Identification and characterization of VapBC toxin-antitoxin system in Bosea sp. PAMC 26642 isolated from Arctic lichens.

Toxin-antitoxin (TA) systems are genetic modules composed of a toxin interfering with cellular processes and its cognate antitoxin, which counteracts the activity of the toxin. TA modules are widespread in bacterial and archaeal genomes. It has been suggested that TA modules participate in the adaptation of prokaryotes to unfavorable conditions. The Bosea sp. PAMC 26642 used in this study was isolated from the Arctic lichen Stereocaulon sp. There are 12 putative type II TA loci in the genome of Bosea sp. PAMC 26642. Of these, nine functional TA systems have been shown to be toxic in Escherichia coli The toxin inhibits growth, but this inhibition is reversed when the cognate antitoxin genes are coexpressed, indicating that these putative TA loci were bona fide TA modules. Only the BoVapC1 (AXW83_01405) toxin, a homolog of VapC, showed growth inhibition specific to low temperatures, which was recovered by the coexpression of BoVapB1 (AXW83_01400). Microscopic observation and growth monitoring revealed that the BoVapC1 toxin had bacteriostatic effects on the growth of E. coli and induced morphological changes. Quantitative real time polymerase chain reaction and northern blotting analyses showed that the BoVapC1 toxin had a ribonuclease activity on the initiator tRNAfMet, implying that degradation of tRNAfMet might trigger growth arrest in E. coli Furthermore, the BoVapBC1 system was found to contribute to survival against prolonged exposure at 4°C. This is the first study to identify the function of TA systems in cold adaptation.

Transformation of galena to pyromorphite produces bioavailable sulfur for neutrophilic chemoautotrophy.

The aqueous concentration of lead [Pb(II)] in geochemical environments is controlled by the solubility of Pb-bearing minerals and their weathering products. In contaminated soils, a common method for in situ stabilization of Pb(II) is the addition of phosphate to convert more redox sensitive sulfide minerals into sparingly soluble pyromorphite [Pb5 (PO4 )3 X]. In this study, we conducted experimental studies to investigate the fate of reduced sulfur during the conversion of galena [PbS] to chloropyromorphite [Pb5 (PO4 )3 Cl]. Powder X-ray diffraction analysis indicated that the reaction of phosphate with galena under oxic conditions resulted in the oxidation of sulfide and formation of elemental sulfur [S8 ]. Under oxic abiotic conditions, the S8 was retained in the solid phase, and negligible concentrations of sulfur as sulfide and thiosulfate were detected in the aqueous phase and only a small amount of sulfate. When PbS reacted in the presence of the chemoautotrophic organism Bosea sp. WAO, the S8 in the secondary mineral was oxidized to sulfate. Strain WAO produced significantly more sulfate from the secondary S8 than from the primary galena. Microscopic analysis of mineral-microbe aggregates on mineral-embedded slide cultures showed that the organism was colocalized and increased in biomass over time on the secondary mineral surface supporting a microbial role. The results of this study indicate that stimulation of sulfur-oxidizing activity may be a direct consequence of phosphate amendments to Pb(II)-contaminated soils.

Extra-slow-growing Tardiphaga strains isolated from nodules of Vavilovia formosa (Stev.) Fed.

Eleven extra-slow-growing strains were isolated from nodules of the relict legume Vavilovia formosa growing in North Ossetia (Caucasus) and Armenia. All isolates formed a single rrs cluster together with the type strain Tardiphaga robiniae LMG 26467(T), while the sequencing of the 16S-23S rDNA intergenic region (ITS) and housekeeping genes glnII, atpD, dnaK, gyrB, recA and rpoB divided them into three groups. North Ossetian isolates (in contrast to the Armenian ones) were clustered separately from the type strain LMG 26467(T). However, all isolates were classified as T. robiniae because the DNA-DNA relatedness between them and the type strain LMG 26467(T) was 69.6% minimum. Two symbiosis-related genes (nodM and nodT) were amplified in all isolated Tardiphaga strains. It was shown that the nodM gene phylogeny is similar to that of ITS and housekeeping genes. The presence of the other symbiosis-related genes in described Tardiphaga strains, which is recently described genus of rhizobia, as well as their ability to form nodules on any plants are under investigation.

Preferential association of endophytic bradyrhizobia with different rice cultivars and its implications for rice endophyte evolution.

Plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. To understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. Samples were collected from various rice (Oryza sativa) tissues and crop rotational systems. The rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation on siratro (Macroptilium atropurpureum). Six bradyrhizobial strains were obtained exclusively from rice grown in a crop rotational system. The isolates were separated into photosynthetic bradyrhizobia (PB) and nonphotosynthetic bradyrhizobia (non-PB). Thai bradyrhizobial strains promoted rice growth of Thai rice cultivars better than the Japanese bradyrhizobial strains. This implies that the rice cultivars possess characteristics that govern rice-bacterium associations. To examine whether leguminous plants in a rice plantation system support the persistence of rice endophytic bradyrhizobia, isolates were tested for legume nodulation. All PB strains formed symbioses with Aeschynomene indica and Aeschynomene evenia. On the other hand, non-PB strains were able to nodulate Aeschynomene americana, Vigna radiata, and M. atropurpureum but unable to nodulate either A. indica or A. evenia. Interestingly, the nodABC genes of all of these bradyrhizobial strains seem to exhibit low levels of similarity to those of Bradyrhizobium diazoefficiens USDA110 and Bradyrhizobium sp. strain ORS285. From these results, we discuss the evolution of the plant-bradyrhizobium association, including nonlegumes, in terms of photosynthetic lifestyle and nod-independent interactions.

[Influence of iron on siderophore and photosynthetic pigments biosynthesis by siderophore-producing Rhodopesudomonnas palustris].

OBJECTIVE: To explore the regulation of iron on siderophore production, cell growth and photosynthetic pigments biosynthesis by siderophore-producing anoxygenic phototrophic bacteria. METHODS: Siderophore production was determined using Chrome Azurol S (CAS) assay. The siderophore types were determined by Arnow method, Csaky test and Shenker test. The compositions and contents of photosynthetic pigments were determined by spectrophotometry and HPLC analysis. RESULTS: Rhodopseudomonas palustris (Rps. palustris) CQV97 was capable of producing hydroxamate-type of siderophore. Siderophore production reached the highest yield in the absence of ferric chloride. With increasing ferric chloride concentrations, the lag phase of cell growth was shortened, and the cell growth rate, final biomass and the total amounts of carotenoid and bacteriochlorophyll a were increased significantly. The characteristic absorption maxima of carotenoids from pigment extracts were blueshifted. Iron concentration had little effect on the compositions and relative contents of bacteriochlorophylls a, whereas predominately affected carotenoid compositions, rhodopin was present as major carotenoid component instead of spirillxanthin. Culture tends to accumulate the Cars having shorter conjugated double bonds at the expense of longer conjugated double bonds as the ferric chloride concentration increased. The changes in carotenoid composition were consistent with those of the blue shift of absorption spectra of pigment extracts. CONCLUSION: Rps. palustris CQV97 can produce siderophore and the changes in microbial growth, siderophore production and photosynthetic pigments accumulation of anoxygenic phototrophic bacteria are related to the iron concentration in the medium.

Cloning of a novel 6-chloronicotinic acid chlorohydrolase from the newly isolated 6-chloronicotinic acid mineralizing Bradyrhizobiaceae strain SG-6C.

A 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. This Bradyrhizobiaceae, designated strain SG-6C, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. This metabolic pathway was confirmed by growth and resting cell assays using HPLC and LC-MS studies. A candidate for the gene encoding the initial dechlorination step, named cch2 (for 6-chloronicotinic acid chlorohydrolase), was identified using genome sequencing and its function was confirmed using resting cell assays on E. coli heterologously expressing this gene. The 464 amino acid enzyme was found to be a member of the metal dependent hydrolase superfamily with similarities to the TRZ/ATZ family of chlorohydrolases. We also provide evidence that cch2 was mobilized into this bacterium by an Integrative and Conjugative Element (ICE) that feeds 6-hydroxynicotinic acid into the existing nicotinic acid mineralization pathway.

[Community structure and spatial distribution of anaerobic ammonium oxidation bacteria in the sediments of Chongming eastern tidal flat in summer].

The objectives of this study were to identify whether there were Anaerobic Ammonium Oxidation (ANAMMOX) bacteria in the surface sediments of Chongming eastern tidal flat in the Yangtze estuary and the feature of their community structure and spatial distribution. Based on the total DNA extracted from the surface sediments of Chongming eastern tidal flat, ANAMMOX-specific 16S rDNA fragments were amplified. PCR products were cloned and sequenced, and an ANAMMOX-specific 16S rDNA gene library was established. Phylogenetic tree was constructed using MEGA5 after the sequences were checked in the GenBank database. Phylogenetic analysis indicated that the clone sequences CM-L-7 and CM-L-18 had 98% identities with ANAMMOX bacteria Candidatus 'Scalindua sp.'. CM-L-13 had 94% identities with Candidatus 'Scalindua wagneri'. CM-M-6 had 94% identities with Candidatus 'Kuenenia sp.'. CM-M-22 had 95% identities with Anaerobic ammonium-oxidizing planctomycete JMK-1. CM-H-15 had 94% identities with Candidatus 'Kuenenia stuttgartiensis'. The results indicated that there were ANAMMOX bacteria in the surface sediments of Chongming eastern tidal flat, but the ANAMMOX species were diverse in different tidal flats: Candidatus 'Scalindua' was the predominant group in the low tidal flat, while Candidatus 'Kuenenia' was the major population in the high tidal flat and the middle tidal flat. In comparison with the high and low tidal flats, the community structure of ANAMMOX bacteria in the middle tidal flat was the most complicated. A portion of the sequences related to uncultivated bacteria outside the known ANAMMOX cluster, probably indicated that there were potential ANAMMOX bacteria in the sediments of Chongming eastern tidal flat.

Phylogeny and photoheterotrophy in the acidophilic phototrophic purple bacterium Rhodoblastus acidophilus.

Norbert Pfennig isolated the first acidophilic purple bacterium over 40 years ago and named the organism Rhodopseudomonas acidophila (now Rhodoblastusacidophilus). Since the original work of Pfennig, no systematic study has been conducted on the phylogeny and carbon nutrition of a collection of strains of Rbl. acidophilus. We have isolated six new strains of Rbl. acidophilus from a Canadian peat bog. These strains, three of the original Pfennig strains and two additional putative R. acidophilus strains isolated several years ago in this laboratory,were characterized as to their pigments, phylogeny, and carbon sources supporting photoheterotrophic growth. Phototrophic cultures were either purple or orange in color,and the color of a particular strain was linked to phylogeny. As for the Pfennig strains of Rbl. acidophilus, all new strains grew photoheterotrophically at pH 5 on a variety of organic and fatty acids. However, in addition to methanol and ethanol, the new strains as well as the Pfennig strains grew on several other primary alcohols, results not reported in the original species description. Our work shows that some phylogenetic and physiological diversity exists within the species Rbl. acidophilus and supports the observation that few species of acidophilic purple bacteria appear to exist in nature.

Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions.

Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H(2) to derive energy for fixation of CO(2). Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H(2) generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME) analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H(2) as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes.

Interaction of CO dehydrogenase with the cytoplasmic membrane monitored by fluorescence correlation spectroscopy.

We have investigated the interaction of carbon monoxide dehydrogenase (CODH), an enzyme that catalyses the oxidation of CO in the aerobic eubacterium Oligotropha carboxidovorans, with the cytoplasmic membrane by using fluorescence correlation spectroscopy (FCS). Our results reveal that in vitro this interaction of CODH is specific for cytoplasmic membranes from CO-grown bacteria.

[Experimental determination of bacterial decay characteristics in biological wastewater treatment system].

The characteristics of cell decay in biological wastewater treatment systems were investigated under aerobic condition, by measuring the decay rate and by determining the death rate with LIVE/DEAD dyeing experiments. It was found that cell decay in biological wastewater treatment systems can be actually described as two parts: decay caused by cell death and decay derived from activity decrease. The experimental results revealed that 60% of cell decay in a nitrifying system was caused by activity decrease and 40% was caused by cell death. In a heterotrophic system, however, activity decrease was responsible for 80% of cell decay, and the other cell decay for 20% was caused by cell death.

Effect of inorganic carbon on nitrite accumulation in an aerobic granule reactor.

Pilot scale experiments were performed to evaluate the potential of nitrite type nitrification process with an airlift reactor and granular biomass. Initially, oxygen limitation was used as the main control parameter for accumulating nitrite in the effluent. After 30 d operation, the maximum nitrite conversion rate reached 2.5 kgNO2-N m(-3) d(-1), average diameter of the granule was 0.7 mm. Nitrite type reaction continued over 100 d, but nitrate formation increased after 150 d of operation. Once nitrate formation increased, oxygen limitation could not eliminate nitrite oxidising bacteria from granule. To overcome nitrate formation, laboratory scale batch experiments were conducted and it revealed a high concentration of inorganic carbon which had a significant effect on nitrite accumulation. Following this new concept, inorganic carbon was fed to the pilot scale reactor by changing pH adjustment reagent from NaOH to Na2CO3 and nitrite accumulation was recovered successfully without changing DO concentration. These results show that a high concentration of inorganic carbon is one of the control parameters for accumulating nitrite in biofilm nitrification system.

Sensitivity analysis of a biofilm model describing mixed growth of nitrite oxidisers in a CSTR.

A simple kinetic model has been developed for describing nitrite oxidation by autotrophic aerobic nitrifiers in a CSTR reactor, in which mixed (suspended and attached) growth conditions are prevailing. In this work, a critical dimensionless parameter is identified containing both biofilm characteristics and microbial kinetic parameters, as well as the specific (per volume) surface of the reactor configuration used. Evaluation of this dimensionless parameter can easily provide information on whether or not wall attachment is critical, and should be taken into account either in kinetic studies or in reactor design, when specific pollutants are to be removed from the waste influent stream. The effect of bulk dissolved oxygen (DO) concentration on the validity of this model is addressed and minimum non-limiting DO concentrations are proposed depending on the reactor configuration.

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

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.

Chemolithoautotrophic nitrifiers in the phyllosphere of a spruce ecosystem receiving high atmospheric nitrogen input.

Evidence is presented for the first time that chemolithoautotrophic ammonia oxidizers (CAO) and chemolithoautotrophic nitrite oxidizers (CNO) colonize in appreciable cell numbers the phyllosphere of spruce trees in a forest ecosystem exposed for decades to high levels of atmospheric nitrogen (The Höglwald Forest, Bavaria, Germany). The results strongly indicate that both, CAO and CNO are predominantly located inside the spruce needles, most likely within the stomatal cavity. These results are further supported by field experiments of NH3 uptake into twigs on intact spruce trees in the presence and absence of 10 Pa acetylene, an inhibitor of the ammonia monooxygenase of CAO. It is clearly demonstrated for the first time that in situ uptake of NH3 from the atmosphere into spruce needles exposed to high levels of atmospheric N is not catalyzed exclusively by the tree, but is the result of combined activities of both, the spruce trees and the chemolithoautotrophic nitrifiers colonizing the needles.

Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation.

Ammonia-oxidizer numbers decreased under conditions of moisture limitation in litter, fermentation and humus layers of forest soil in the field, but the extent of regrowth after rehydration varied between layers. Nitrosospira 16S rRNA genes were amplified from all layers, regardless of moisture content or soil pH which varied between 4.1 and 5.2. Nitrosomonas spp. were detected less often, but appeared to exhibit more rapid recovery than the Nitrosospira spp. when drought conditions were relieved by rainfall.

Microenvironments and distribution of nitrifying bacteria in a membrane-bound biofilm.

The distribution of nitrifying bacteria of the genera Nitrosomonas, Nitrosospira, Nitrobacter and Nitrospira was investigated in a membrane-bound biofilm system with opposed supply of oxygen and ammonium. Gradients of oxygen, pH, nitrite and nitrate were determined by means of microsensors while the nitrifying populations along these gradients were identified and quantified using fluorescence in situ hybridization (FISH) in combination with confocal laser scanning microscopy. The oxic part of the biofilm which was subjected to high ammonium and nitrite concentrations was dominated by Nitrosomonas europaea-like ammonia oxidizers and by members of the genus Nitrobacter. Cell numbers of Nitrosospira sp. were 1-2 orders of magnitude lower than those of N. europaea. Nitrospira sp. were virtually absent in this part of the biofilm, whereas they were most abundant at the oxic-anoxic interface. In the totally anoxic part of the biofilm, cell numbers of all nitrifiers were relatively low. These observations support the hypothesis that N. europaea and Nitrobacter sp. can out-compete Nitrosospira and Nitrospira spp. at high substrate and oxygen concentrations. Additionally, they suggest microaerophilic behaviour of yet uncultured Nitrospira sp. as a factor of its environmental competitiveness.

Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Northwestern Mediterranean Sea.

The aim of this study was to determine if there were differences between the types of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria associated with particulate material and planktonic samples obtained from the northwestern Mediterranean Sea. A nested PCR procedure performed with ammonia oxidizer-selective primers was used to amplify 16S rRNA genes from extracted DNA. The results of partial and full-length sequence analyses of 16S rRNA genes suggested that different groups of ammonia-oxidizing bacteria were associated with the two sample types. The particle-associated sequences were predominantly related to Nitrosomonas eutropha, while the sequences obtained from the planktonic samples were related to a novel marine Nitrosospira group (cluster 1) for which there is no cultured representative yet. A number of oligonucleotide probes specific for different groups of ammonia oxidizers were used to estimate the relative abundance of sequence types in samples of clone libraries. The planktonic libraries contained lower proportions of ammonia oxidizer clones (0 to 26%) than the particulate material libraries (9 to 83%). Samples of the planktonic and particle-associated libraries showed that there were depth-related differences in the ammonia oxidizer populations, with the highest number of positive clones in the particle-associated sample occurring at a depth of 700 m. The greatest difference between planktonic and particle-associated populations occurred at a depth of 400 m, where only 4% of the clones in the planktonic library were identified as Nitrosomonas clones, while 96% of these clones were identified as clones that were related to the marine Nitrosospira species. Conversely, all ammonia oxidizer-positive clones obtained from the particle-associated library were members of the Nitrosomonas group. This is the first indication that Nitrosomonas species and Nitrosospira species may occupy at least two distinct environmental niches in marine environments. The occurrence of these groups in different niches may result from differences in physiological properties and, coupled with the different environmental conditions associated with these niches, may lead to significant differences in the nature and rates of nitrogen cycling in these environments.