Polysulfide as a possible substrate for sulfur-reducing bacteria

Because of its low solubility it is unlikely that elemental sulfur serves as the direct substrate for sulfur-reducing bacteria. To test the hypothesis that polysulfide may represent a soluble intermediate of sulfur reduction, the maximal polysulfide concentrations formed from elemental sulfur in aqueous sulfide solutions were measured at near neutral pH and at temperatures up to 90°C. The saturation concentrations decreased by two orders of magnitude when the pH was lowered from 7 to 6 at a given temperature, and increased about tenfold when the temperature was raised from 37°C to 90°C at a given pH. The dissolution of 0.1 mM zerovalent sulfur in 1 mM sulfide (H₂S+HS^–) required a pH of 7.5 at 20°C and of only 6.1 at 100°C. A comparison with the growth optima of sulfur-reducers suggests that polysulfide is present at sufficient concentration at the growth conditions of the Bacteria and the moderately acidophilic Archaea. Polysulfide is apparently not available at the growth conditions of the extremely acidophilic Archaea. Alternative mechanisms for the sulfur utilization under these conditions are discussed.Abbreviations MOPS Morpholinopropanesulfonate - PIPES 1,4 piperazine-N,N-bis(2-ethanesulfonate) - HEPES N-2-hydroxy-ethylpiperazine-N-ethanesulfonate     

Factors influencing odour production by actinomycetes

Odour production by actinomycete (Streptomyces spp.) strains isolated from hypereutrophic natural waters in which muddy odours in fish have occurred, were studied by the ISP (International Streptomyces Project) carbon utilization method. The streptomycete strains were isolated from water, bottom mud and aquatic plants. Nine different carbon sources were used. Odour character was determined by sniffing the cultures. Odour production varied depending on the strain and the carbon source used. Some of the strains produced similar odours in all media regardless of the carbon source. In other strains, the odour varied depending on the carbohydrate used. The total colony counts of actinomycetes may not necessarily indicate the role of actinomycetes in odour problems in the aquatic environment because the odour production by actinomycetes depends on environmental factors.     

Isolation and characterization of halotolerant Streptomyces radiopugnans from Antarctica soil

An actinomycete wild strain PM0626271 (= MTCC 5447), producing novel antibacterial compounds, was isolated from soil collected from Antarctica. The taxonomic status of the isolate was established by polyphasic approach. Scanning electron microscopy observations and the presence of LL‐Diaminopimelic acid in the cell wall hydrolysate confirmed the genus Streptomyces. Analysis of 16S rRNA gene sequence showed highest sequence similarity to Streptomyces radiopugnans (99%). The phylogenetic tree constructed using near complete 16S rRNA gene sequences of the isolate and closely related strains revealed that although the isolate fell within the S. radiopugnans gene subclade, it was allocated a different branch in the phylogenetic tree, separating it from the majority of the radiopugnans strains. Similar to type strain, S. radiopugnans R97^T, the Antarctica isolate displayed thermo tolerance as well as resistance to ⁶⁰Co gamma radiation, up to the dose of 15 kGy. However, media and salt tolerance studies revealed that, unlike the type strain, this isolate needed higher salinity for its growth. This is the first report of S. radiopugnans isolated from the Antarctica region. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Streptomyces radiopugnans MTCC 5447 is JQ723477 .

Significance and Impact of the Study

The study presents the first report of isolation of Streptomyces radiopugnans from Antarctica. To date, there is only one publication regarding S. radiopugnans R97^T isolated from radiation‐polluted soil. Like the type strain, Antarctica isolate was thermotolerant and radiotolerant, but in addition, it required salts for growth and did not degrade phenol. We envisaged that metabolic pattern of the same species varies based on acclimatization in its native ecological habitat. Additionally, Antarctica isolate had produced novel antibacterial compounds (patent‐US2012/0156295). The study highlighted that least explored extreme regions like Antarctica are rich resources of novel microbial strains producing novel bioactive compounds.     

Acidic Cave-Wall Biofilms Located in the Frasassi Gorge,Italy

Acidic biofilms present on cave walls in the sulfidic region of the Frasassi Gorge, Italy, were investigated to determine their microbial composition and their potential role in cave formation and ecosystem functioning. All biofilm samples examined had pH values < 1.0. Scanning electron microscopy of the biofilms revealed the presence of various filaments and rods associated in large clusters with mineral crystals. Qualitative energy-dispersive x-ray analysis was used to determine that the crystals present on the cave walls, associated with the microbial biofilm, were composed of calcium and barium sulfate. Ribosomal RNA-based methods to determine the microbial composition of these biofilms revealed the presence of at least two strains of potential acidophilic, sulfur-oxidizing bacteria, belonging to the genera Thiobacillus and Sulfobacillus. An acid-producing strain of Thiobacillus sp. also was obtained in pure culture. Stable isotope ratio analysis of carbon and nitrogen showed that the wall biofilms are isotopically light, suggesting that in situ chemoautotrophic activity plays an important role in this subsurface ecosystem.     

Acidophilic granulocytes of the marine fish gilthead seabream (<Emphasis Type="Italic">Sparus aurata</Emphasis> L.) produce interleukin-1β following infection with<Emphasis Type="Italic"> Vibrio anguillarum</Emphasis>

The fish immune response to Gram-negative bacteria is poorly understood. In this study, we use a monoclonal antibody (mAb) specific to acidophilic granulocytes from the marine fish gilthead seabream (Sparus aurata L.), together with an antiserum specific to interleukin-1 (IL-1) from this species, in order to investigate whether these cells are involved in the immune response against the pathogenic bacterium Vibrio anguillarum and, in particular, in the production of the pro-inflammatory cytokine IL-1. We found that gilthead seabream head-kidney, peritoneal exudate and peripheral blood leukocytes accumulated proIL-1 intracellularly when challenged in vitro with V. anguillarum, whereas only peritoneal exudate and blood leukocytes were able to accumulate proIL-1 following infection. Importantly, the blood leukocytes from infected animals that accumulated proIL-1 were shown to be the acidophilic granulocytes. A rapid mobilization of such cells from the head-kidney to the site of inflammation following infection with V. anguillarum was also observed. This work was supported by the Spanish Ministry of Science and Technology (grants BIO2001-2324-C02-02 and AGL2002-03529, and fellowship to J. García-Castillo), Spanish Ministry of Education, Culture and Sport (fellowship to E. Chaves-Pozo) and Fundación Séneca, Coordination Centre for Research (grant PI-51/00782/FS/01 and fellowship to P. Pelegrín).E. Chaves-Pozo and P. Pelegrín contributed equally to this work.     

Microbial cycling of iron and sulfur in sediments of acidic and pH-neutral mining lakes in Lusatia (Brandenburg, Germany)

A vast number of lakes developed in the abandoned opencast lignite mines of Lusatia (East Germany) contain acidic waters (mmolSm^–2a^–). Potential Fe(III) reduction measured by the accumulation of Fe(II) during anoxic incubation yielded similar rates in both types of sediments, however, the responses towards the supplementation of Fe(III) and organic carbon were different. Sulfate reduction rates estimated with ³⁵S-radiotracer were much lower in the slightly acidic sediment than in the pH-neutral sediment (156 v.s. 738mmolSO₄ ^2–m^–2a^–1). However, sulfate reduction rates were increased by the addition of organic carbon. Severe limitation of sulfate-reducing bacteria under acidic conditions was also reflected by low most probable numbers (MPN). High MPN of acidophilic iron- and sulfur-oxidizing bacteria in acidic sediments indicated a high reoxidation potential. The results show that potentials for reductive processes are present in acidic sediments and that these are determined mainly by the availability of oxidants and organic matter.     

NAD+-dependent DNA ligases of Mycobacterium tuberculosis and Streptomyces coelicolor

Sequencing of the genomes of Mycobacterium tuberculosis H37Rv and Streptomyces coelicolor A3(2) identified putative genes for an NAD(+)-dependent DNA ligase. We have cloned both open reading frames and overexpressed the protein products in Escherichia coli. In vitro biochemical assays confirm that each of these proteins encodes a functional DNA ligase that uses NAD(+) as its cofactor. Expression of either protein is able to complement E. coli GR501, which carries a temperature-sensitive mutation in ligA. Thus, in vitro and in vivo analyses confirm predictions that ligA genes from M. tuberculosis and S. coelicolor are NAD(+)-dependent DNA ligases.     

Towards an ecological basis for the conservation of subalpine heath-grassland on the upper ridges of the Vosges

Abstract. The subalpine oligotrophic heath-grasslands, assigned to the Pulsatillo-Vaccinietum and Violo-Nardetum, occurring at the upper ridges in the Vosges at 1100 - 1300 m a.s.l. are of conservational interest because they form natural, mature and stable ecosystems. The Pulsatillo-Vaccinietum is particularly rich in endemic plant species and subspecies due to a local oceanic-subarctic climate and the continuous occurrence of the community throughout the Holocene period, when the association was not affected by changes in the prevailing environmental conditions. After a period of abandonment during and after World War II, agriculture was intensified through mineral fertilization and liming, sometimes mowing, and even ploughing and sowing. Seven pastures were selected to estimate the present plant biodiversity. Losses of biodiversity were assessed on the Kastelberg ridge by diachronic analysis of the vegetation composition and structure over the last 30 years. Species diversity changed in both associations through a decrease in the abundance of oligotrophic, acidophilic species, typical of the mountains of western Europe, and an extension of grassland types of the Violo-Nardetum trifolietosum. Strategies for a return to more natural conditions include the abandonment of fertilization and liming, except locally around farms. Regular mowing is needed in order to decrease the nutrient level of the sites.     

Structural insights into the acidophilic pH adaptation of a novel endo-1,4-β-xylanase from Scytalidium acidophilum

In this study, the crystal structure of a novel endo-1,4-β-xylanase from Scytalidium acidophilum, XYL1, was solved at 1.9 Å resolution. This is one of the few solved crystal structures of acidophilic proteins. The enzyme has the overall fold typical to family 11 xylanases. Comparison of this structure with other homologous acidophilic, neutrophilic and alkalophilic xylanases provides additional insights into the general features involved in low pH adaptation (stability and activity). Several sequence and structure modifications appeared to be responsible for the acidophilic characteristic: (a) the presence of an aspartic acid H bonded to the acid/base catalyst (b) the nature of specifically conserved residues in the active site (c) the negative potential at the surface (d) the decreased number of salt bridges and H bonds in comparison with highly alkaline enzymes.     

Distribution and seasonal variability in the benthic eukaryotic community of Río Tinto (SW, Spain), an acidic, high metal extreme environment

The eukaryotic community of the Río Tinto (SW, Spain) was surveyed in fall, winter and spring through the combined use of traditional microscopy and molecular approaches, including Denaturing Gradient Gel Electrophoresis (DGGE) and sequence analysis of 18S rRNA gene fragments. Eukaryotic assemblages of surface sediment biofilms collected in January, May and September 2002 were compared from 13 sampling stations along the river. Physicochemical data revealed extremely acidic conditions (the pH ranged from 0.9 to 2.5) with high concentrations of heavy metals, including up to 20 mg l(-1) Fe, 317 mg l(-1) Zn, 47 mg l(-1) As, 42 mg l(-1) Cd and 4 mg l(-1) Ni. In total, 20 taxa were identified, including members of the Bacillariophyta, Chlorophyta and Euglenophyta phyla as well as ciliates, cercomonads, amoebae, stramenopiles, fungi, heliozoans and rotifers. In general, total cell abundances were highest in fall and spring but decreased drastically in winter, and the sampling stations with the most extreme conditions showed the lowest number of cells, as well as the lowest diversity. Species diversity did not vary much during the year. Only the filamentous algae showed a dramatic seasonal change, since they almost disappeared in winter and reached the highest biomass during the summer. Principal Components Analysis (PCA) showed a high inverse correlation between pH and most of the heavy metals analyzed, as well as Dunaliella sp., while Chlamydomonas sp. was directly related to pH during May and September. Three heavy metals (Zn, Cu and Ni) remained separate from the rest and showed an inverse correlation with most of the species analyzed, except for Dunaliella sp.