on colon and breast cancer. Our study is the first on its possible chemoprevention effects against prostate cancer. For this purpose an androgen-dependent prostate cancer cell line, LNCaP, was used to examine effects in vitro. Purple corn color inhibited the proliferation of LNCaP cells by decreasing the expression of Cyclin D1 and inhibiting the G1 stage of the cell cycle. Thirty-six male transgenic rats for adenocarcinoma of prostate were fed basic diet or diet with purple corn color for 8 weeks. Purple corn color decreased the incidence of adenocarcinoma in the lateral prostate and slowed down the progression of prostate cancer. A lower Ki67 positive rate, a decrease of the expression of Cyclin D1, and downregulation of the activation of Erk1/2 and p38 MAPK were observed in the group consuming purple corn color in the diet. Since purple corn color is a mixture, determining its active component should help in the understanding and usage of purple corn color for prostate cancer chemoprevention. Therefore, the three major anthocyanins in purple corn color, cyanidin-3-glucoside, pelargonidin-3-glucoside and peonidin-3-glucoside, were tested with LNCaP cells. The results suggested that cyanidin-3-glucoside and pelargonidin-3-glucoside are the active compounds. © 2012 Japanese Cancer Association.

Anthocyanins and flavonols are responsible for purple color of Lablab purpureus (L.) sweet pods.

PubMed

Cui, Baolu; Hu, Zongli; Zhang, Yanjie; Hu, Jingtao; Yin, Wencheng; Feng, Ye; Xie, Qiaoli; Chen, Guoping

2016-06-01

Lablab pods, as dietary vegetable, have high nutritional values similar to most of edible legumes. Moreover, our studies confirmed that purple lablab pods contain the natural pigments of anthocyanins and flavonols. Compared to green pods, five kinds of anthocyanins (malvidin, delphinidin and petunidin derivatives) were found in purple pods by HPLC-ESI-MS/MS and the major contents were delphinidin derivatives. Besides, nine kinds of polyphenol derivatives (quercetin, myricetin, kaempferol and apigenin derivatives) were detected by UPLC-ESI-MS/MS and the major components were quercetin and myricetin derivatives. In order to discover their molecular mechanism, expression patterns of biosynthesis and regulatory gens of anthocyanins and flavonols were investigated. Experimental results showed that LpPAL, LpF3H, LpF3'H, LpDFR, LpANS and LpPAP1 expressions were significantly induced in purple pods compared to green ones. Meanwhile, transcripts of LpFLS were more abundant in purple pods than green or yellow ones, suggestind that co-pigments of anthocyanins and flavonols are accumulated in purple pods. Under continuously dark condition, no anthocyanin accumulation was detected in purple pods and transcripts of LpCHS, LpANS, LpFLS and LpPAP1 were remarkably repressed, indicating that anthocyanins and flavonols biosynthesis in purple pods was regulated in light-dependent manner. These results indicate that co-pigments of anthocyanins and flavonols contribute to purple pigmentations of pods. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Bioleaching mechanism of Co and Li from spent lithium-ion battery by the mixed culture of acidophilic sulfur-oxidizing and iron-oxidizing bacteria.

PubMed

Xin, Baoping; Zhang, Di; Zhang, Xian; Xia, Yunting; Wu, Feng; Chen, Shi; Li, Li

2009-12-01

The bioleaching mechanism of Co and Li from spent lithium-ion batteries by mixed culture of sulfur-oxidizing and iron-oxidizing bacteria was investigated. It was found that the highest release of Li occurred at the lowest pH of 1.54 with elemental sulfur as an energy source, the lowest occurred at the highest pH of 1.69 with FeS(2). In contrast, the highest release of Co occurred at higher pH and varied ORP with S + FeS(2), the lowest occurred at almost unchanged ORP with S. It is suggested that acid dissolution is the main mechanism for Li bioleaching independent of energy matters types, however, apart from acid dissolution, Fe(2+) catalyzed reduction takes part in the bioleaching process as well. Co(2+) was released by acid dissolution after insoluble Co(3+) was reduced into soluble Co(2+) by Fe(2+) in both FeS(2) and FeS(2) + S systems. The proposed bioleaching mechanism mentioned above was confirmed by the further results obtained from the experiments of bioprocess-stimulated chemical leaching and from the changes in structure and component of bioleaching residues characterized by XPS, SEM and EDX.

Hydrogeology of the Sulphur Springs area, Tampa, Florida

USGS Publications Warehouse

Stewart, J.W.; Mills, L.R.

1984-01-01

The Sulfur Springs area includes about 56 square miles in west-central Hillsborough County, Florida. The north-central part of the city of Tampa is highly urbanized; the north-west part of the area is rural or undeveloped. The area has numerous sinkholes, two of which are used as retention basins for urban storm runoff. An intermittent stream discharges into a sinkhole that is hydraulically connected with the Floridian aquifer. A well-developed cavity system occurs in the upper part of the aquifer in the southwestern and southeastern parts of the area. Groundwater velocities of 4,200 to 9,200 feet per day were determined from dye tests conducted in a sinkhole area north of Sulfur Springs. Sulfur Springs provides the city of Tampa a supplemental water supply of 20 million gallons per day. Periodically, the spring pool is closed to swimming because of the high bacteria counts in the water. The source of bacteria appears to be an internally drained sinkhole area north of the spring. In 1980, groundwater use in the study area, excluding withdrawals from Sulphur Springs, was 7.2 million gallons per day, largely for public water supplies. The city of Tampa pumped an average of 48.5 million gallons per day from the Tampa Dam Reservoir on the Hillsborough River. (USGS)

Characterisation and stability of anthocyanins in purple-fleshed sweet potato P40.

PubMed

Xu, Jianteng; Su, Xiaoyu; Lim, Soyoung; Griffin, Jason; Carey, Edward; Katz, Benjamin; Tomich, John; Smith, J Scott; Wang, Weiqun

2015-11-01

Purple-fleshed sweet potato P40 has been shown to prevent colorectal cancer in a murine model. This study is to identify anthocyanins by using HPLC/MS-MS and assess the stability during various cooking conditions. P40 possesses a high content of anthocyanins up to 14 mg/g dry matter. Total 12 acylated anthocyanins are identified. Top three anthocyanins, e.g., cyanidin 3-caffeoyl-p-hydroxybenzoyl sophoroside-5-glucoside, peonidin 3-caffeoyl sophoroside-5-glucoside, and cyanidin 3-(6"-caffeoyl-6"-feruloylsophoroside)-5-glucoside, account for half of the anthocyanin contents. Over 80% of anthocyanins measured by acid hydrolysis were cyanidin derivatives, indicating P40 is unique when compared with other purple-fleshed sweet potatoes that usually contain more peonidin than cyanidin. Steaming, pressure cooking, microwaving, and frying but not baking significantly reduced 8-16% of total anthocyanin contents. Mono-acylated anthocyanins showed a higher resistance against heat than di- and non-acylated. Among of which, cyanidin 3-p-hydroxybenzoylsophoroside-5-glucoside exhibited the best thermal stability. The stable acylated and cyanidin-predominated anthocyanins in P40 may provide extra benefits for cancer prevention. Copyright © 2014 Elsevier Ltd. All rights reserved.

View of Sally May/Purple Mountain Siphon Intake. Looking southeast ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

View of Sally May/Purple Mountain Siphon Intake. Looking southeast - Childs-Irving Hydroelectric Project, Childs System, Sally May-Purple Mountain Siphon Intake, Forest Service Road 708/502, Camp Verde, Yavapai County, AZ

System evaluation and microbial analysis of a sulfur cycle-based wastewater treatment process for Co-treatment of simple wet flue gas desulfurization wastes with freshwater sewage.

PubMed

Qian, Jin; Liu, Rulong; Wei, Li; Lu, Hui; Chen, Guang-Hao

2015-09-01

A sulfur cycle-based wastewater treatment process, namely the Sulfate reduction, Autotrophic denitrification and Nitrification Integrated process (SANI(®) process) has been recently developed for organics and nitrogen removal with 90% sludge minimization and 35% energy reduction in the biological treatment of saline sewage from seawater toilet flushing practice in Hong Kong. In this study, sulfate- and sulfite-rich wastes from simple wet flue gas desulfurization (WFGD) were considered as a potential low-cost sulfur source to achieve beneficial co-treatment with non-saline (freshwater) sewage in continental areas, through a Mixed Denitrification (MD)-SANI process trialed with synthetic mixture of simple WFGD wastes and freshwater sewage. The system showed 80% COD removal efficiency (specific COD removal rate of 0.26 kg COD/kg VSS/d) at an optimal pH of 7.5 and complete denitrification through MD (specific nitrogen removal rate of 0.33 kg N/kg VSS/d). Among the electron donors in MD, organics and thiosulfate could induce a much higher denitrifying activity than sulfide in terms of both NO3(-) reduction and NO2(-) reduction, suggesting a much higher nitrogen removal rate in organics-, thiosulfate- and sulfide-based MD in MD-SANI compared to sulfide alone-based autotrophic denitrification in conventional SANI(®). Diverse sulfate/sulfite-reducing bacteria (SRB) genera dominated in the bacterial community of sulfate/sulfite-reducing up-flow sludge bed (SRUSB) sludge without methane producing bacteria detected. Desulfomicrobium-like species possibly for sulfite reduction and Desulfobulbus-like species possibly for sulfate reduction are the two dominant groups with respective abundance of 24.03 and 14.91% in the SRB genera. Diverse denitrifying genera were identified in the bacterial community of anoxic up-flow sludge bed (AnUSB) sludge and the Thauera- and Thiobacillus-like species were the major taxa. These results well explained the successful operation of the lab-scale MD-SANI process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Variations of Escherichia coli O157:H7 Survival in Purple Soils

PubMed Central

Zhang, Taoxiang; Hu, Suping; Yang, Wenhao

2017-01-01

Escherichia coli O157:H7 is a well-recognized cause of human illness. Survival of Escherichia coli O157:H7 in five purple soils from Sichuan Province was investigated. The dynamics of E. coli O157:H7 survival in purple soils were described by the Weibull model. Results showed that this model is suitable to fit survival curves of E. coli O157:H7 in purple soils, with the calculated td value (survival time needed to reach the detection limit of 100 CFU·g−1) ranging from 2.99 days to 26.36 days. The longest survival time of E. coli O157:H7 was observed in neutral purple soils (24.49 days), followed by alkalescent purple soil (18.62 days) and acid purple soil (3.48 days). The redundancy analysis (RDA) revealed that td values were significantly enhanced by soil nutrition (total organic carbon (OC), total nitrogen (TN), available potassium (AK) and the ratio of humic acid to fulvic acid (Ha/Fa)), but were significantly suppressed by iron and aluminum oxide. PMID:29057845

Stromatolitic structures associated with sulfur-bearing limestones from the Miocene (Badenian) of the Carpathian Foredeep (S Poland)

NASA Astrophysics Data System (ADS)

Siewicz, Andrzej Gä; Olchowy, Piotr

2010-05-01

The Middle Badenian (Miocene) evaporitic unit is widespread in the Miocene of the Carpathian Foredeep (South Poland). The unit is predominated by sulfates (gypsum + anhydrite) and locally in the northern marginal part of the foredeep contains carbonate complexes up to 45 m thick. The carbonate series are lithologically heterogenous and change from clayey and marl interlayers through marly to pure limestones and may be either sulfur-bearing or barren limestones locally intercalated by sulfate beds and layers. The bulk of the limestones consist of more or less calcareous, either non-bedded or bedded, laminated or streaky mudstones. The series is locally intercalated by breccia, rudstone (nodular) and gypsum-ghost facies. A characteristic feature of the carbonate mudstones lithofacies is the presence of variously developed sparse, thin and finely laminated layers and small (up to few centimeters in height) domal forms clearly resembling stromatolitic structures. The laminated layers usually are up to about 20 cm, discontinuous (up to a few tens meters long) and occur in various stratigraphic positions. The structures reveal wavy or flat, thin and subtle lamination consisting of intercalation of discontinuous native sulfur and calcareous laminae. They are lacking of gypsum selenite relics. There are two kinds of laminae: 1) thicker ones composed of finer to coarser crystalline calcite, sometimes with various clay admixtures and 2) thinner, commonly more or less discontinuous composed of subtle, fine crystalline and pure native sulfur. The calcite laminae are commonly barren with microfossils. The native sulfur laminae are commonly re-crystallized but often contain honey-comb like structures and local pockets with variously preserved sulfur microbial remains. The microfossils are poorly preserved and include coccoid and filamentous remains. The microbial structures are locally associated with irregular patches of structureless amorphous material resembling mucilage associated with many recent microorganisms. The calcite laminae are characterized by variable 18O values ranging in between -3.3 and -6.8‰ PDB and 13C ones from -31.7 to -57.2‰ PDB. The native sulfur forming laminae has positive 34S values changing from 4.6 to 17.2‰ CDT. Both the structural and isotopic data allow to interpret the stromatolitic structures as a result of microbial activity of syntropic sulfate-reducing and methanotrophic consortia + sulfide oxidizing bacteria. As it may be inferred from sedimentological and geochemical features of both the sulfur stromatolitic structures and associated sulfur-bearing limestones, the environment was generally shallow water, penesaline and euxinic, interrupted by meteoric influxes with precipitation of calcite and native sulfur, supply of both detrital and produced in situ organic matter. Such laminated structures have commonly been believed as a lithological equivalent of stromatolitic gypsum beds preserved due to massive replacement of solid gypsum by limestones and limestones + native sulfur. However, a more detailed comparison of geometry and distribution, sedimentological and petrologic features, as well as geochemical signatures accordingly exclude the native sulfur stromatolites as an analogue of the stromatolitic gypsum selenites. It argues against epigenetic replacement of solid sulfates and for syndepositional origin sulfur-bearing limestones.

Decoupling the Impacts of Heterotrophy and Autotrophy on Sulfuric Acid Speleogenesis

NASA Astrophysics Data System (ADS)

Jones, A. A.; Bennett, P.

2013-12-01

Within caves such as Movile Caves (Romania), the Frasassi Caves (Italy), and Lower Kane Cave (LKC, Wyoming, USA) the combination of abiotic autoxidation and microbiological oxidation of H2S produces SO42- and H+ that promotes limestone dissolution through sulfuric-acid speleogenesis (SAS). Microbial sulfide oxidation by sulfur-oxidizing bacteria (SOB) has been shown recently to be the dominant process leading to speleogenesis in these caves. However, due to the inherently large diversity of microbial communities within these environments, there are a variety of metabolic pathways that can impact limestone dissolution and carbon cycling to varying degrees. In order to investigate these variations we outfitted a continuous flow bioreactor with a Picarro Wavelength-Scanned Cavity Ring Down Spectrometer (WS-CRDS) that continuously monitored and logged 12CO2 and 13CO2 at ppmv sensitivity and isotope ratios at <0.3‰ precision in simulated cave atmospheres. Bioreactors containing Madison Limestone were inoculated with either a monoculture of the mixotrophic sulfur-oxidizing Thiothrix unzii or a mixed environmental (LKC) sulfur-metabolizing community. Ca2+ and pH were also continuously logged in order to quantify the impact of microbial metabolism on limestone dissolution rate. We found an order of magnitude of variability in limestone dissolution rates that were closely tied to microbial metabolism. In monocultures, limestone dissolution was inhibited by excessive reduced sulfur as T. unzii prefers to store sulfur internally as So under these conditions, generating no acidity. The headspace was depleted in 13C when sulfur was being stored as So and enriched in 13C when sulfur was being converted to SO42-. This suggests a preference for a heterotrophy during periods of high sulfur input and autotrophy when sulfur input is low. This was corroborated by an increase in SO42- during low sulfide input and microscope images showed loss of internal sulfur within the filaments during these periods. In both monoculture and LKC environmental cultures, dissolution rates were highest when sulfur-substrate was limited and CO2 was supplied with no organic carbon. Under these conditions δ13C values were as much as 20‰ higher than abiotic conditions and signifies autotrophic carbon fixation which discriminates against 13C. 16S rRNA sequences confirm that autotrophic SOB dominate within this reactor. In contrast, when acetate was supplied with no supplied CO2, δ13C was relatively constant, maintaining values between -31‰ and as low as -37‰. This signifies heterotrophic metabolism where lighter 12C is preferentially consumed resulting in lighter CO2 in the headspace. 16S rRNA sequences confirm that heterotrophic sulfur-reducing bacteria dominate the community within this reactor. When both acetate and CO2 were supplied the heterotrophic behavior appeared to dominate the system which resulted in a significant drop (15‰) in δ13C and a correlative drop in limestone dissolution rate. These results suggest that chemoautotrophy increases the rate of SAS and CO2 flux within the cave environment while heterotrophy leads to slower SAS or even calcite precipitation. Furthermore, changes in carbon substrate (CO2 vs. Acetate) or sulfur substrate concentrations caused an immediate microbial response that could be observed in all measured chemical variables.

A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

NASA Astrophysics Data System (ADS)

Barabash, Yu. M.; Lyamets, A. K.

2016-12-01

The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions (A(t)={sum}_{i=1}^n{a}_i{e}^{-{k}_it}) is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

Trace and minor element variations and sulfur isotopes in crystalline and colloform ZnS: Incorporation mechanisms and implications for their genesis

USGS Publications Warehouse

Pfaff, Katharina; Koenig, Alan; Wenzel, Thomas; Ridley, Ian; Hildebrandt, Ludwig H.; Leach, David L.; Markl, Gregor

2011-01-01

Various models have been proposed to explain the formation mechanism of colloform sphalerite, but the origin is still under debate. In order to decipher influences on trace element incorporation and sulfur isotope composition, crystalline and colloform sphalerite from the carbonate-hosted Mississippi-Valley Type (MVT) deposit near Wiesloch, SW Germany, were investigated and compared to sphalerite samples from 52 hydrothermal vein-type deposits in the Schwarzwald ore district, SW Germany to study the influence of different host rocks, formation mechanisms and fluid origin on trace element incorporation. Trace and minor element incorporation in sphalerite shows some correlation to their host rock and/or origin of fluid, gangue, paragenetic minerals and precipitation mechanisms (e.g., diagenetic processes, fluid cooling or fluid mixing). Furthermore, crystalline sphalerite is generally enriched in elements like Cd, Cu, Sb and Ag compared to colloform sphalerite that mainly incorporates elements like As, Pb and Tl. In addition, sulfur isotopes are characterized by positive values for crystalline and strongly negative values for colloform sphalerite. The combination of trace element contents, typical minerals associated with colloform sphalerite from Wiesloch, sulfur isotopes and thermodynamic considerations helped to evaluate the involvement of sulfate-reducing bacteria in water-filled karst cavities. Sulfate-reducing bacteria cause a sulfide-rich environment that leads in case of a metal-rich fluid supply to a sudden oversaturation of the fluid with respect to galena, sphalerite and pyrite. This, however, exactly coincides with the observed crystallization sequence of samples involving colloform sphalerite from the Wiesloch MVT deposit.

Bacillus subtilis UBTn7, a potential producer of L - Methioninase isolated from mangrove, Rhizophora mucronata

NASA Astrophysics Data System (ADS)

Prihanto, A. A.

2018-04-01

L-methioninase is an enzyme that degrades sulfur-containing amino acids to α-keto acids, ammonia, and thiols. L-methioninase could be found in plants, bacteria, and fungi. The aims of this study was to obtain L-methioninase-producing endophytic bacteria isolated from mangrove Rhizophora mucronata. The mangrove was collected from Jenu Beach, Tuban, East Java, Indonesia. The samples were roots, stems, and leaves of Rhizophora mucronata. Endophytic bacteria were pure isolated using LB agar medium. Each bacteria were screened its capability to produce L-methioninase using selective media namely modified Czapek Dox agar. The best producer of enzyme was further identified with morphological and biochemical analysis. The result showed that three bacteria produced L-methioninase. Based on the result of morphological and biochemical analysis, the best producer was Bacillus subtilis UBTn7.

The use of lysozyme modified with fluorescein for the detection of Gram-positive bacteria.

PubMed

Arabski, Michał; Konieczna, Iwona; Tusińska, Ewa; Wąsik, Sławomir; Relich, Inga; Zając, Krzysztof; Kamiński, Zbigniew J; Kaca, Wiesław

2015-01-01

Lysozyme (1,4-β-N-acetylmuramidase) is commonly applied in the food, medical, and pharmaceutical industries. In this study, we tested a novel application of fluorescein-modified lysozyme (using carboxyfluorescein with a triazine-based coupling reagent) as a new tool for the detection of Gram-positive soil bacteria. The results, obtained by cultivation methods, fluorescence analysis, and laser interferometry, showed that, after optimization, fluorescein-modified lysozyme could be used to evaluate the prevalence of Gram-positive bacteria essential in bioremediation of soils with low pH, such as those degraded by sulfur. Copyright © 2014 Elsevier GmbH. All rights reserved.

Fermentation, degradation and microbial nitrogen partitioning for three forage colour phenotypes within anthocyanidin-accumulating Lc-alfalfa progeny.

PubMed

Jonker, Arjan; Gruber, Margaret Y; Wang, Yuxi; Narvaez, Nelmy; Coulman, Bruce; McKinnon, John J; Christensen, David A; Azarfar, Arash; Yu, Peiqiang

2012-08-30

Alfalfa has the disadvantage of having a rapid initial rate of protein degradation, which results in pasture bloat, low efficiency of protein utilisation and excessive nitrogen (N) pollution into the environment for cattle. Introducing a gene that stimulates the accumulation of monomeric/polymeric anthocyanidins might reduce the ruminal protein degradation rate (by fixing protein and/or direct interaction with microbes) and additionally reduce methane emission. The objectives of this study were to evaluate in vitro fermentation, degradation and microbial N partitioning of three forage colour phenotypes (green, light purple-green (LPG) and purple-green (PG)) within newly developed Lc-progeny and to compare them with those of parental green non-transgenic (NT) alfalfa. PG-Lc accumulated more anthocyanidin compared with Green-Lc (P < 0.05), with LPG-Lc intermediate. Volatile fatty acids and potentially degradable dry matter (DM) and N were similar among the four phenotypes. Gas, methane and ammonia accumulation rates were slower for the two purple-Lc phenotypes compared with NT-alfalfa (P < 0.05), while Green-Lc was intermediate. Effective degradable DM and N were lower in the three Lc-phenotypes (P < 0.05) compared with NT-alfalfa. Anthocyanidin concentration was negatively correlated (P < 0.05) with gas and methane production rates and effective degradability of DM and N. The Lc-alfalfa phenotypes accumulated anthocyanidin. Fermentation and degradation parameters indicated a reduced rate of fermentation and effective degradability for both purple anthocyanidin-accumulating Lc-alfalfa phenotypes compared with NT-alfalfa. Copyright © 2012 Society of Chemical Industry.

Condensed tannins affect bacterial and fungal microbiomes and mycotoxin production during ensiling and upon aerobic exposure.

PubMed

Peng, Kai; Jin, Long; Niu, Yan D; Huang, Qianqian; McAllister, Tim A; Yang, Hee Eun; Denise, Hubert; Xu, Zhongjun; Acharya, Surya; Wang, Shunxi; Wang, Yuxi

2017-12-15

Purple prairie clover (PPC; Dalea purpurea Vent.) containing 84.5 g/kg DM of condensed tannin (CT) was ensiled without (Control) or with polyethylene glycol (PEG) for 76 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics were determined and bacterial and fungal communities were assessed using metagenomic sequencing. Addition of PEG that deactivated CT at ensiling increased ( P < 0.05∼0.001) soluble N, non-protein N, lactic acid, total volatile fatty acids, ammonia N, deoxynivalenol (DON) and ochratoxin A (OTA), but decreased ( P < 0.001) pH and water soluble carbohydrates. Concentration of DON and OTA increased ( P < 0.001) for both silages with the extent of increase being greater for Control than for PEG treated silage during aerobic exposure. The PEG treated silage exhibited higher ( P < 0.01∼0.001) copy numbers of total bacteria, Lactobacillus , yeasts and fungi than Control. Addition of PEG decreased ( P < 0.01) bacterial diversity during both ensiling and aerobic exposure, whereas it increased ( P < 0.05) fungal diversity during aerobic exposure. Addition of PEG at ensiling increased ( P < 0.05) abundances of Lactobacillus and Pediococcus , but decreased ( P < 0.01) abundances of Lactococcus and Leuconostoc Filamentous fungi were found in the microbiome at ensiling and after aerobic exposure, whereas the Bacillus were the dominate bacteria after aerobic exposure. In conclusion, CT decreased protein degradation and improved aerobic stability of silage. These desirable outcomes likely reflect the ability of PPC CT to inhibit those microorganisms involved in lowering silage quality and in the production of mycotoxins. IMPORTANCE The present study reports the effects of condensed tannins on the complex microbial communities involved in ensiling and aerobic exposure of purple prairie clover. This study documents the ability of condensed tannins to lower mycotoxin production and associated microbiome. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillus as a result of aerobic exposure. It is interesting to observe that condensed tannins decreased bacterial diversity during both ensiling and aerobic exposure but increased fungal diversity during aerobic exposure only. The present study indicates that the effects of condensed tannins on microbial communities lead to a reduced lactic acid and total volatile fatty acids production, proteolysis and mycotoxin concentration in the terminal silage and an improved aerobic stability. Condensed tannins could be used as additive to control unfavorable microbial development and maybe enhanced feed safety. © Crown copyright 2017.

[Relationships between vegetation characteristics and soil properties at different restoration stages on slope land with purple soils in Hengyang of Hunan Province, South-central China].

PubMed

Yang, Ning; Zou, Dong-Sheng; Yang, Man-Yuan; Hu, Li-Zhen; Zou, Fang-Ping; Song, Guang-Tao; Lin, Zhong-Gui

2013-01-01

By using space series to replace time series, this paper studied the relationships between the vegetation characteristics and soil properties at different restoration stages on the slope land with purple soils in Hengyang of Hunnan Province South-central China. There existed obvious differences in the soil physical and chemical properties at different restoration stages. From grassplot, grass-shrub, shrub to shrub-arbor, the soil organic matter, total and available N, and moisture contents increased markedly, soil bulk density had an obvious decrease, soil total and available P contents changed little, and soil pH decreased gradually, but no significant differences were observed among different restoration stages. At different restoration stages, the biomass of plant community had effects on the quantity and composition of soil microbes. The quantities of soil bacteria and fungi had significant positive correlations with the aboveground biomass of plant community, but the quantity of soil actinomycetes had less correlation with plant community's aboveground biomass. At different restoration stages, the activities of soil urease, protease, alkaline phosphatase, invertase, cellulase, catalase, and polyphenol oxidase decreased with increasing soil layer, and had significant positive correlations with plant community's richness and aboveground biomass.

Optimization of multifunnel traps for emerald ash borer (Coleoptera: Buprestidae): influence of size, trap coating, and color.

PubMed

Francese, Joseph A; Rietz, Michael L; Mastro, Victor C

2013-12-01

Field assays were conducted in southeastern and south-central Michigan in 2011 and 2012 to optimize green and purple multifunnel (Lindgren funnel) traps for use as a survey tool for the emerald ash borer, Agrilus planipennis Fairmaire. Larger sized (12- and 16-unit) multifunnel traps caught more beetles than their smaller-sized (4- and 8-unit) counterparts. Green traps coated with untinted (white) fluon caught almost four times as many adult A. planipennis as Rain-X and tinted (green) fluon-coated traps and almost 33 times more beetles than untreated control traps. Purple multifunnel traps generally caught much lower numbers of A. planipennis adults than green traps, and trap catch on them was not affected by differences in the type of coating applied. However, trap coating was necessary as untreated control purple traps caught significantly less beetles than traps treated with Rain-X and untinted or tinted (purple) fluon. Proportions of male beetles captured were generally much higher on green traps than on purple traps, but sex ratios were not affected by trap coating. In 2012, a new shade of purple plastic, based on a better color match to an attractive purple paint than the previously used purple, was used for trapping assays. When multifunnel traps were treated with fluon, green traps caught more A. planipennis adults than both shades of purple and a prism trap that was manufactured based on the same color match. Trap catch was not affected by diluting the fluon concentration applied to traps to 50% (1:1 mixture in water). At 10%, trap catch was significantly lowered.

Life detection at an Arctic analog to Europa

NASA Astrophysics Data System (ADS)

Gleeson, D. F.; Pappalardo, R. T.; Anderson, M. S.; Grasby, S. E.; Wright, K.; Templeton, A. S.

2010-12-01

Europa is a high priority for astrobiological investigations. Future missions to the icy surface of this moon will query the arguably sulfur-rich materials for potential indications of the presence of life carried to the surface by mobile ice or partial melt. Cold sulfur-rich environments are rare on the Earth, and the potential for the generation and preservation of biosignatures under these conditions remains largely unconstrained. Here we describe investigations into the biogenicity of analogous sulfur deposits from the surface of an Arctic glacier at Borup Fiord pass, Ellesmere Island. Optical and electron microscopy indicate that the sulfur in field samples is present in the form of clumps of mineral grains and spherical mineral aggregates, in close association with microbial sheaths. The morphologies of these materials are consistent with observations of the sulfur generated by sulfide-oxidizing bacteria cultivated from field samples in previous studies. X-ray diffraction measurements provide some evidence for the presence of rosickyite, a metastable form of sulfur previously recognized to be associated with the presence of life. Infrared spectroscopy reveals the presence of organics at parts per million levels, and organic functional groups diagnostic of proteins and fatty acids are identified. Organic components were below the detection limit for Raman spectra, which were dominated by sulfur peaks. These combined investigations indicate that sulfur minerals have the potential to contain identifiable biosignatures that low-temperature conditions help stabilize and preserve. Borup Fiord Pass represents a useful testing ground for instruments and techniques relevant to future astrobiological exploration at Europa.

Iron and Sulfur Species and Sulfur Isotopic Compositions of Authigenic Pyrite in Gas Hydrate-Bearing Sediments from Hydrate Ridge, Cascadia Margin (ODP Leg 204): A Proposal of Conceptual Models to Indicate the Non-Steady State Depositional and Diagenetic Processes

NASA Astrophysics Data System (ADS)

Liu, C.; Jiang, S. Y.; Su, X.

2017-12-01

Two accretionary sediment sequences from Sites 1245 and 1252 recovered during Ocean Drilling Program (ODP) Leg 204 at Hydrate Ridge, Cascadia Margin were investigated to explore the non-steady state depositional and diagenetic history. Five iron species and three sulfur species were chemically extracted, and their concentrations and the sulfur isotopic compositions of pyrite were determined. After the mineral recognitions of these species and detailed comparative analyses, the aerobic history of bottom seawater has been determined. The formation of pyrite is thought to be controlled by the limited production of hydrogen sulfide relative to the supply of reactive iron. Also, the intrusion of oxygen by bioturbation would oxidize the reduced sulfur species and further suppress pyritization. To explain the geochemical relationship between pyrite and siderite and the sulfur isotope characteristics of pyrite, we propose seven conceptual models based on the variations in depositional rate and methane flux, and the models succeed in explaining the geochemical results and are validated by the observed non-steady state events. These models may contribute to the reconstruction of the non-steady state processes in other research areas in the future.

Microbial colonization and growth on metal sulfides and other mineral surfaces

NASA Technical Reports Server (NTRS)

Caldwell, D.; Sundquist, A. R.; Lawrence, J.; Doyle, A. P.

1985-01-01

To determine whether a bacterial film forms on sulfur minerals in situ, various sulfur containing and other minerals were incubated in Penitencia Creek. The rate of cell growth and attachment within the surface microenvironment of mineral surfaces was also determined. To determine whether surfaces enriched with soluble sulfur substrates (cysteine, glutathione, thioglycolate, sulfite, and thiosulfate) increased the rate of growth or attachment of natural communities, membrane enrichments were incubated. These rates were determined as described by Caldwell et al. (1981, 1983). The growth of Pseudomonas fluorescens, a heterotrophic sulfur oxidizer, was studied in batch cell suspensions and in continuous culture. In batch culture the cells were oxygen limited (growth rate 0.33 per hour under oxygen limitations and 0.52 per hour when vigorously aerated). Growth within the film was glucose limited. Several behavioral phenomena were observed for cells growing within the hydrodynamic boundary layer. Despite a flow of 10 cm per second in the environment, the bacteria were able to move freely in both directions within the hydrodynamic boundary layer.

Identification of a chondroitin synthase from an unexpected source, the green sulfur bacterium Chlorobium phaeobacteroides.

PubMed

Green, Dixy E; DeAngelis, Paul L

2017-05-01

Glycosaminoglycans (GAGs) are known to be present in all animals as well as some pathogenic microbes. Chondroitin sulfate is the most abundant GAG in mammals where it has various structural and adhesion roles. The Gram-negative bacteria Pasteurella multocida Type F and Escherichia coli K4 produce extracellular capsules composed of unsulfated chondroitin or a fructosylated chondroitin, respectively. Such polysaccharides that are structurally related to host molecules do not generally provoke a strong antibody response thus are thought to be employed as molecular camouflage during infection. We observed a sequence from the photosynthetic green sulfur bacteria, Chlorobium phaeobacteroides DSM 266, which was very similar (~62% identical) to the open reading frames of the known bifunctional chondroitin synthases (PmCS and KfoC); some segments are strikingly conserved amongst the three proteins. Recombinant E. coli-derived Chlorobium enzyme preparations were found to possess bona fide chondroitin synthase activity in vitro. This new catalyst, CpCS, however, has a more promiscuous acceptor usage than the prototypical PmCS, which may be of utility in novel chimeric GAG syntheses. The finding of such a similar chondroitin synthase enzyme in C. phaeobacteroides is unexpected for several reasons including (a) a free-living nonpathogenic organism should not "need" an animal self molecule for protection, (b) the Proteobacteria and the green sulfur bacterial lineages diverged ~2.5-3 billion years ago and (c) the ecological niches of these bacteria are not thought to overlap substantially to facilitate horizontal gene transfer. CpCS provides insight into the structure/function relationship of this class of enzymes. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Single-cell genomics reveals co-metabolic interactions within uncultivated Marine Group A bacteria

NASA Astrophysics Data System (ADS)

Hawley, A. K.; Hallam, S. J.

2016-02-01

Marine Group A (MGA) bacteria represent a ubiquitous and abundant candidate phylum enriched in oxygen minimum zones (OMZs) and the deep ocean. Despite MGA prevalence little is known about their ecology and biogeochemistry. Here we chart the metabolic potential of 26 MGA single-cell amplified genomes sourced from different environments spanning ecothermodynamic gradients including open ocean waters, OMZs and methanogenic environments including a terephthalate-degrading bioreactor. Metagenomic contig recruitment to SAGs combined with tetra-nucleotide frequency distribution patterns resolved nine MGA population genome bins. All population genomes exhibited genomic streamlining with open ocean MGA being the most reduced. Different strategies for carbohydrate utilization, carbon fixation energy metabolism and respiratory pathways were identified between population genome bins, including various roles in the nitrogen and sulfur cycles. MGA inhabiting OMZ oxyclines encoded genes for partial denitrification with potential to feed into anammox and nitrification as well as a polysulfide reductase with a potential role in the cryptic sulfur cycle. MGA inhabiting anoxic waters, encoded NiFe hydrogenase and nitrous oxide reductase with the potential to complete partial denitrification pathways previously linked to sulfur oxidation in SUP05 bacteria. MGA from methanogenic environments encoded genes mediating cascading syntrophic interactions with fatty acid degraders and methanogens including reverse electron transport potential. The MGA phylum appears to have evolved alternative metabolic innovations adapting specific subgroups to occupy specific niches along ecothermodynamic gradients. Additionally, expression of MGA genes from different OMZ environments supports that these subgroups manifest an increasing propensity for co-metabolic interactions under energy limiting conditions that mandates a cooperative mode of existence with important implications for C, N and S cycling in marine ecosystems.

Redox regulation of energy transfer efficiency in antennas of green photosynthetic bacteria

NASA Technical Reports Server (NTRS)

Blankenship, R. E.; Cheng, P.; Causgrove, T. P.; Brune, D. C.; Wang, J.

1993-01-01

The efficiency of energy transfer from the peripheral chlorosome antenna structure to the membrane-bound antenna in green sulfur bacteria depends strongly on the redox potential of the medium. The fluorescence spectra and lifetimes indicate that efficient quenching pathways are induced in the chlorosome at high redox potential. The midpoint redox potential for the induction of this effect in isolated chlorosomes from Chlorobium vibrioforme is -146 mV at pH 7 (vs the normal hydrogen electrode), and the observed midpoint potential (n = 1) decreases by 60 mV per pH unit over the pH range 7-10. Extraction of isolated chlorosomes with hexane has little effect on the redox-induced quenching, indicating that the component(s) responsible for this effect are bound and not readily extractable. We have purified and partially characterized the trimeric water-soluble bacteriochlorophyll a-containing protein from the thermophilic green sulfur bacterium Chlorobium tepidum. This protein is located between the chlorosome and the membrane. Fluorescence spectra of the purified protein indicate that it also contains groups that quench excitations at high redox potential. The results indicate that the energy transfer pathway in green sulfur bacteria is regulated by redox potential. This regulation appears to operate in at least two distinct places in the energy transfer pathway, the oligomeric pigments in the interior of the chlorosome and in the bacteriochlorophyll a protein. The regulatory effect may serve to protect the cell against superoxide-induced damage when oxygen is present. By quenching excitations before they reach the reaction center, reduction and subsequent autooxidation of the low potential electron acceptors found in these organisms is avoided.

Application of indigenous sulfur-oxidizing bacteria from municipal wastewater to selectively bioleach phosphorus from high-phosphorus iron ore: effect of particle size.

PubMed

Shen, Shaobo; Rao, Ruirui; Wang, Jincao

2013-01-01

The effects of ore particle size on selectively bioleaching phosphorus (P) from high-phosphorus iron ore were studied. The average contents of P and Fe in the iron ore were 1.06 and 47.90% (w/w), respectively. The particle sizes of the ores used ranged from 58 to 3350 microm. It was found that the indigenous sulfur-oxidizing bacteria from municipal wastewater could grow well in the slurries of solid high-phosphorus iron ore and municipal wastewater. The minimum bioleaching pH reached for the current work was 0.33. The P content in bioleached iron ore reduced slightly with decreasing particle size, while the removal percentage of Fe decreased appreciably with decreasing particle size. The optimal particle size fraction was 58-75 microm, because the P content in bioleached iron ore reached a minimum of 0.16% (w/w), the removal percentage of P attained a maximum of 86.7%, while the removal percentage of Fe dropped to a minimum of 1.3% and the Fe content in bioleached iron ore was a maximum of 56.4% (w/w) in this case. The iron ores thus obtained were suitable to be used in the iron-making process. The removal percentage of ore solid decreased with decreasing particle size at particle size range of 106-3350 microm. The possible reasons resulting in above phenomena were explored in the current work. It was inferred that the particle sizes of the iron ore used in this work have no significant effect on the viability of the sulfur-oxidizing bacteria.

Purple loosestrife volunteers

USGS Publications Warehouse

Middleton, Beth A.

2004-01-01

Purple loosestrife (Lythrum salicaria) is a perennial plant native to Eurasia where it grows along streams, rivers, and wet seepage areas (fig. 1). Seeds were inadvertently brought to North American territories in the ballast water of ships. Purple loosestrife was also intentionally planted throughout North America for its ornamental flowers but has since escaped cultivation to spread to wetlands.Some purple loosestrife plants release millions of seeds during the summer season, and these seeds readily disperse to new wetlands via water, animals, and even on people’s shoes. In addition, both its roots and stem fragments can sprout and begin new plants.When purple loosestrife invades a wetland, the species sometimes becomes more dominant than the original native wetland species, such as cattails and sedges. While many people think that purple loosestrife reduces the value of wetlands for wildlife, these claims are disputed. Most people agree, however, that purple loosestrife grows more prolifically in North America than elsewhere, probably because the species has left its native enemies behind in Eurasia and Australia. Although we do not understand how well the species grows in various climates, there is some thought that purple loosetrife may never fully invade the southern United States. Studies looking at the species’ response to temperature and analyses of its growth patterns across latitudes can help us determine its future threat to uninvaded portions of the United States. This is where volunteers come in.Volunteers in North America, Eurasia, and Australia are helping assess purple loosestrife growth in their regions (fig. 2). The program is part of Dr. Beth Middleton’s project to compare the role of purple loosestrife in its native and invasive habitats. Anyone can participate, and volunteers currently include high school and college students, retirees, professionals from all disciplines, agency personnel, and university faculty. Volunteers collect data by marking off a sampling area, recording the number and height of purple loosestrife, and observing the sunlight and water conditions at each location. Data collection only occurs once in each wetland and takes less than 30 minutes (see form below). The results of the study will help efforts to control and predict the future spread of this species.

On Light-Induced Photoconversion of B800 Bacteriochlorophylls in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum.

PubMed

Kell, Adam; Jassas, Mahboobe; Hacking, Kirsty; Cogdell, Richard J; Jankowiak, Ryszard

2017-11-02

The B800-850 LH2 antenna from the photosynthetic purple sulfur bacterium Allochromatium vinosum exhibits an unusual spectral splitting of the B800 absorption band; i.e., two bands are well-resolved at 5 K with maxima at 805 nm (B800 R ) and 792 nm (B800 B ). To provide more insight into the nature of the B800 bacteriochlorophyll (BChl) a molecules, high-resolution hole-burning (HB) spectroscopy is employed. Both white light illumination and selective laser excitations into B800 R or B800 B lead to B800 R → B800 B phototransformation. Selective excitation into B800 B leads to uncorrelated excitation energy transfer (EET) to B800 R and subsequent B800 R → B800 B phototransformation. The B800 B → B800 R EET time is 0.9 ± 0.1 ps. Excitation at 808.4 nm (into the low-energy side of B800 R ) shows that the lower limit of B800 R → B850 EET is about 2 ps, as the B800 R → B800 B phototransformation process could contribute to the corresponding zero-phonon hole width. The phototransformation of B800 R leads to a ∼ 200 cm -1 average blue-shift of transition energies, i.e., B800 R changes into B800 B . We argue that it is unlikely that B800-B850 excitonic interactions give rise to a splitting of the B800 band. We propose that the latter is caused by different protein conformations that can lead to both strong or weak hydrogen bond(s) between B800 pigments and the protein scaffolding. Temperature-dependent absorption spectra of B800, which revealed a well-defined isosbestic point, support a two-site model, likely with strongly and weakly hydrogen-bonded B800 BChls. Thus, BChls contributing to B800 R and B800 B could differ in the position of the proton in the BChl carbonyl-protein hydrogen bond, i.e., proton dynamics along the hydrogen bond may well be the major mechanism of this phototransformation. However, the effective tunneling mass is likely larger than the proton mass.

Fire and nitrogen effects on purple threeawn invaded plant communities

USDA-ARS?s Scientific Manuscript database

Purple threeawn (Aristida purpurea) is a native grass capable of rapidly increasing on rangelands, forming near monocultures, and arresting ecological succession. Productive rangelands throughout the Great Plains and Intermountain West have experienced increases in purple threeawn abundance, leadin...

Light response, oxidative stress management and nucleic acid stability in closely related Linderniaceae species differing in desiccation tolerance.

PubMed

Dinakar, Challabathula; Bartels, Dorothea

2012-08-01

In the present study, three closely related Linderniaceae species which differ in their sensitivity to desiccation are compared in response to light and oxidative stress defence. Lindernia brevidens, a desiccation-tolerant plant, displayed intense purple pigmentation in leaves under long-day conditions in contrast to Craterostigma plantagineum (desiccation tolerant) and Lindernia subracemosa (desiccation sensitive). The intense pigmentation in leaves does not affect the desiccation tolerance behaviour but seems to be related to oxidative stress protection. Green leaves of short-day and purple leaves of long-day plants provided suitable material for comparing basic photosynthetic parameters. An increase in non-photochemical quenching in purple leaves appears to prevent photoinhibition. Treatment with methyl viologen decreased the photochemical activities in both long-day and short-day plants but long-day plants which accumulate anthocyanins maintained a higher non-photochemical quenching than short-day plants. No differences were seen in the expression of desiccation-induced proteins and proteins involved in carbohydrate metabolism in short-day and long-day grown plants, whereas differences were observed in the expression of transcripts encoding chloroplast-localised stress proteins and transcripts encoding antioxidant enzymes. While the expression of genes encoding antioxidant enzymes were either constitutive or up-regulated during desiccation in C. plantagineum, the expression was down-regulated in L. subracemosa. RNA expression analysis indicated degradation of mRNA during desiccation in L. subracemosa but not in desiccation tolerant species. These results indicate that a better oxidative stress management and mRNA stability are correlated with desiccation tolerance.

Two-step rapid sulfur capture. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1994-04-01

The primary goal of this program was to test the technical and economic feasibility of a novel dry sorbent injection process called the Two-Step Rapid Sulfur Capture process for several advanced coal utilization systems. The Two-Step Rapid Sulfur Capture process consists of limestone activation in a high temperature auxiliary burner for short times followed by sorbent quenching in a lower temperature sulfur containing coal combustion gas. The Two-Step Rapid Sulfur Capture process is based on the Non-Equilibrium Sulfur Capture process developed by the Energy Technology Office of Textron Defense Systems (ETO/TDS). Based on the Non-Equilibrium Sulfur Capture studies the rangemore » of conditions for optimum sorbent activation were thought to be: activation temperature > 2,200 K for activation times in the range of 10--30 ms. Therefore, the aim of the Two-Step process is to create a very active sorbent (under conditions similar to the bomb reactor) and complete the sulfur reaction under thermodynamically favorable conditions. A flow facility was designed and assembled to simulate the temperature, time, stoichiometry, and sulfur gas concentration prevalent in the advanced coal utilization systems such as gasifiers, fluidized bed combustors, mixed-metal oxide desulfurization systems, diesel engines, and gas turbines.« less