Rufibacter radiotolerans sp. nov., a novel gamma-radiation-resistant bacterium isolated from rice field.

A red-pigmented isolate, designated DG31DT, was isolated from the soil of a rice field in South Korea. Cells were strictly aerobic, short rod-shaped, Gram-negative, oxidase-positive, and catalase-positive. The major polar lipid was phosphatidylethanolamine (PE), and the predominant respiratory quinone was MK-7. DG31DT showed high resistance to both the UV and gamma radiations. Based on the 16S rRNA gene sequence, strain DG31DT was related to Rufibacter immobilis MCC P1T (97.1%) and Rufibacter tibetensis 1351T (96.5%). The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the strain DG31DT and the related Rufibacter sp. were between 74.1-77.6% and 19.9-21.9%, respectively. Strain DG31DT grew between 15 and 30 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and tolerated up to 1.0% NaCl (w/v). The major cellular fatty acids of the novel strain were summed feature 3 (C16:1 ω7c/C16:1 ω6c) and C16:1 ω5c. Flexirubin-type pigments were absent. On the basis of the phenotypic, phylogenetic, and chemotaxonomic data, strain DG31DT represents a novel species of the genus Rufibacter, for which the name Rufibacter radiotolerans sp. nov. is proposed. The type strain is DG31DT (= JCM 19446T = KCTC 32454T).

Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island.

A novel Gram-stain negative, aerobic, rod-shaped, non-motile and pink-coloured bacterium, designated strain 17J68-5T, was isolated from soil in Jeju Island, Korea. The strain was found to grow at 18-37 °C (optimum 25 °C) in R2A medium at pH (6.0 to 7.5; optimum 6.5) in the presence of 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 17J68-5T forms a distinct lineage within the family Hymenobacteraceae and is closely related to Hymenobacter daecheongensis DSM 21074T (94.9% 16S rRNA gene sequence similarity), Hymenobacter rutilus K2-33028T (94.6%) and Hymenobacter tibetensis XTM003T (94.3%). The draft genome sequence of strain 17J68-5Tis 5.1 Mb size. The calculated average nucleotide identity and the digital DNA-DNA hybridization between strain 17J68-5T and closely related type strains were 81.3 to 84.1  % and 25.5 to 28.1%. The major cellular fatty acids (≥ 10%) of the strain 17J68-5T were identified as summed feature 3 (C16:1ω6c/C16:1ω7c; 21.2%), iso-C15:0 (19.1%), summed feature 4 (C17:1 iso I/C17:1 anteiso B; 17.9%) and C16:1ω5c (13.1%). The predominant respiratory quinones were found to be menaquinone 7 and 6 (MK-7 and MK-6). The major polar lipid was found to be phosphatidylethanolamine. The genomic DNA G + C content based on the whole genome sequence is 59.6 mol %. The phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate 17J68-5T represents a novel species within the genus Hymenobacter, for which the name Hymenobacter jejuensis sp. nov. is proposed. The type strain of Hymenobacter jejuensis is 17J68-5T (= KCTC 62224T = JCM 33182T).

Antarctic heterotrophic bacterium Hymenobacter nivis P3T displays light-enhanced growth and expresses putative photoactive proteins.

Hymenobacter nivis P3T is a heterotrophic bacterium isolated from Antarctic red snow generated by algal blooms. Despite being non-photosynthetic, H. nivis was dominantly found in the red snow environment that is exposed to high light and UV irradiation, suggesting that this species can flourish under such harsh conditions. In order to further understand the adaptive strategies on the snow surface environment of Antarctica, the genome of H. nivis P3T was sequenced and analyzed, which identified genes putatively encoding for light-reactive proteins such as proteorhodopsin, phytochrome, photolyase and several copies of cryptochromes. Culture-based experiments revealed that H. nivis P3T growth was significantly enhanced under light conditions, while dark conditions had increased extracellular polymeric substances. Furthermore, the expression of several putative light-reactive proteins was determined by proteomic analysis. These results indicate that H. nivis P3T is able to potentially utilize light, which may explain its dominance on the red snow surface environment of Antarctica. ORIGINALITY-SIGNIFICANCE STATEMENT: The role of proteorhodopsin in heterotrophic bacteria is not well-characterized, as only a handful of proteorhodopsin-harbouring isolates were shown to have a light-enhanced phenotype through culture-based experiments to date. This is the first study that demonstrates light-stimulated growth and protein expression evidence of photoactive proteins for a non-marine psychrophile and for a member of the genus Hymenobacter. It is also the first study that provides comprehensive proteome information for this genus. This study presents significant results in understanding the adaptive mechanism of a heterotrophic non-photosynthetic bacterium thriving on the snow surface environment of Antarctica as well as demonstrating the role of light-utilization in promoting growth, possibly through proteorhodopsin.

Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge.

Comparative analyses of bacterial and archaeal community structures and dynamics in three biogas digesters during start-up and subsequent operation using microwaved, ultrasonicated or untreated waste activated sludge were performed based on 454 pyrosequencing datasets of part of 16S ribosomal RNA sequences and quantitative PCR. The pre-treatment increased the solubility, and thus the availability of the substrate for microbial degradation and significantly affected the succession of the anaerobic community structure over the course of the digestion. Bacteroidetes, Proteobacteria and Firmicutes were the dominant phyla in all digesters throughout operation. Proteobacteria decreased in relative abundance from 23-26 % to 11-13 % in association with enhanced substrate availability. Negative correlations between relative abundance of Alpha-, Beta- and Gammaproteobacteria and the substrate availability and/or biogas production were disclosed in statistical analyses. Clostridiales was the dominant order in Firmicutes, and Clostridiales, Clostridia and Firmicutes relative abundance and richness were shown to positively correlate with substrate availability and biogas generation. Methanogenic communities had a fairly restricted structure, highly dominated by Methanosaeta and Methanobrevibacter phylotypes. A gradual decline in Methanobrevibacter and increased representation of Methanosaeta concilii over time were particularly apparent in the digester receiving untreated waste activated sludge, whereas more diversified archaeal communities were maintained in the pre-treatment digesters. The quantitative PCR analyses revealed a methanogenic community distribution that coincided with the 454 pyrosequencing data.

[Diversity and Physiological and Biochemical Properties of Heterotrophic Bacteria. Isolated from Lake Baikal Neuston.]

For heterotrophic microorganisms (44 strains) isolated-from the surface film of Lake Baikal, iden- tification was carried out and their. physiological and biochemical characteristics were determined. Com- pared to the water column, diversity of cultured heterotrophs was low, indicating formation of stable micro- bial communities at the air-water interphase interface. Heterotrophic bacteria isolated from the surface mi- crolayer exhibited the enzymatic activity comparable to that for strains form other biofilm associations. Deinococcusfi6us strain NA202 'vas the most active component of the community, capable of utilization of the broadest spectrum of mono- and disaccharides,'sugars, and amino acids. This strain possessed the highest diversity of extracellular enzymes and was the most resistant to UV radiation. The physiological and bio- chemical properties of this strain may-be responsible for its adaptation to survival in extreme conditions of the surface microlayer. Our results improve our understanding of occurrence of UV-resistant strains in freshwater ecosystems.

Sunlight inactivation of human polymerase chain reaction markers and cultured fecal indicators in river and saline waters.

Decay rates for sunlight inactivation of polymerase chain reaction (PCR) markers for total Bacteroidales, human-specific Bacteroidales, Escherichia coli, and Bifidobacterium adolescentis relative to cultured E. coli were investigated. The experiment used 100-L chambers of fresh water and seawater (paired with dark controls) seeded with human sewage and exposed to natural sunlight over three summer days. Culturable E. coli levels in sunlight-exposed chambers decreased by at least 3 logs on day 1, and by day 3 a total reduction of 4.5 to 5.5 logs was achieved in fresh water and seawater, respectively. In contrast, PCR detection of the four gene targets in sunlight-exposed chambers reduced by no more than 2 logs over the duration of the study (k(t) < 0.071 log(e) units h(-1)). Under these experimental conditions, PCR markers are considerably more conservative than culturable E. coli and can persist for extended periods of time following inactivation of E. coli.

Interspecies variation in survival and growth of filamentous heterotrophic bacteria in response to UVC radiation.

Ultraviolet radiation is an important environmental constraint on the evolution of life. In addition to its harmful effects, ultraviolet radiation plays an important role in generating genetic polymorphisms and acting as a selective agent. Understanding how prokaryotes cope with high radiation can give insights on the evolution of life on Earth. Four representative filamentous bacteria from the family Cytophagaceae with different pigmentation were selected and exposed to different doses of UVC radiation (15-32,400Jm(-2)). The effect of UVC radiation on bacterial survival, growth and morphology were investigated. Results showed high survival in response to UVC for Rudanella lutea and Fibrisoma limi, whereas low survival was observed for Fibrella aestuarina and Spirosoma linguale. S. linguale showed slow growth recovery after ultraviolet exposure, R. lutea and F. limi showed intermediate growth recovery, while F. aestuarina had the fastest recovery among the four tested bacteria. In terms of survival, S. linguale was the most sensitive bacterium whereas R. lutea and F. limi were better at coping with UVC stress. The latter two resumed growth even after 2h exposure (∼10,800Jm(-2)). Additionally, the ability to form multicellular filaments after exposure was tested using two bacteria: one representative of the high (R. lutea) and one of the low (F. aestuarina) survival rates. The ability to elongate filaments due to cell division was preserved but modified. In R. lutea 10min exposure reduced the average filament length. The opposite was observed in F. aestuarina, where the 5 and 10min exposures increased the average filament length. R. lutea and F. limi are potential candidates for further research into survival and resistance to ultraviolet radiation stress.

Effects of radiation (Cobalt-60) on the elimination of Brevipalpus phoenicis (Acari: Tenuipalpidae) Cardinium endosymbiont.

Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) is a polyphagous mite with worldwide distribution and it is also a vector of several plant viruses. In citrus, B. phoenicis transmits Citrus leprosis virus (CiLV), the causal agent of leprosis, a disease that costs millions of dollars per year for its prevention and control. Brevipalpus phoenicis mites reproduce through thelytokous parthenogenesis, producing haploid females. This characteristic is attributable to the presence of an endosymbiont bacterium of the genus Cardinium; however, very little is known about the biological and ecological implications of the presence of this endosymbiont in Brevipalpus mites. In order to investigate the role of Cardinium in the transmission of CiLV to citrus plants, our goal was to eliminate the bacterium from the mite. We assessed the effectiveness of different doses of radiation from a Cobalt-60 source to cure B. phoenicis populations from Cardinium sp. The efficiency of irradiation on the elimination of the endosymbiont was determined by counting the number of females and males obtained in the F(1) generation after irradiation and confirming the presence of the endosymbiont by PCR. Both radiation treatments influenced the oviposition period and the number of eggs laid by irradiated females. Also, irradiation eliminated the Cardinium endosymbiont and increased the number of males in progeny of the exposed populations. Although macroscopic morphological abnormalities were not observed among the treated mites, the mortality was higher compared to the non-irradiated control group.

[Changes in viability of two Antarctic marine bacteria exposed to solar radiation in the water column: influence of vertical mixing]. / Cambios en la viabilidad de dos bacterias marinas antárticas expuestas a la radiación solar en la columna de agua: influencia de la mezcla vertical.

The effect of UV radiation on two Antarctic marine bacterial strains (UVps and UVvi) was studied in the water column of Potter Cove (South Shetland, Antarctica). Quartz flasks were filled with the bacterial suspensions and exposed to solar radiation at 0 m, 1 m and 3 m depth. Assays using flasks exposed to direct solar radiation and others using flasks covered with/by interferential filters which discriminate between UVA and UVB, were performed. In other assays, a vertical mixing of 4 m/h was simulated. Both strains showed a significant decrease in viability (expressed as colony - forming units) when exposed to a surface UVB dose of 8.4 kJ m(-2). Studies with interferential filters showed a significant decrease at 0 and 1 m depth under both UV treatments. The UVps strain appeared to be more sensitive to UVB than to UVA. Damage produced by UVB was attenuated by the vertical mixing when the surface UVB dose was 4.8 kJ m(-2). This effect was not observed when surface UVB dose was 7.7 kJ m(-2). These results show that the negative effect caused by UVB radiation on the bacterioplankton would be significant only in the first meter of water column of the Antarctic coastal waters with high levels of suspended particulate material.

Cambios en la viabilidad de dos bacterias marinas antárticas expuestas a la radiación solar en la columna de agua: influencia de la mezcla vertical / Changes in viability of two Antarctic marine bacteria exposed to solar radiation in the water column: influence of vertical mixing

Se estudió el efecto de la radiación ultravioleta (RUV) sobre dos cepas bacterianas marinas antárticas (UVps y UVvi) en la columna de agua de la caleta Potter (Shetland del Sur, Antártida). Frascos de cuarzo con las cepas en estudio fueron expuestos a la radiación solar en superficie, a 1 m y a 3 m de profundidad. Se realizaron ensayos con exposición directa y con filtros interferenciales que discriminaron la radiación UVA y la UVB. En otros ensayos se simuló una mezcla vertical de 4 m/h. Ambas cepas mostraron una disminución significativa del número de unidades formadoras de colonias, tanto en superficie como a 1 m de profundidad, luego de exponerlas a dosis superficiales de UVB de 8,4 kJ m-2. El estudio con filtros interferenciales mostró una disminución significativa de la viabilidad en ambos tratamientos UV en superficie y a 1 m. La cepa UVps mostró mayor sensibilidad a la UVB que a la UVA. La mezcla vertical amortiguó el daño causado por la UVB cuando la dosis en superficie fue de 4,8 kJ m-2. Este efecto amortiguador no se observó cuando la dosis en superficie fue de 7,7 kJ m-2. Estos resultados muestran que el efecto negativo de la RUV sobre el bacterioplancton sería particularmente importante en el primer metro de profundidad de las aguas costeras antárticas con abundante material particulado en suspensión.

The effect of UV radiation on two Antarctic marine bacterial strains (UVps and UVvi) was studied in the water column of Potter Cove (South Shetland, Antarctica). Quartz flasks were filled with the bacterial suspensions and exposed to solar radiation at 0 m, 1 m and 3 m depth. Assays using flasks exposed to direct solar radiation and others using flasks covered with/by interferential filters which discriminate between UVA and UVB, were performed. In other assays, a vertical mixing of 4 m/h was simulated. Both strains showed a significant decrease in viability (expressed as colony - forming units) when exposed to a surface UVB dose of 8.4 kJ m-2. Studies with interferential filters showed a significant decrease at 0 and 1 m depth under both UV treatments. The UVps strain appeared to be more sensitive to UVB than to UVA. Damage produced by UVB was attenuated by the vertical mixing when the surface UVB dose was 4.8 kJ m-2. This effect was not observed when surface UVB dose was 7.7 kJ m-2. These results show that the negative effect caused by UVB radiation on the bacterioplankton would be significant only in the first meter of water column of the Antarctic coastal waters with high levels of suspended particulate material.

Functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration.

The recent discovery of a carotenoid light-harvesting antenna in xanthorhodopsin, a retinal-based proton pump in Salinibacter ruber, made use of photoinhibition of respiration in whole cells to obtain action spectra [Balashov et al. Science 309, (2005) 2061-2064]. Here we provide further details of this phenomenon, and compare action spectra in three different systems where carotenoids have different functions or efficiencies of light-harvesting. The kinetics of light-induced inhibition of respiration in Salinibacter ruber was determined with single short flashes, and the photochemical cross section of the photoreaction was estimated. These measurements confirm that the xanthorhodopsin complex includes no more than a few, and most likely only one, carotenoid molecule, which is far less than the core complex antenna of photosynthetic bacteria. Although the total cross-section of light absorption in the purple bacterium Rhodospirillum rubrum greatly exceeds that in Salinibacter, the cross-sections are roughly equivalent in the shared wavelength range. We show further that despite interaction of bacterioruberin with archaerhodopsin, another retinal-based proton pump, there is no significant energy transfer from this carotenoid. This emphasizes the uniqueness of the salinixanthin-retinal interaction in xanthorhodopsin, and indicates that bacterioruberin in Halorubrum species has a structural or photoprotective rather than energetic role.