Fibrisoma montanum sp. nov., isolated from soil of Mountain Danxia, China.

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium, designated HYT19T, was isolated from soil of Mountain Danxia in southern China. It showed the highest similarity of 16S rRNA gene sequence (97.0%) and formed a monophyletic clade with Fibrisoma limi BUZ 3T. Strain HYT19T grew at 16-37 °C (optimum 28-30 °C) and at pH 6-7. The draft genome size of strain HYT19T was 7.8 Mb with a DNA G+C content of 54.0 mol%. The digital DDH and average nucleotide identity values between strain HYT19T and F. limi BUZ 3T were 28.8% and 85.1%, respectively. MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, unidentified aminophospholipid, two unidentified aminolipids, unidentified phospholipid and unidentified lipid. The strain contained C16:1ω5c, iso-C15:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0, iso-C17:0 3-OH and anteiso-C15:0 as the major fatty acids. On the basis of phylogenetic, genomic, phenotypic and chemotaxonomic analysis, we propose a new species Fibrisoma montanum sp. nov. of genus Fibrisoma. The type strain is HYT19T (= CCTCC AB 2018342T = JCM 33105T).

Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil.

A Gram-negative, yellow-pigmented, long-rod shaped bacterial strain designated DY10(T) was isolated from a soil sample collected at Mt. Deogyusan, Jeonbuk province, South Korea. Optimum growth observed at 30°C and pH 7. No growth was observed above 1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain DY10(T) belonged to the genus Spirosoma and was distantly related to Spirosoma arcticum R2-35(T) (91.0%), Spirosoma lingual DSM 74(T) (90.8%), Spirosoma endophyticum EX36(T) (90.7%), Spirosoma panaciterrae DSM 21099(T) (90.5%), Spirosoma rigui WPCB118(T) (90.2%), Spirosoma spitsbergense DSM 19989(T) (89.8%), Spirosoma luteum DSM 19990(T) (89.6%), Spirosoma oryzae RHs22(T) (89.6%), and Spirosoma radiotolerans DG5A(T) (89.1%). Strain DY10(T) showed resistance to gamma and ultraviolet radiation. The chemotaxonomic characteristics of strain DY10(T) were consistent with those of the genus Spirosoma, with the quinone system with MK-7 as the predominant menaquinone, iso-C15:0, C16:1 ω5c, and summed feature3 (C16:1 ω7c/C16:1 ω6c), and phosphatidylethanolamine as the major polar lipid. The G+C content of the genomic DNA was 53.0 mol%. Differential phenotypic properties with the closely related type strains clearly distinguished strain DY10(T) from previously described members of the genus Spirosoma and represents a novel species in this genus, for which the name Spirosoma montaniterrae sp. nov. is proposed. The type strain is DY10(T) (=KCTC 23999(T) =KEMB 9004-162(T) =JCM 18492(T)).

Impacts of single-walled carbon nanotubes on microbial community structure in activated sludge.

AIMS: Single-walled carbon nanotubes (SWNTs) are likely to become increasingly widespread and yet their environmental impact is not well understood. The purpose of the current study was to evaluate the impact of SWNTs on microbial communities in a 'sentinel' environmental system, activated sludge batch-scale reactors. METHODS AND RESULTS: Triplicate batch reactors were exposed to SWNTs and compared to control reactors exposed to impurities associated with SWNTs. Automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterial community structure in each reactor. SWNT exposure was found to impact microbial community structure, while SWNT-associated impurities had no effect, compared to controls. 16S rRNA gene sequence analysis indicated that dominant phylotypes detected by ARISA included members of the families Sphingomonadaceae and Cytophagacaceae and the genus Zoogloea. ARISA results indicated an adverse impact of SWNTs on the sphingomonad relative to other community members. Changes in community structure also occurred in both SWNT-exposed and control reactors over the experimental time period and with the date on which activated sludge was obtained from a wastewater treatment facility. CONCLUSIONS: These results indicate that SWNTs differentially impact members of the activated sludge reactor bacterial community. SIGNIFICANCE AND IMPACT OF THE STUDY: The finding that community structure was affected by SWNTs indicates that this emerging contaminant differentially impacted members of the activated sludge bacterial community and raises the concern that SWNTs may also affect the services it provides.

Antibiotic effects of three strains of chrysophytes (Ochromonas, Poterioochromonas) on freshwater bacterial isolates.

We investigated the antibiotic effects of extracts of freeze-dried biomass and culture supernatants from the mixotrophic chrysophyte species Ochromonas danica, Poterioochromonas sp. strain DS, and Poterioochromonas malhamensis on bacterial strains isolated from lake water. Methanolic biomass extracts inhibited the growth of all tested strains, albeit to a different extent, whereas aqueous biomass extracts only affected bacteria of the genus Flectobacillus. The antibiotic action of supernatants from flagellate cultures could be mostly attributed to lipophilic substances, but the growth of bacteria affiliated with Flectobacillus and Sphingobium was also affected by hydrophilic compounds. A comparison of biomass extracts from light- and dark-adapted cultures of Poterioochromonas sp. strain DS showed that the growth-inhibiting factor was unrelated to chlorophyll derivatives. Supernatants from a dark-adapted, phagotrophically grown flagellate culture had stronger antibiotic effects and affected more bacterial strains than the supernatant from a light-adapted culture. Significant growth reduction of a Flectobacillus isolate was already induced by extremely low concentrations of lipophilic extracts from these supernatants. Our results show that metabolites of the studied flagellates - either released actively or during cell lysis - may selectively affect the growth of some aquatic bacteria even in very small doses and thus potentially affect microbial community composition. Moreover, the antibiotic potential of mixotrophic chrysophytes may change with their nutritional mode.

Assessing niche separation among coexisting Limnohabitans strains through interactions with a competitor, viruses, and a bacterivore.

We investigated potential niche separation in two closely related (99.1% 16S rRNA gene sequence similarity) syntopic bacterial strains affiliated with the R-BT065 cluster, which represents a subgroup of the genus Limnohabitans. The two strains, designated B4 and D5, were isolated concurrently from a freshwater reservoir. Differences between the strains were examined through monitoring interactions with a bacterial competitor, Flectobacillus sp. (FL), and virus- and predator-induced mortality. Batch-type cocultures, designated B4+FL and D5+FL, were initiated with a similar biomass ratio among the strains. The proportion of each cell type present in the cocultures was monitored based on clear differences in cell sizes. Following exponential growth for 28 h, the cocultures were amended by the addition of two different concentrations of live or heat-inactivated viruses concentrated from the reservoir. Half of virus-amended treatments were inoculated immediately with an axenic flagellate predator, Poterioochromonas sp. The presence of the predator, of live viruses, and of competition between the strains significantly affected their population dynamics in the experimentally manipulated treatments. While strains B4 and FL appeared vulnerable to environmental viruses, strain D5 did not. Predator-induced mortality had the greatest impact on FL, followed by that on D5 and then B4. The virus-vulnerable B4 strain had smaller cells and lower biomass yield, but it was less subject to grazing. In contrast, the seemingly virus-resistant D5, with slightly larger grazing-vulnerable cells, was competitive with FL. Overall, our data suggest contrasting ecophysiological capabilities and partial niche separation in two coexisting Limnohabitans strains.

Heme uptake by Microscilla marina and evidence for heme uptake systems in the genomes of diverse marine bacteria.

The ability to acquire diverse and abundant forms of iron would be expected to confer a survival advantage in the marine environment, where iron is scarce. Marine bacteria are known to use siderophores and inorganic iron, but their ability to use heme, an abundant intracellular iron form, has only been examined preliminarily. Microscilla marina, a cultured relative of a bacterial group frequently found on marine particulates, was used as a model organism to examine heme uptake. Searches of the genome revealed analogs to known heme transport proteins, and reverse transcription-quantitative PCR analysis of these genes showed that they were expressed and upregulated under iron stress and during growth on heme. M. marina was found to take up heme-bound iron and could grow on heme as a sole iron source, supporting the genetic evidence for heme transport. Similar putative heme transport components were identified in the genomes of diverse marine bacteria. These systems were found in the genomes of many bacteria thought to be particle associated but were lacking in known free-living organisms (e.g., Pelagibacter ubique and marine cyanobacteria). This distribution of transporters is consistent with the hydrophobic, light-sensitive nature of heme, suggesting that it is primarily available on phytoplankton or detritus or in nutrient-rich environments.

Grazer and virus-induced mortality of bacterioplankton accelerates development of Flectobacillus populations in a freshwater community.

We present a detailed analysis of the effects of distinct bacterial mortality factors, viral lysis and heterotrophic nanoflagellates (HNF) bacterivory, associated with the development of filamentous Flectobacillus populations. Reservoir bacterioplankton communities were subjected to additions of both HNF and viruses together, or HNF alone, and then incubated in situ in dialyses bags. For distinct bacterial groups, mortality or growth stimulation was analysed by examining bacterial prey ingested in HNF food vacuoles with fluorescence in situ hybridization (FISH) and via FISH with microautoradiography (MAR-FISH). We also developed a semi-quantitative MAR-FISH-based estimation of relative activities of Flectobacillus populations (targeted by the R-FL615 probe). Bacterial groups vulnerable to HNF predation (mainly clusters of Betaproteobacteria), or discriminated against (Actinobacteria), were detected. Bacterial lineages most vulnerable to virus-lysis (mainly the Betaproteobacteria not targeted by the R-BT065 probe, of the Polynucleobacter cluster) were identified by comparing treatments with HNF alone to HNF and viruses together. Filaments affiliated with the Flectobacillus cluster appeared in both treatments, but were about twice as abundant, long and active as in incubations with viruses and HNF as compared with HNF alone. Viruses appeared to selectively suppress several bacterial groups, perhaps enhancing substrate availability thus stimulating growth and activity of filamentous Flectobacillus.

A carotenoid synthesis gene cluster from Algoriphagus sp. KK10202C with a novel fusion-type lycopene beta-cyclase gene.

A carotenoid synthesis gene cluster was isolated from a marine bacterium Algoriphagus sp. strain KK10202C that synthesized flexixanthin. Seven genes were transcribed in the same direction, among which five of them were involved in carotenoid synthesis. This cluster had a unique gene organization, with an isoprenoid gene, ispH (previously named lytB), being present among the carotenoid synthesis genes. The lycopene beta-cyclase encoded by the crtY ( cd ) gene appeared to be a fusion of bacterial heterodimeric lycopene cyclase CrtY(c) and CrtY(d). This was the first time that a fusion-type of lycopene beta-cyclase was reported in eubacteria. Heterologous expression of the Algoriphagus crtY ( cd ) gene in lycopene-accumulating Escherichia coli produced bicyclic beta-carotene. A biosynthesis pathway for monocyclic flexixanthin was proposed in Algoriphagus sp. strain KK10202C, though several of the carotenoid synthesis genes not linked with the cluster have not yet been cloned.

Direct and indirect effects of protist predation on population size structure of a bacterial strain with high phenotypic plasticity.

We studied the impact of grazing and substrate supply on the size structure of a freshwater bacterial strain (Flectobacillus sp.) which showed pronounced morphological plasticity. The cell length varied from 2 to >40 microm and encompassed rods, curved cells, and long filaments. Without grazers and with a sufficient substrate supply, bacteria grew mainly in the form of medium-sized rods (4 to 7 microm), with a smaller proportion (<10%) of filamentous forms. Grazing experiments with the bacterivorous flagellate Ochromonas sp. showed that freely suspended cells of <7 microm were highly vulnerable to grazers, whereas filamentous cells were resistant to grazing and became enriched during predation. A comparison of long-term growth in carbon-limited chemostats with and without grazers revealed that strikingly different bacterial populations developed: treatments with flagellates were composed of >80% filamentous cells. These attained a biomass comparable to that of populations in chemostats without grazers, which were composed of medium-sized rods and c-shaped cells. Carbon starvation resulted in a fast decrease in cell length and a shift towards small rods, which were highly vulnerable to grazing. Dialysis bag experiments in combination with continuous cultivation revealed that filament formation was significantly enhanced even without direct contact of bacteria with bacterivores and was thus probably stimulated by grazer excretory products.

[Relations of oligotrophic bacteria to oxygen].

Polluted air and the derived photochemical smog are the sources of free radicals in the atmosphere. Organic peroxides present in the smog mediate formation of peroxide radical. Oxygen species are formed by purely physical mechanisms, for instance, energy consumption converts molecular oxygen to an excited singlet state. Six active oxygen species are known: ozone, atomic oxygen, perhydroxyl, superoxide, and singlet oxygen. Singlet oxygen is the most harmful oxygen product for living cells, while hydrogen peroxide is the least harmful. Molecular oxygen is hardly toxic for prokaryotes due to an efficient protection of microbial cells by specific enzymes. This work experimentally confirms the harmlessness of molecular oxygen.

Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm.

A Gram-negative bacterium was isolated from a freshwater biofilm developed on a stainless steel surface under a fluid velocity of 0.26 m s(-1). The strain, MBRG1.5(T), was cultivated on R2A agar and formed pink colonies. Light microscopy and negative staining in a transmission electron microscope showed that the cells were rod-shaped, approximately 2.8-4.1 microm long by 0.9-1.7 microm wide in size and produced large quantities of extracellular fibrillar material. Additionally, following growth in batch culture, transmission electron microscopy showed that many cells plasmolysed. Stationary-phase cells were more variable in size and shape. The DNA G+C content was 40.0 mol%. The most abundant fatty acids were 15 : 0 iso (22.5 %), followed by 16 : 1omega5c (16.9 %) and 15 : 0 iso 2-OH (16.5 %). Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the family 'Flexibacteraceae' of the Cytophaga-Flavobacterium-Bacteroides group. Phenotypic and genotypic analyses indicated that the strain could not be assigned to any recognized genus; therefore a novel genus and species, Adhaeribacter aquaticus gen. nov., sp. nov., is proposed, with MBRG1.5(T) (=DSM 16391(T)=NCIMB 14008(T)) as the type strain.

Biological hydrogen production using a membrane bioreactor.

A cross-flow membrane was coupled to a chemostat to create an anaerobic membrane bioreactor (MBR) for biological hydrogen production. The reactor was fed glucose (10,000 mg/L) and inoculated with a soil inoculum heat-treated to kill non-spore-forming methanogens. Hydrogen gas was consistently produced at a concentration of 57-60% in the headspace under all conditions. When operated in chemostat mode (no flow through the membrane) at a hydraulic retention time (HRT) of 3.3 h, 90% of the glucose was removed, producing 2200 mg/L of cells and 500 mL/h of biogas. When operated in MBR mode, the solids retention time (SRT) was increased to SRT = 12 h producing a solids concentration in the reactor of 5800 mg/L. This SRT increased the overall glucose utilization (98%), the biogas production rate (640 mL/h), and the conversion efficiency of glucose-to-hydrogen from 22% (no MBR) to 25% (based on a maximum of 4 mol-H(2)/mol-glucose). When the SRT was increased from 5 h to 48 h, glucose utilization (99%) and biomass concentrations (8,800 +/- 600 mg/L) both increased. However, the biogas production decreased (310 +/- 40 mL/h) and the glucose-to-hydrogen conversion efficiency decreased from 37 +/- 4% to 18 +/- 3%. Sustained permeate flows through the membrane were in the range of 57 to 60 L/m(2) h for three different membrane pore sizes (0.3, 0.5, and 0.8 microm). Most (93.7% to 99.3%) of the membrane resistance was due to internal fouling and the reversible cake resistance, and not the membrane itself. Regular backpulsing was essential for maintaining permeate flux through the membrane. Analysis of DNA sequences using ribosomal intergenic spacer analysis indicated bacteria were most closely related to members of Clostridiaceae and Flexibacteraceae, including Clostridium acidisoli CAC237756 (97%), Linmingia china AF481148 (97%), and Cytophaga sp. MDA2507 AF238333 (99%). No PCR amplification of 16s rRNA genes was obtained when archaea-specific primers were used.

Isolation and characterization of aerobic heterotrophic bacteria from natural spring waters in the Lanjaron area (Spain).

Aerobic, heterotrophic bacteria were isolated from nine natural mineral water springs in the Lanjaron area of Spain over the period July 1980 to May 1981. The mineral waters contained few bacteria (mean counts 26-5275 cfu per 100 ml) and the bacterial flora of all nine springs was very similar. Most of the isolates were Gram-negative rods (90%), and among these Pseudomonas spp. and members of the Flavobacterium-Cytophaga-Flexibacter group were numerically dominant. Aeromonas-Vibrio and Enterobacteriaceae isolates were an important fraction of the total number, but isolates from remaining groups (Acinetobacter, Chromobacterium, Alcaligenes and Gram-positive organisms) constituted only a small proportion of the flora. The comparatively small number of species isolated, and the occurrence of no more than three or four different bacterial types in spring water of different chemical and physical composition is discussed.

SQ 28,332, a new monobactam produced by a Flexibacter sp. Taxonomy, fermentation, isolation, structure determination and biological properties.

A new monobactam SQ 28,332 has been isolated from fermentations of a Flexibacter sp. and the structure 3 was deduced from its spectroscopic properties. SQ 28,332 exhibits weak antibacterial activity.

Two new monobactam antibiotics produced by a Flexibacter sp. I. Taxonomy, fermentation, isolation and biological properties.

Two new beta-lactam antibiotics, namely SQ 28,502 and SQ 28,503, have been isolated from fermentations of a Flexibacter sp. They are demethoxy monobactams with oligopeptide side chains and have molecular weights of 1,462 and 1,446, respectively. These beta-lactams show a high degree of stability to a variety of beta-lactamases and act as potent irreversible inactivators of P99 beta-lactamase from Enterobacter cloacae. They exhibit weak antibacterial activity.

[Aquatic myxobacteria (Sporocytophaga cauliformis) and the order "Myxobacterales" (author's transl)]. / Wassermyxobakterien (Sporocytophaga cauliformis) und die Ordnung "Myxobacterales".

The indicator function of aquatic myxobacteria for the purpose of evaluating drinking water quality as well as their occurrence in sewage effluent make it desirable to describe these hitherto little known organisms in more detail. To this end, a comparative investigation of anaerobic myxobacteria of the genus Sphaerocytophaga, two typical representatives of the Order Myxobacterales (Myxococcus fulvus, Sporocytophage cauliformis), and a strain ov Vitrepscilla (Vitroescilla proteolytica) was undertaken. With respect to culture morphology, the migratory fringe surrounding colonies of Sphaerocytophaga similar to the other strains studies was a prominent characteristic. In particular, the similarity with colonies of Sporocytophaga cauliformis was apparent. The gliding motility typical of Sphaerocytophaga could be demonstrated in all of the strains investigated. Scanning electron micrographs revealed an amorphous layer of slime covering the cell surfaces in all strains compared in this study, thus excluding the existence of more rigid organelles of locomotion. Taxonomically, the anaerobec myxobacteria of the oral cavity (Sphaerocytophaga) belong to the Order "Myxobacterales" and not the "Eubacterales", i.e., to the genus Fusobacterium. This is clearly suggested by their motility lacking flagella and, above all, by their cell morphology which differs from the Eubacterales.

Capnocytophaga: new genus of gram-negative gliding bacteria. II. Morphology and ultrastructure.

Gram-negative, anaerobic gliding bacteria were isolated from normal supragingival plaque and from periodontal lesions. Isolates could be divided into two size classes: small 2.4-4.2 micrograms x 0.38-0.5 microgram and large 4.8-5.8 micrograms x 0.42-0.6 microgram cells. The outer membrane was either loose-fitting and wavy, or taut, and of variable thickness. An electron-dense fuzz was discernible on several of the isolates. The periplasmic region was of variable electron-density. The genus Capnocytophaga has been proposed for these organisms based on morphological and cultural characteristics.

Capnocytophaga: new genus of gram-negative gliding bacteria. III. Physiological characterization.

Sixty-eight strains of capnophilic fusiform Gram-negative rods from the human oral cavity were subjected to extensive physiologic characterization, tested for susceptibility to various antibiotics, and the mol-percent guanine plus cytosine of each isolate determined. The characteristics of the isolates were compared with 10 fresh and 2 stock isolates of Fusobacterium nucleatum. The isolates clearly differed from the Fusobacterium species on the basis of mol-percent guanine plus cytosine, end products, growth in a capnophilic environment and fermentation of carbohydrates. All of the gliding isolates required CO2 and formed acetate and succinate, but not H2S, indole or acetylmethylcarbinol. All fermented glucose, sucrose, maltose and mannose. The organisms may be differentiated on the basis of fermentation of additional carbohydrates, hydrolysis of polymers and reduction nitrate. Three species are proposed: Capnocytophaga ochracea, Capnocytophaga sputigena and Capnocytophaga gingivalis. Ten isolates did not fit into the proposed species.