Isolation and characterization of novel potassium-solubilizing purple nonsulfur bacteria from acidic paddy soils using culture-dependent and culture-independent techniques.

The current research as aimed (i) to isolate and select the purple nonsulfur bacteria (PNSB) possessing the potassium-solubilizing ability from acid paddy fields and (ii) to evaluate the ability to release the plant growth-promoting substances (PGPS) of selected PNSB. A total of 35 acid sulfate (AS) soil samples were collected in An Giang province, Vietnam. Then, 70 PNSB strains were isolated from the AS soil samples. In the current study, the isolated strains were screened and selected according to their tolerability to acidic conditions, ability to solubilize potassium, and characteristics of a plant growth promoter on basic isolation media with various incubation conditions. Therein, three strains, TT07.4, AN05.1, and AC04.1, presented the highest potassium solubilization under the microaerobic light (11.8-17.7 mg L-1) and aerobic dark (16.4-24.7 mg L-1) conditions and stresses from Al3+, Fe2+, and Mn2+ toxicity. The selected strains were identified as Rhodopseudomonas pentothenatexigens by the 16S rDNA sequence, with 99% similarity. The selected acidic-resistant strains possessed the traits of biofertilizers under both microaerobic light and aerobic dark conditions, with abilities to fix nitrogen (0.17-6.24; 7.93-11.2 mg L-1); solubilize phosphorus from insoluble compounds with 3.22-49.9 and 9.49-11.2 mg L-1 for Al-P, 21.9-25.8 and 20.2-25.1 mg L-1 for Ca-P, and 10.1-29.8 and 18.9-23.2 mg L-1 for Fe-P; produce 5-aminolevulinic acid (0.63-3.01; 1.19-6.39 mg L-1), exopolymeric substances (0.14-0.76; 0.21-0.86 mg L-1), indole-3-acetic acid (12.9-32.6; 13.6-17.8 mg L-1), and siderophores (28.4-30.3; 6.15-10.3%). The selected potassium-solubilizing strains have a great potential to apply in liquid form into rice seed and solid form in AS soils to supply nutrients and PGPS for enhancing rice growth and grain yield.

In-situ fermentation with gellan gum adding to produce bacterial cellulose from traditional Chinese medicinal herb residues hydrolysate.

In this study, bacterial cellulose was synthesized by Taonella mepensis from traditional Chinese medicinal herb residues hydrolysate. To overcome the inhibitory effect of fermentation environment, in-situ fermentation with gellan gum adding was carried out for the first time. After 10 days' static fermentation, both high-acyl gellan gum and low-acyl gellan gum adding showed certain beneficial effects for bacterial cellulose production that the highest bacterial cellulose yield (0.866 and 0.798 g/L, respectively) was 59% and 47% higher than that (0.543 g/L) without gellan gum adding. Besides, gellan gum based bacterial cellulose showed some better texture characteristics. Gellan gum was loaded in the nano network of bacterial cellulose, and gellan gum adding had some influence on the crystal structure and thermal degradation behaviors of bacterial cellulose but affected little on its functional groups. Overall, this in-situ fermentation technology is attractive for bacterial cellulose production from low-cost but inhibitory substrates.

Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes.

The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.

Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum.

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913T and R5959T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C19 : 0 cyclo ω8c and C16 : 0; in addition, C18 : 1ω7c was also found as a predominant fatty acid in strain R5913T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913T and R5959T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656T, Dongia mobilis CGMCC 1.7660T, Dongia soli D78T and Dongia rigui 04SU4-PT. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae, for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913T=DSM 109816T=CECT 9472T) and Hypericibacter adhaerens sp. nov. (type strain R5959T=DSM 109817T=CECT 9620T).

Genomic insights into the metabolism of 'Candidatus Defluviicoccus seviourii', a member of Defluviicoccus cluster III abundant in industrial activated sludge.

Filamentous cluster III Defluviicoccus (DF3) are known to proliferate and cause bulking issues in industrial wastewater treatment plants. Members of the genus Defluviicoccus are also known to exhibit the glycogen accumulating organism (GAO) phenotype, which is suggested to be detrimental to enhanced biological phosphorus removal (EBPR). Despite the reported negative impact members of the DF3 have on activated sludge wastewater treatment systems, limited research has focused on understanding the physiological traits that allow them to compete in these environments. In this study, a near complete genome of an abundant filamentous DF3 named 'Candidatus Defluviicoccus seviourii' was obtained from a full-scale sequencing batch reactor (SBR) treating winery wastewater. Annotation of the 'Ca. D. seviourii' genome revealed interesting metabolic features that help to understand the abundance of this microorganism in industrial wastewater treatment plants. Their potential for the storage of polyhydroxyalkanoates (PHA) is suggested to favour these organisms with the intermittent availability of carbon in these systems. An ability to fix nitrogen and take up urea may provide them with an additional advantage with the characteristically high carbon to nitrogen content of industrial waste. The genome and preliminary findings of this study provide a foundation for further research into these biotechnologically relevant organisms.

Enhanced crude oil biodegradative potential of natural phytoplankton-associated hydrocarbonoclastic bacteria.

Phytoplankton have been shown to harbour a diversity of hydrocarbonoclastic bacteria (HCB), yet it is not understood how these phytoplankton-associated HCB would respond in the event of an oil spill at sea. Here, we assess the diversity and dynamics of the bacterial community associated with a natural population of marine phytoplankton under oil spill-simulated conditions, and compare it to that of the free-living (non phytoplankton-associated) bacterial community. While the crude oil severely impacted the phytoplankton population and was likely conducive to marine oil snow formation, analysis of the MiSeq-derived 16S rRNA data revealed dramatic and differential shifts in the oil-amended communities that included blooms of recognized HCB (e.g., Thalassospira, Cycloclasticus), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential (Olleya, Winogradskyella, and members of the inconspicuous BD7-3 phylum). Notably, the oil biodegradation potential of the phytoplankton-associated community exceeded that of the free-living community, and it showed a preference to degrade substituted and non-substituted polycyclic aromatic hydrocarbons. Our study provides evidence of compartmentalization of hydrocarbon-degrading capacity in the marine water column, wherein HCB associated with phytoplankton are better tuned to degrading crude oil hydrocarbons than that by the community of planktonic free-living bacteria.

Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples.

A Gram-negative, aerobic, motile, spiral-shaped bacterium, strain H5569(T), was isolated from a human blood sample. Phenotypic and molecular characteristics of the isolate were investigated. Optimal growth was found to occur at 35 °C under aerobic conditions on Heart Infusion Agar supplemented with 5 % rabbit blood. The major fatty acids present in the cells were identified as C16:0, C16:1ω7c and C18:1ω7c. The predominant respiratory quinone was found to be ubiquinone-Q10. The G+C content of genomic DNA for strain H5569(T) was found to be 49.9 %. Based on 16S rRNA gene sequence analysis results, 13 additional isolates were also analysed in this study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism, represented by strain H5569(T), forms a distinct lineage within the family Rhodospirillaceae, closely related to two Novispirillum itersonii subspecies (93.9-94.1 %) and two Caenispirillum sp. (91.2-91.6 %). Based on these results, the isolate H5569(T) is concluded to represent a new genus and species for which the name Haematospirillum jordaniae gen. nov., sp. nov. is proposed. The type strain is H5569(T) (=DSM(T) 28903 = CCUG 66838(T)).

Impact of butyrate on microbial selection in enhanced biological phosphorus removal systems.

Microbial selection in an enhanced biological phosphorus removal system was investigated in a laboratory-scale sequencing batch reactor fed exclusively with butyrate as a carbon source. As reported in the few previous studies, butyrate uptake was slow and phosphorus (P) release occurred during the entire anaerobic period. Polyphosphate-accumulating organism (PAO), i.e. Candidatus Accumulibacter phosphatis (named as Accumulibacter), glycogen-accumulating organisms (GAOs), i.e. Candidatus Competibacter phosphatis (named as Competibacter) and Defluviicoccus-related, tetrad-forming alphaproteobacteria (named as Defluviicoccus) were identified using fluorescence in situ hybridization analysis. The results show that Accumulibacter and Defluviicoccus were selected in the butyrate-fed reactor, whereas Competibacter was not selected. P removal was efficient at the beginning of the experiment with an increasing percentage relative abundance (% RA) of PAOs. The % RA of Accumulibacter and Defluviicoccus increased from 13% to 50% and 8% to 16%, respectively, and the % RA of Competibacter decreased from 8% to 2% during the experiment. After 6 weeks, P removal deteriorated with the poor correlation between the percentage of P removal and % RA of GAOs.

Metagenomic characterization of 'Candidatus†Defluviicoccus tetraformis strain TFO71', a tetrad-forming organism, predominant in an anaerobic-aerobic membrane bioreactor with deteriorated biological phosphorus removal.

In an acetate-fed anaerobic-aerobic membrane bioreactor with deteriorated enhanced biological phosphorus removal (EBPR), Defluviicoccus-related tetrad-forming organisms (DTFO) were observed to predominate in the microbial community. Using metagenomics, a partial genome of the predominant DTFO, 'Candidatus Defluviicoccus tetraformis strain TFO71', was successfully constructed and characterized. Examining the genome confirmed the presence of genes related to the synthesis and degradation of glycogen and polyhydroxyalkanoate (PHA), which function as energy and carbon storage compounds. TFO71 and 'Candidatus Accumulibacter phosphatis' (CAP) UW-1 and CAP UW-2, representative polyphosphate-accumulating organisms (PAO), have PHA metabolism-related genes with high homology, but TFO71 has unique genes for PHA synthesis, gene regulation and granule management. We further discovered genes encoding DTFO polyphosphate (polyP) synthesis, suggesting that TFO71 may synthesize polyP under untested conditions. However, TFO71 may not activate these genes under EBPR conditions because the retrieved genome does not contain all inorganic phosphate transporters that are characteristic of PAOs (CAP UW-1, CAP UW-2, Microlunatus phosphovorus NM-1 and Tetrasphaera species). As a first step in characterizing EBPR-associated DTFO metabolism, this study identifies important differences between DTFO and PAO that may contribute to EBPR community competition and deterioration.

Optimization of polygalacturonase production from a newly isolated Thalassospira frigidphilosprofundus to use in pectin hydrolysis: statistical approach.

The present study deals with the production of cold active polygalacturonase (PGase) by submerged fermentation using Thalassospira frigidphilosprofundus, a novel species isolated from deep waters of Bay of Bengal. Nonlinear models were applied to optimize the medium components for enhanced production of PGase. Taguchi orthogonal array design was adopted to evaluate the factors influencing the yield of PGase, followed by the central composite design (CCD) of response surface methodology (RSM) to identify the optimum concentrations of the key factors responsible for PGase production. Data obtained from the above mentioned statistical experimental design was used for final optimization study by linking the artificial neural network and genetic algorithm (ANN-GA). Using ANN-GA hybrid model, the maximum PGase activity (32.54 U/mL) was achieved at the optimized concentrations of medium components. In a comparison between the optimal output of RSM and ANN-GA hybrid, the latter favored the production of PGase. In addition, the study also focused on the determination of factors responsible for pectin hydrolysis by crude pectinase extracted from T. frigidphilosprofundus through the central composite design. Results indicated 80% degradation of pectin in banana fiber at 20 °C in 120 min, suggesting the scope of cold active PGase usage in the treatment of raw banana fibers.

Genome sequence of Thalassospira xiamenensis type strain M-5.

Thalassospira xiamenensis M-5(T) was isolated from the surface water of a waste oil pool at the oil storage dock in the city of Xiamen, Fujian Province, China. Here, we present the draft genome of strain M-5(T), which contains 4,705,237 bp with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA genes.

Antibiotic resistance of mixed biofilms in cystic fibrosis: impact of emerging microorganisms on treatment of infection.

Cystic fibrosis (CF) is a genetic disorder associated with multispecies infections where interactions between classical and newly identified bacteria might be crucial to understanding the persistent colonisation in CF lungs. This study investigated the interactions between two emerging species, Inquilinus limosus and Dolosigranulum pigrum, and the conventional CF pathogen Pseudomonas aeruginosa by evaluating the ability to develop biofilms of mixed populations and then studying their susceptibility patterns to eight different antimicrobials. Monospecies biofilms formed by I. limosus and D. pigrum produced significantly less biomass than P. aeruginosa and displayed greater sensitivity to antimicrobials. However, when in dual-species biofilms with P. aeruginosa, the emerging species I. limosus and D. pigrum were crucial in increasing tolerance of the overall consortia to most antibiotics, even without a change in the number of biofilm-encased cells. These results may suggest that revising these and other species interactions in CF might enable the development of more suitable and effective therapies in the future.

Inquilinus ginsengisoli sp. nov., isolated from soil of a ginseng field.

A Gram-reaction-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (strain Gsoil 080(T)) was isolated from soil collected in a ginseng field in Pocheon Province, South Korea, and was investigated by using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 080(T) was related most closely to Inquilinus limosus strains AU0476(T) and AU1979 (98.9 % similarity to both). Strain Gsoil 080(T) shared ≤91.3 % 16S rRNA gene sequence similarity with the type strains of other recognized species examined. The genus Inquilinus belongs to the family Rhodospirillaceae in the order Rhodospirillales, class Alphaproteobacteria. The predominant ubiquinone was Q-10 and the major fatty acids were summed feature 7 (C(18 : 1)ω9c/ω12t/ω7c) and C(19 : 0) cyclo ω8c. The G+C content of the genomic DNA of strain Gsoil 080(T) was 69.9 mol%. The level of DNA-DNA relatedness between strain Gsoil 080(T) and I. limosus LMG 20952(T) was 12 %. The results of genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Gsoil 080(T) represents a novel species of the genus Inquilinus, for which the name Inquilinus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 080(T) (=KCTC 12574(T) =LMG 23638(T)).

Purple nonsulfur bacteria diversity in activated sludge and its potential phosphorus-accumulating ability under different cultivation conditions.

This study investigates the diversity and the potential phosphorus-accumulating ability among the purple nonsulfur (PNS) bacteria. Traditional methods and molecular biotechniques were applied. Microscopic visualization using 4',6-diamidino-2-phenylindole staining as well as chemical analysis demonstrated that most of the isolated PNS bacteria presented different levels of phosphorus accumulation. Four of the pure cultures, denoted as Rhodopseudomonas palustris CC1, CC7, G11, and GE1, based on their differences in the PNS's pufM gene, exhibited higher internal phosphorus content compared to other isolated strains in this study. In addition, substantial polyphosphate accumulation was observed after the bacteria entered their stationary growth phase. Among them, the isolated R. palustris G11 could accumulate internal phosphorus up to 13%-15% of its cell dry weight under anaerobic illuminated incubation conditions. When the incubation status was switched from anaerobic to aerobic, the bacterial phosphorus content had a tendency to decrease slightly or remain about the same throughout the whole aerobic stage. The growth rate and biomass were higher when the PNS bacteria grew under photoheterotrophic conditions rather than the chemoheterotrophic ones. Furthermore, the environmental pH value could affect the contents of internal bacterial phosphate. Results of this study demonstrated that PNS bacteria are a group of the polyphosphate-accumulating organisms, of which this ability had never been properly studied. The conditions that PNS bacteria accumulating polyphosphate presented from this study were unique and showed characteristics that were different from the well-known enhanced biological phosphorus removal model.

Applications of photosynthetic bacteria for medical fields.

The medical applications of photosynthetic bacteria are summarized. Photosynthetic bacteria can produce various types of physiological active substance such as vitamin B(12), ubiquinone (coenzyme Q10), 5-aminolevulinic acid (ALA), porphyrins and RNA. In particular, photosynthetic bacterial ALA was commercially applied to cancer diagnosis and treatment. Recently, ALA has been applied to the treatment of acne vulgaris and the suppression of the inflammatory response to coronary and iliac injuries. In addition, the recent applications of RNA from a marine photosynthetic bacterium as a medical supplement for immune improvement and suppression of infection are described. Furthermore, the feasible application of a biopolymer consisting of RNA from a photosynthetic bacterium as a drug delivery system (DDS) to cancer treatment is described.