Sulfidogenesis in hypersaline chloride-sulfate lakes of Kulunda Steppe (Altai, Russia)

The activity and culturable diversity of sulfidogens were investigated in anoxic sediments of four hypersaline lakes with pH 7.6-8.2 in the Kulunda Steppe (Altai, Russia). Sulfate reduction rates were low, varying from 0.1 to 6.0 nmol HS(-) /(cm(3) h) with a maximum in the top 10 cm layer. Potential sulfidogenic rates with thiosulfate and sulfur as the e-acceptors were higher than with sulfate and were stimulated by formate, lactate, and acetate. Sulfidogenesis was optimal at salt concentrations below 2 M NaCl. Cultivation at 2 M NaCl resulted in the isolation of several strains of moderately halophilic SRB, but no growth of SRB was observed at 4 M NaCl. At lithotrophic conditions (i.e., with formate or H(2) as e-donors), several closely related alkalitolerant strains belonging to the genus Desulfonatronovibrio were isolated. Enrichments at heterotrophic conditions with lactate, propionate, acetate, or butyrate using sulfate or thiosulfate as e-acceptors yielded isolates related to Desulfosalsimonas propionicica, Desulfohalobium utahense, and Desulfocella halophila. Sulfur-reducing enrichments at 2 M NaCl with ethanol produced a member of the genus Halanaerobium, while enrichments at 4 M NaCl with acetate were dominated by archaea, demonstrating for the first time such type of catabolism in haloarchaea.     

Low-temperature modulation of the redox properties of the acceptor side of photosystem II: photoprotection through reaction centre quenching of excess energy

Although it has been well established that acclimation to low growth temperatures is strongly correlated with an increased proportion of reduced Q_A in all photosynthetic groups, the precise mechanism controlling the redox state of Q_A and its physiological significance in developing cold tolerance in photoautotrophs has not been fully elucidated. Our recent thermoluminescence (TL) measurements of the acceptor site of PSII have revealed that short‐term exposure of the cyanobacterium Synechococcus sp. PCC 7942 to cold stress, overwintering of Scots pine (Pinus sylvestris L.), and acclimation of Arabidopsis plants to low growth temperatures, all caused a substantial shift in the characteristic T_M of S₂Q_B^– recombination to lower temperatures. These changes were accompanied by much lower overall TL emission, restricted electron transfer between Q_A and Q_B, and in Arabidopsis by a shift of the S₂Q_A^–‐related peak to higher temperatures. The shifts in recombination temperatures are indicative of a lower activation energy for the S₂Q_B^– redox pair and a higher activation energy for the S₂Q_A^– redox pair. This results in an increase in the free‐energy gap between P680⁺Q_A^– and P680⁺Pheo^– and a narrowing of the free energy gap between Q_A and Q_B electron acceptors. We propose that these effects result in an increased population of reduced Q_A (Q_A^–), facilitating non‐radiative P680⁺Q_A^– radical pair recombination within the PSII reaction centre. The proposed reaction centre quenching could be an important protective mechanism in cyanobacteria in which antenna and zeaxanthin cycle‐dependent quenching are not present. In herbaceous plants, the enhanced capacity for dissipation of excess light energy via PSII reaction centre quenching following cold acclimation may complement their capacity for increased utilization of absorbed light through CO₂ assimilation and carbon metabolism. During overwintering of evergreens, when photosynthesis is inhibited, PSII reaction centre quenching may complement non‐photochemical quenching within the light‐harvesting antenna when zeaxanthin cycle‐dependent energy quenching is thermodynamically restricted by low temperatures. We suggest that PSII reaction centre quenching is a significant mechanism enabling cold‐acclimated organisms to acquire increased resistance to high light.     

Sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake with an unprecedented high sulfide content

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 10(7) 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.     

The serine-rich N-terminal region of <Emphasis Type="Italic">Arabidopsis</Emphasis> phytochrome A is required for protein stability

Deletion or substitution of the serine-rich N-terminal stretch of grass phytochrome A (phyA) has repeatedly been shown to yield a hyperactive photoreceptor when expressed under the control of a constitutive promoter in transgenic tobacco or Arabidopsis seedlings retaining their native phyA. These observations have lead to the proposal that the serine-rich region is involved in negative regulation of phyA signaling. To re-evaluate this conclusion in a more physiological context we produced transgenic Arabidopsis seedlings of the phyA-null background expressing Arabidopsis PHYA deleted in the sequence corresponding to amino acids 6–12, under the control of the native PHYA promoter. Compared to the transgenic seedlings expressing wild-type phyA, the seedlings bearing the mutated phyA showed normal responses to pulses of far-red (FR) light and impaired responses to continuous FR light. In yeast two-hybrid experiments, deleted phyA interacted normally with FHY1 and FHL, which are required for phyA accumulation in the nucleus. Immunoblot analysis showed reduced stability of deleted phyA under continuous red or FR light. The reduced physiological activity can therefore be accounted for by the enhanced destruction of the mutated phyA. These findings do not support the involvement of the serine-rich region in negative regulation but they are consistent with a recent report suggesting that phyA turnover is regulated by phosphorylation. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Growth physiology and competitive interaction of obligately chemolithoautotrophic,haloalkaliphilic, sulfur-oxidizing bacteria from soda lakes

Two different groups of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria belonging to the genera Thioalkalimicrobium and Thioalkalivibrio have recently been discovered in highly alkaline and saline soda lakes. To understand response to their extreme environment and different occurrence in soda lakes, the growth kinetics and competitive behavior of several representatives have been characterized in detail using batch and pH-controlled continuous cultivation. The bacteria belong to the true alkaliphiles, growing within the pH range 7.5-10.6 with maximum growth rate and maximum growth yield at pH 9.5-10. On the basis of their response to salt content, three groups can be identified. All the Thioalkalimicrobium strains and some of the Thioalkalivibrio strains belonged to the moderate halophiles. Some of the Thioalkalivibrio strains from hypersaline soda lakes were extremely salt-tolerant and capable of growth in saturated soda brines. The Thioalkalimicrobium strains demonstrated relatively high specific growth rates, low growth yield, high maintenance, and extremely high rates of thiosulfate and sulfide oxidation. In contrast, the Thioalkalivibrio strains, in general, were slow-growing, high-yield organisms with lower maintenance and much lower rates of oxidation of sulfide and thiosulfate. Moreover, the latter survived starvation much better than Thioalkalimicrobium. Different growth characteristics and salt resistance appear to determine the outcome of the enrichment cultures from different soda lakes: Thioalkalimicrobium dominated in the enrichments with freshly obtained samples from diluted soda lakes at low-medium salinity, while Thioalkalivibrio was the predominant organism in enrichments from aged samples and at hypersaline conditions. In mixed thiosulfate-limited chemostat cultures at low salinity, Thioalkalimicrobium strains (mu(max)=0.33 h(-1)) out-competed Thioalkalivibrio strains (mu(max)=0.15 h(-1)) at D>0.02 h(-1). The overall results suggest that Thioalkalimicrobium and Thioalkalivibrio represent two different ecological strategies.     

Genetic evolution and diversity of common carp Cyprinus carpio L.

Knowledge of genetic variation and population structure of existing strains of both farmed and wild common carp Cyprinus carpio L. is absolutely necessary for any efficient fish management and/or conservation program. To assess genetic diversity in common carp populations, a variety of molecular markers were analyzed. Of those, microsatellites and mitochondrial DNA were most frequently used in the analysis of genetic diversity and genome evolution of common carp. Using microsatellites showed that the genome evolution in common carp exhibited two waves of rearrangements: one whole-genome duplication (12–16 million years ago) and a more recent wave of segmental duplications occurring between 2.3 and 6.8 million years ago. The genome duplication event has resulted in tetraploidy since the common carp currently harbors a substantial portion of duplicated loci in its genome and twice the number of chromosomes (n = 100–104) of most other cyprinid fishes. The variation in domesticated carp populations is significantly less than that in wild populations, which probably arises from the loss of variation due to founder effects and genetic drift. Genetic differentiation between the European carp C.c. carpio and Asian carp C.c. haematopterus is clearly evident. In Asia, two carp subspecies, C.c. haematopterus and C.c. varidivlaceus, seem to be also genetically distinct.     

Mutant loxP vectors for selectable marker recycle and conditional knock-outs

Background  

Gene disruption by targeted integration of transfected constructs becomes increasingly popular for studies of gene function. The chicken B cell line DT40 has been widely used as a model for gene knock-outs due to its high targeted integration activity. Disruption of multiple genes and complementation of the phenotypes is, however, restricted by the number of available selectable marker genes. It is therefore highly desirable to recycle the selectable markers using a site-specific recombination system like Cre/loxP.     

Complete genome sequence of Thioalkalivibrio sp. K90mix

Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.