Biomarker indications for microbial contribution to Recent and Late Jurassic carbonate deposits

Summary Biomarker investigations were applied to the hydrocarbon fractions of three Recent (cyanobacterial mat, Lake Van microbialite and Lake Satonda microbialite) and two Late Jurassic carbonate samples obtained from sponge bioherms. The relative concentrations ofn-alkanes, monomethyl alkanes, acyclic isoprenoids, steroids and hopanoids in these samples are studied and their probable biological precursors are discussed. Normal alkanes with carbon chain lengths ranging from C₁₅ to C₃₄ and monomethyl alkanes ranging from C₁₇ to C₂₁ with a varying methyl branching pattern are found. The major hydrocarbons are low molecular weight (LMW)n-alkanes (C₁₅–C₂₁) with a slight to strong predominance ofn-heptadecane (C₁₇). High molecular weight (HMW)n-alkanes occur in low to moderate relative concentrations showing a preference of odd-carbon numbered compounds with a maximum at C₂₉. Within the acyclic isoprenoids, pristane, phytane/phytene, pentamethyl-eicosane, squalane and lycopane could be identified. Polycyclic terpenoids of the sterane and/or hopane type are present in all carbonate samples. The carbon numbers of these components range from 27 to 29 and 27 to 32, respectively. These organic compounds identified can be attributed to various source organisms such as cyanobacteria, archaebacteria, algae and vascular plants. All hydrocarbon fractions of the samples are characterized by moderate to high relative concentrations of compounds derived from cyanobacteria, signifying the role of these organisms as contributors to the Recent as well as to the Late Jurassic carbonate deposits.     

Natronogracilivirga saccharolytica gen. nov., sp. nov. and Cyclonatronum proteinivorum gen. nov., sp. nov., haloalkaliphilic organotrophic bacteroidetes from hypersaline soda lakes forming a new family Cyclonatronaceae fam. nov. in the order Balneolales

Two heterotrophic bacteroidetes strains were isolated as satellites from autotrophic enrichments inoculated with samples from hypersaline soda lakes in southwestern Siberia. Strain Z-1702^T is an obligate anaerobic fermentative saccharolytic bacterium from an iron-reducing enrichment culture, while Ca. Cyclonatronum proteinivorum Omega^T is an obligate aerobic proteolytic microorganism from a cyanobacterial enrichment. Cells of isolated bacteria are characterized by highly variable morphology. Both strains are chloride-independent moderate salt-tolerant obligate alkaliphiles and mesophiles. Strain Z-1702^T ferments glucose, maltose, fructose, mannose, sorbose, galactose, cellobiose, N-acetyl-glucosamine and alpha-glucans, including starch, glycogen, dextrin, and pullulan. Strain Omega^T is strictly proteolytic utilizing a range of proteins and peptones. The main polar lipid fatty acid in both strains is iso-C_15:0, while other major components are various C₁₆ and C₁₇ isomers. According to pairwise sequence alignments using BLAST Gracilimonas was the nearest cultured relative to both strains (<90% of 16S rRNA gene sequence identity). Phylogenetic analysis placed strain Z-1702^T and strain Omega^T as two different genera in a deep-branching clade of the new family level within the order Balneolales with genus. Based on physiological characteristics and phylogenetic position of strain Z-1702^T it was proposed to represent a novel genus and species Natronogracilivirga saccharolityca gen. nov., sp. nov. (= DSMZ 109061^T =JCM 32930^T =VKM B 3262^T). Furthermore, phylogenetic and phenotypic parameters of N. saccharolityca and C. proteinivorum gen. nov., sp. nov., strain Omega^T (=JCM 31662^T, =UNIQEM U979^T), make it possible to include them into a new family with a proposed designation Cyclonatronaceae fam. nov..     

The chemistry and crustacean zooplankton of the Seewinkel pans: a review of recent conditions

A number of shallow pans was investigated between May 1982 and May 1985 in the Seewinkel region between Neusiedlersee and the Hungarian border. Chemical and zooplankton samples were obtained at three monthly intervals. Analyses indicated some changes during the past decades. Human activity has resulted in some changes to water chemistry and zooplankton composition in a few pans, and many smaller pans have now disappeared.     

Characterization of Microbial Arsenate Reduction in the Anoxic Bottom Waters of Mono Lake,California

Dissimilatory reduction of arsenate (DAsR) occurs in the arsenic-rich, anoxic water column of Mono Lake, California, yet the microorganisms responsible for this observed in situ activity have not been identified. To gain insight as to which microorganisms mediate this phenomenon, as well as to some of the biogeochemical constraints on this activity, we conducted incubations of arsenate-enriched bottom water coupled with inhibition/amendment studies and Denaturing Gradient Gel Electrophoresis (DGGE) characterization techniques. DAsR was totally inhibited by filter-sterilization and by nitrate, partially inhibited (~50%) by selenate, but only slightly (~25%) inhibited by oxyanions that block sulfate-reduction (molybdate and tungstate). The apparent inhibition by nitrate, however, was not due to action as a preferred electron acceptor to arsenate. Rather, nitrate addition caused a rapid, microbial re-oxidation of arsenite to arsenate, which gave the overall appearance of no arsenate loss. A similar microbial oxidation of As(III) was also found with Fe(III), a fact that has implications for the recycling of As(V) in Mono Lake's anoxic bottom waters. DAsR could be slightly (10%) stimulated by substrate amendments of lactate, succinate, malate, or glucose, but not by acetate, suggesting that the DAsR microflora is not electron donor limited. DGGE analysis of amplified 16S rDNA gene fragments from incubated arsenate-enriched bottom waters revealed the presence of two bands that were not present in controls without added arsenate. The resolved sequences of these excised bands indicated the presence of members of the epsilon ( Sulfurospirillum ) and delta ( Desulfovibrio ) subgroups of the Proteobacteria , both of which have representative species that are capable of anaerobic growth using arsenate as their electron acceptor.     

A test of traditional diversity measures and taxonomic distinctness indices on benthic diatoms of soda pans in the Carpathian basin

Saline lakes are threatened all over the world and their conservation has been a key issue. Various diversity indices are available for ecological status assessments, however, with poorly explored relevance and applicability in saline, alkaline pans. Therefore, traditional diversity measures (species richness and Shannon diversity) and taxonomic distinctness indices (Average [AvTD] and Variance of Taxonomic Distinctness [VarTD]) were tested in more than 100 sampling sites of 39 soda pans in Central-Europe to find sufficient indicators of the ecological condition and simultaneously to facilitate their preservation according to the modern conservation practices. Results of the analyses showed that healthy soda pan ecosystems with high level of natural stress and reduced habitat heterogeneity are characterized by low diversity diatom assemblages. In soda pans where the stress can be extremely high from natural reasons, oligopoly of closely related species can develop: the average taxonomic distinctness appeared between genus and family level. The non-DNA-sequence based phylogenetic diversity measures (AvTD and VarTD), were generally sensitive to the trophic state of the lakes, in contrast to traditional diversity metrics, which were unequivocally indicative for the special physical and chemical parameters (e.g. conductivity, pH) of the soda pans. In some cases, when the response of the diversity measures for a given environmental variable (pH, temperature) overlapped, the AvTD was found to be a more precise indicator of the environmental changes (pH) than traditional ones. The decreasing tendency of the AvTD along the intensified natural impact may be explained by the long available time for the species to adapt to these special environments.     

Halomonas magadii sp. nov., a new member of the genus Halomonas, isolated from a soda lake of the East African Rift Valley

A number of novel alkaliphilic organotrophic bacteria have been isolated from several saline and alkaline East African soda lakes. The new isolates grow at pH values between 7.0 and 11.0, with pH optima for growth between 9.0 and 10.0. Growth occurs at total salts concentration between 0% and 20% (w/v) with optimum at 0%–7% (w/v). Phylogenetic analyses based on 16S rDNA sequence comparison indicate that these isolates are related (>96% similarity) to members of the Halomonadaceae within the γ-3 subdivision of the Proteobacteria. These analyses indicate that existing species within the Halomonadaceae fell within three main groups, one group comprising the type species of Halomonas, Halomonas elongata, and a number of other known species including one soda lake isolate. A second group constituting most of the remaining known species of Halomonas and related Chromohalobacter spp. includes 3 soda lake isolates with high DNA–DNA homologies. The third group included Halomonas halodenitrificans, Halomonas desiderata, Halomonas cupida, and 13 soda lake isolates. Phenotypic comparisons indicated that the majority of soda lake strains shared similar morphological, phenotypic, and chemotaxonomic properties to known strains of Halomonas but grew under alkaline conditions. The 3 soda lake isolates with high DNA–DNA homologies were, however, significantly different in antibiotic sensitivity pattern and in the utilization of several substrates, were unable to reduce nitrite, and showed low DNA–DNA homologies with known halomonads in the same group. We propose that these isolates comprise a new species of the genus Halomonas that we name Halomonas magadii sp. nov. The type strain is strain 21 MI (NCIMB 13595). Received: July 20, 1999 / Accepted: October 29, 1999     

<Emphasis Type="Italic">Tindallia texcoconensis</Emphasis> sp. nov., a new haloalkaliphilic bacterium isolated from lake Texcoco,Mexico

A new alkaliphilic and moderately halophilic, strictly anaerobic, fermentative bacterium (strain IMP-300^T) was isolated from a groundwater sample in the zone of the former soda lake Texcoco in Mexico. Strain IMP-300^T was Gram-positive, non-sporulated, motile and rod-shaped. It grew within a pH range from 7.5 to 10.5, and an optimum at 9.5. The organism was obligately dependent on the presence of sodium salts. Growth showed an optimum at 35°C with absence of growth above 45°C. It fermented peptone and a few amino acids, preferentially arginine and ornithine, with production of acetate, propionate, and ammonium. Its fatty acid pattern was mainly composed of straight chain saturated, unsaturated, and cyclopropane fatty acids. The G + C content of genomic DNA was 40.0 mol%. Analysis of the 16S rRNA gene sequence indicated that the new isolate belongs to the genus Tindallia, in the low G + C Gram-positive phylum. Phylogenetically, strain IMP-300^T has Tindallia californiensis, as closest relative with a 97.5% similarity level between their 16S rDNA gene sequences, but the DNA–DNA re-association value between the two DNAs was only 42.2%. On the basis of differences in genotypic, phenotypic, and phylogenetic characteristics, strain IMP-300^T is proposed as a new species of the genus Tindallia, T. texcoconensis sp. nov. (type strain IMP-300^T = DSM 18041^T = JCM 13990^T).     

Description of a new species of Potamonautes MacLeay, 1838, from the iSimangaliso Wetland Park,South Africa

A new species of freshwater crab, Potamonautes isimangaliso sp. n., is described from the western shores of False Bay, Hluhluwe, within the iSimangaliso Wetland Park, South Africa. While bearing a superficial resemblance to Potamonautes lividus, the new species has been found to be genetically distinct, diverging from the former by 7.4–7.8% in mtDNA. Potamonautes isimangaliso most closely resembles Potamonautes lividus, but is distinguished by a unique suite of carapace characters, colouration, and size. The new species also lives in close association with oxygen-poor, fresh ephemeral pans, while the habitat of Potamonautes lividus is well above the surface water line of the closest water body. An updated identification key for the Potamonautes species of South Africa is provided.     

Cellulase activity of a haloalkaliphilic anaerobic bacterium, strain Z-7026

Summary The cellulolytic activity of an alkaliphilic obligate anaerobic bacterium, Z-7026, which was isolated from the microbial community of soda-lake sediments and belongs to the cluster III of Clostridia with low G+C content, was studied. The bacterium was capable of growing in media with cellulose or cellobiose as the sole energy sources. Its maximal growth rate on cellobiose (0.042–0.046 h^–1) was observed at an initial pH value of 8.5–9.0, whereas the maximal rate of cellulase synthesis, assayed by using a novel fluorimetric approach, was found to be 0.1 h^–1 at pH 8–8.5. Secreted proteins revealed high affinity for cellulose and were represented by two major forms of molecular masses of 75 and 84 kDa, whereas the general protein composition of the precipitated and cellulose-bound preparations was similar to cellulosome subunits of Clostridium thermocellum. The optimum pH of the partially purified enzyme preparation towards both amorphous and crystalline cellulose was in the range 6–9, with more than 70% and less than 50% of maximal activity being retained at pH 9.2 and 5.0, respectively.     

Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors

Thiopaq biotechnology for partial sulfide oxidation to elemental sulfur is an efficient way to remove H₂S from biogases. However, its application for high-pressure natural gas desulfurization needs upgrading. Particularly, an increase in alkalinity of the scrubbing liquid is required. Therefore, the feasibility of sulfide oxidation into elemental sulfur under oxygen limitation was tested at extremely haloalkaline conditions in lab-scale bioreactors using mix sediments from hypersaline soda lakes as inoculum. The microbiological analysis, both culture dependent and independent, of the successfully operating bioreactors revealed a domination of obligately chemolithoautotrophic and extremely haloalkaliphilic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio. Two subgroups were recognized among the isolates. The subgroup enriched from the reactors operating at pH 10 clustered with Thioalkalivibrio jannaschii–Thioalkalivibrio versutus core group of the genus Thioalkalivibrio. Another subgroup, obtained mostly with sulfide as substrate and at lower pH, belonged to the cluster of facultatively alkaliphilic Thioalkalivibrio halophilus. Overall, the results clearly indicate a large potential of the genus Thiolalkalivibrio to efficiently oxidize sulfide at extremely haloalkaline conditions, which makes it suitable for application in the natural gas desulfurization. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Nucleotide sequence accession numbers: The GenBank/EMBL accession numbers of the 16S rRNA gene sequence determined in this study are EU709849–EU709878.