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In order to evaluate the corrosive action of microorganisms on 316L metal exposed directly to a marine environment, a system was designed to immerse coupons in seawater. After periods of 30, 60 and 90 days, the coupons were recovered, the corrosion rates evaluated and the biofilm samples on their surface were analyzed by 16S rRNA gene sequencing. The results of the corrosion rate showed an acceleration over the entire experimental period. Alpha diversity measurements showed higher rates after 60 days of the experiment, while abundance measurements showed higher rates after 90 days of exposure to the marine environment. The beta-diversity results showed a clear separation between the three conditions and proximity in the indices between replicates of the same experimental condition. The results of 16S rRNA gene sequencing showed that after 30 days of exposure to seawater, there was massive representativeness of the pioneer bacteria, Gamma and Alphaproteobacteria, with emphasis on the genera Alcanivorax, Oceanospirillum and Shewanella. At the 60-day analysis, the Gammaproteobacteria class remained dominant, followed by Alphaproteobacteria and Flavobacteria, and the main representatives were Flexibacter and Pseudoalteromonas. In the last analysis, after 90 days, a change in the described bacterial community profile was observed. The Gammaproteobacteria class was still the largest in diversity and OTUs. The most predominant genera in number of OTUs were Alteromonas, Bacteriovorax and, Nautella. Our results describe a change in the microbial community over coupons directly exposed to the marine environment, suggesting a redirection to the formation of a mature biofilm. The conditions created by the biofilm structure suggest said condition favor biocorrosion on the analyzed coupons.

The increasing use of cerium oxide nanoparticles (CeO2 NPs) has caused concerns regarding their potential environmental risks. However, their effects on bacterial communities and network interactions in activated sludge process are still unclear. In this study, we carried out long-term exposure experiments (210 d) to investigate the influence of CeO2 NPs on wastewater treatment performance, bacterial community structure and network interactions in activated sludge systems. The results showed that long-term exposure to 1 mg/L CeO2 NPs induced the deterioration of denitrifying process, which was consistent with the inhibition of enzyme activities of nitrite oxidoreductase and nitrate reductase under CeO2 NPs. CeO2 NPs decreased the bacterial diversity and altered the overall bacterial community structure in activated sludge. Some dominant denitrifying bacteria, such as Flexibacter and Acinetobacter decreased significantly. Molecular ecological network analysis showed that CeO2 NPs decreased the network complexity of bacterial community, and probably promoted the competition in bacterial communities of activated sludge. These changes of denitrifying bacteria and the bacterial network may be relevant to the deterioration of denitrifying process. This study provides insights into how the bacteria community and their molecular ecological network respond to CeO2 NPs in activated sludge systems.

The composition and diversity of microbial communities from the cold ultra-fresh oligotrophic seeps and River Sukhoe Ubzhogoe of the National Park "Alkhanai" were determined via culture-dependent vs. culture-independent approaches. The microbial community of six groundwater seeps determined by 16S rDNA cloning, and sequencing consisted of four dominant genera belonging to the classes Betaproteobacteria and Gammaproteobacteria; they were Duganella sp., Janthinobacterium sp., and Pseudomonas sp., Serratia sp., respectively. Uncultured bacteria were presented by the phylum Bacteroidetes, classes Flavobacteriia (Flavobacterium sp.), Cytophagia (Flexibacter sp.), and Chitinophagia (Sediminibacterium sp.); the phylum Proteobacteria, classes Betaproteobacteria (Comamonadaceae) and Gammaproteobacteria (Acinetobacter sp.); and the phylum Actinobacteria, class Actinomycetia (Rhodococcus sp.). The same chemoorganoheterotrophic bacteria were cultivated as dominant species from the waters of the investigated seeps. Still, differences in the microbial communities were found in a proper combination of the four dominant forms of bacteria in the appropriate ecosystems. One of the peculiarities of the cultivable bacteria was the production of colored pigments violacein and prodigiosin, known for their therapeutic properties. The subject is promising for fundamental and applied research. Curative properties of cold seeps were discussed, and it was proposed that the water quality could assume medicinal qualities due to the specific composition of microorganisms.

Bacteria on biocathode can facilitate cathodic reduction reaction for a microbial fuel cells. This study profiled the cathodic bacterial community with high reduction activity using the Illumina pyrosequencing method, from which the highly diversified and novel population structure was found. The cathodic biofilm had a community structure dominated by Proteobacteria (42.7%), Firmicutes (25.0%), 9.7% Bacteroidetes (9.7%), Actinobacteria (7.7%) and Aquificae (7.1%). And the species of Acidovorax, Soehngenia, Clostridium, Sulfurihydrogenibium, Flexibacter, Mycobacterium and others were the predominant populations. Function composition analysis showed that the membrane transport is the most important metabolic activity for this community.

In this study, a total of 172 putative omega-3 producers were isolated from 28 sediment samples from the Arabian Gulf employing a selective isolation procedure using marine agar containing 0·1% triphenyl tetrazolium chloride (TTC). Out of these 172 isolates, 19 isolates produced eicosapentaenoic acid (EPA) as confirmed by Gas Chromatography-Mass Spectrometry (GC-MS). The EPA content of the isolated bacterial strain varied from 1·76 to 6·52% of total fatty acids. Among the 19 isolates of EPA producers, while 17 isolates harboured both pfaA gene and Δ6 desaturase gene, only five isolates harboured Δ5 desaturase gene. Two of the EPA positive strains harbour none of the three genes tested. The 16s RNA identification of these isolates revealed that except one, all the EPA producers were Gram-positive marine bacteria belonging to the phylum Firmicutes, family Bacillacea, genera Bacillus and Oceanobacillus. Halomonas pacifica was the only Gram-negative Gamma-Proteobacteria detected to produce EPA from this region. SIGNIFICANCE AND IMPACT OF THE STUDY: Recently, marine bacteria are considered as a promising source of polyunsaturated fatty acid (PUFA) over marine fishes and microalgae. PUFA producers reported from polar and deep-sea sources were restricted to five well-known marine genera under two distinct domains of bacteria such as proteobacteria (Shewanella, Colwellia, and Moritella) and cytophaga group (Flexibacter, Psychroflexus). This study revealed that subtropical marine environment could also be the source of PUFA producing bacteria, and they predominantly belonged to the class of Firmibacteria. This finding opens up new avenue for research to study the inherent mechanism and physiology of such organisms from this unique environment.

A novel bacterial strain, designated DCY106(T), was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY106(T) is Gram-negative, yellow-pigmented, non-flagellate, motile, non-spore-forming, rod-shaped, and strictly aerobic. The strain grows optimally at 25-30 °C and pH 6.5-7.5. Phylogenetically, strain DCY106(T) is closely related to Flavobacterium arsenitoxidans KCTC 22507(T) (98.41 %), followed by Flavobacterium cutihirudini LMG 26922(T) (97.67 %), Flavobacterium nitrogenifigens LMG 28694(T) (97.59 %), Flexibacter auranticus LMG 3987(T) (97.38 %), Flavobacterium defluvi KCTC 12612(T) (97.21 %) and Flavobacterium chilense LMG 26360(T) (97.05 %). The 16S rRNA gene sequence similarities to all other Flavobacterium species were below 97 %. The DNA G+C content of strain DCY106(T) is 34.2 mol% and the DNA-DNA relatedness between strain DCY106(T) and F. cutihirudini LMG 26922(T), F. auranticus LMG 3987(T), F. defluvi KCTC 12612(T) and F. chilense LMG 26360(T) were below 40.0 %. The menaquinone of the type MK-6 was found to be the predominant respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids (APL1, APL6) and one unidentified lipid L2. C15:0, iso-C15:0 and summed feature 3 (iso-C15:0 2OH/C16:1 ω7c) were identified as the major fatty acids present in DCY106(T). The results of physiological and biochemical tests allowed strain DCY106(T) to be differentiated phenotypically from other recognized species belonging to the genus Flavobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Flavobacterium panacis sp. nov. is proposed with the type strain designated as DCY106(T) (= JCM 31468(T)= KCTC 42747(T)).

To assess the effect of addition of probiotics and carbon source on the microbial community structure within the shrimp culture, an enclosure system simulating a high density, intensive aquaculture of Litopenaeus vannamei was set up in Dianbai, Maoming, Guangdong province, China. The phylogenetic profiles of microbial communities in the enclosure system after addition of Bacillus and molasses were studied in the middle and final culture season (on the 45th, 75th and 95th day) using polymerase chain reaction-denaturing gradient gel electrophoresis. A total of four groups, each containing a triplicate were set up: Group A (control), Group B (64% of daily feed was provided as molasses with Bacillus sp.), Group C (50% of daily feed amount provided as molasses with Bacillus sp.) and Group D (64% of daily feed amount as molasses alone). The results showed that α-Proteobacteria, δ-Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacteria. Moreover, the relative proportion of α-Proteobacteria increased and that of Bacteroidetes decreased gradually with time. Pathogenic Flexibacter was the dominant genus in Group A on the 45th day, while the functional strains (Sphingomonas sp., Erythrobacter sp., Roseobacter sp., and Rhodobacter sp.) were detected multiple times in Groups B and C. Bacillus sp. was the cultivable, dominant bacterium in Groups B and C on the 95th day. Therefore, the combined use of Bacillus and molasses helped increase diversity of the microbial community, effectively inhibit pathogens, and promote the formation and development of a beneficial microbial community structure in the high density, intensive aquaculture of L. vannamei.

Microbial community patterns vary in glaciers worldwide, presenting unique responses to global climatic and environmental changes. Four bacterial clone libraries were established by 16S rRNA gene amplification from four ice layers along the 42-m-long ice core MuztB drilled from the Muztag Ata Glacier. A total of 151 bacterial sequences obtained from the ice core MuztB were phylogenetically compared with the 71 previously reported sequences from three ice cores extracted from ice caps Malan, Dunde, and Puruogangri. Six phylogenetic clusters Flavisolibacter, Flexibacter (Bacteroidetes), Acinetobacter, Enterobacter (Gammaproteobacteria), Planococcus/Anoxybacillus (Firmicutes), and Propionibacter/Luteococcus (Actinobacteria) frequently occurred along the Muztag Ata Glacier profile, and their proportion varied by seasons. Sequence analysis showed that most of the sequences from the ice core clustered with those from cold environments, and the sequence clusters from the same glacier more closely grouped together than those from the geographically isolated glaciers. Moreover, bacterial communities from the same location or similarly aged ice formed a cluster, and were clearly separate from those from other geographically isolated glaciers. In summary, the findings provide preliminary evidence of zonal distribution of microbial community, and suggest biogeography of microorganisms in glacier ice.

Opportunistic pathogens, including Legionella spp. and non-tuberculous mycobacteria, can thrive in building hot water systems despite municipal and traditional on-site chlorine disinfection. Monochloramine is a relatively new approach to on-site disinfection, but the microbiological impact of on-site chloramine use has not been well studied. We hypothesized that comparison of the microbial ecology associated with monochloramine treatment versus no on-site treatment would yield highly dissimilar bacterial communities. Hot water samples were collected monthly from 7 locations for three months from two buildings in a Pennsylvania hospital complex supplied with common municipal water: (1) a hospital administrative building (no on-site treatment) and (2) an adjacent acute-care hospital treated on-site with monochloramine to control Legionella spp. Water samples were subjected to DNA extraction, rRNA PCR, and 454 pyrosequencing. Stark differences in the microbiome of the chloraminated water and the control were observed. Bacteria in the treated samples were primarily Sphingomonadales and Limnohabitans, whereas Flexibacter and Planctomycetaceae predominated in untreated control samples. Serendipitously, one sampling month coincided with dysfunction of the on-site disinfection system that resulted in a Legionella bloom detected by sequencing and culture. This study also demonstrates the potential utility of high-throughput DNA sequencing to monitor microbial ecology in water systems.

Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa . Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes . Levels of DNA–DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and β-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga , named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

To enumerate the secondary microbial infection due to isopod parasites. One gram of tissue from the infected and uninfected part (body surface) was taken and homogenized with sterilized seawater. Samples were taken for enumeration of total heterotrophic bacteria (THB) and fungi. For enumeration of THB and fungi the pour plating technique was adopted. THB was enumerated using Zobel marine agar and fungi using 2 % Malt extract agar. The total count was expressed as colony forming unit/g. Gram stain is a differential staining method to identify bacteria based on the chemical and physical properties of their cell wall. The THB count in the infected fishes was significantly higher than in uninfected fishes. From the biochemical identification to identified isolates are Flavobacterium, Aeromonas hydrophila, Pseudomonas fluorescens, P. putida, Citrobacter, Photobacterium, Bacillus, Mycobacterium marinum, Flexibacter, Vibrio salmonicida, A. salmonicida, Bacillus sp. Fungal strains were identified as Exophiala salmonis, Ichthyosporidiosis based on the microscopic, morphological characters. Present study that the parasitation of Carangid fishes by the isopods lead to secondary infection by pathogenic microbes which may affect the fish population. It is observed to create more possibilities for secondary infection by bacteria and fungi due to their higher density area of the fishes.

Composting is a promising method for the management of agricultural wastes. However, results for wheat straw composts with different carbon-to-nitrogen ratios revealed that wheat straw was only partly degraded after composting for 25days, with hemicellulose and cellulose content decreasing by 14% and 33%, respectively. No significant changes in community structure were found after composting according to 454-pyrosequencing. Bacterial communities were represented by Proteobacteria and Bacteroidetes throughout the composting process, including relatively high abundances of pathogenic microbes such as Pseudomonas and Flexibacter, suggesting that innocent treatment of the composts had not been achieved. Besides, the significant lignocellulose degrader Thermomyces was not the exclusively dominant fungus with relative abundance only accounting for 19% of fungal communities. These results indicated that comparing with maize straw, wheat straw was an inefficient substrate for rapid natural lignocellulose-based composting, which might be due to the recalcitrance of wheat straw.

Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of Gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.

Individual bacterial populations are known to respond differently toward substrate availability. To test how the availability of either pure phenol or natural humic matter (HM) selects for specific pelagic bacteria phylotypes from a humic lake (Lake Grosse Fuchskuhle, northeastern Germany), we used culture-dependent and -independent approaches. Using a batch approach, the bacterial community composition (BCC) differed depending on both the quantity and the quality of added substrates. Using a dilution-to-extinction approach, distinct BCC were detected by eliminating less abundant species. Most bacteria that were common in the lake were favored by phenol, and yet different subsets of the native BCC were enriched by HM. Specific bacterial groups with different growth requirements were consistently present, negatively influenced, or positively enriched following substrate additions. This study comprises the first explicit demonstration that bacteria such as Methylobacterium, Methylophilus, and Methylosinus spp. can be enriched on phenol or HM. Our isolation approaches led to the successful cultivation of a variety of native bacteria from the lake, such as Novosphingobium (Alphaproteobacteria) and Flexibacter (Bacteroidetes), or phenol-utilizing bacteria such as members of Actinobacteria or Burkholderia (Betaproteobacteria). Enrichment and cultivation on phenol and HM as substrates revealed highly specialized bacterial communities that resemble those found in many HM-rich lakes.

One of them is the problem of disease Argulus sp. is ektoparasite which often attacked in activity of good conducting of sea water and also freshwater. Argulus sp. attacking at part of fin, husk, gill and entire all its body exterior of him. attacked by fish is Argulus sp. will seen is thin, often rub body and arise red pock which later can generate secondary infection. Utilize to prove the existence of bacterium which emerge effect of lession (secondary infection) which because of bite of Argulus sp. that is by identifying bacterium and biochemical test. Media which used in identifying bacterium for example that is TSA (Tryptic Soy Agar), TSIA (Triple Soy Iron Agar), MIO (Motility Indol Ornithin), O/F medium (Oksidative/Fermentative), sugar test medium (maltosa, laktosa, arabinosa, inositol, manitol, sukrosa). Target of this research is to know the existence of gram negative bacterium and gram negative bacterium any kind of which is found at fish hurt of gold fish (Carassius auratus) effect of infestation by ectoparasite Argulus sp. Research which is use descriptive method. That is with infestation of Argulus sp. into containing aquarium of gold fish counted 1 tail and Argulus sp. counted 5, 10, 15, 20 tail. After Argulus sp. patch all at gold fish is later then perceived until gold fish arise lession effect of bite of Argulus sp. is afterwards identifyed by bacterium to know the bacterium that were formed on gold fish lesions. The result showed that the lesions of gold fish, isolation at TSA medium and identified by biochemical test to diagnose bacteriums found on gold fish lession. Identifications of the three gram negative bacterium as follow : Aeromonas hydrophilla, Pseudomonas flourescens, Flexibacter columnaris while for the Edwardsiella tarda was not be found in this study

The foam-forming filamentous bacteria can result in serious membrane fouling problems, not only in traditional activated sludge processes, but also in membrane bioreactors (MBR). In this study, we examine the influence of the hydrophobicity of the membrane on membrane fouling in a submerged MBR using two sets of polytetrafluoroethylene membranes with different surface hydrophobicity. We also identify and compare the foam-forming filamentous bacteria via the Eikelboom method, the combination of a polymerase chain reaction with DNA sequencing, and the fluorescent in situ hybridization (FISH) approach based on non-cultured and cultured methods. The experimental results showed that during foaming period, the transmembrane pressure of the high hydrophobicity membrane increased as the flux decreased; but no significant influence was observed for the low hydrophobicity membrane. Of the foam-forming bacteria identified by non-cultured method, only Actinomycetes and Nosotcoida limicola III were observed using Eikelboom identification keys I and II, while high G + C content Gram-positive (HGC) bacteria was the predominant filamentous bacteria identified via the FISH approach. On the other hand, the Microthrix parvicella, Eikelboom type 1851, Eikelboom type 0092, and Flexibacter were identified as the predominant type of filamentous bacteria using the culture method with Eikelboom identification key I. The HGC bacteria made up 77.1% of the total isolates. Finally, the results of 16S rRNA sequences screened by the Eikelboom method showed that the genera Gordonia and Cytophaga, which contributed 75.7% and 20.1%, respectively, were the predominant filamentous bacteria.

Summary Aerated lagoons are commonly used for domestic and industrial wastewater treatment due to their low cost and minimal need of operational requirements. However, little information is known regarding microbial communities that inhabit these ecosystems. In this study, a 16S-DGGE approach was used to estimate bacterial diversity and to monitor community changes in two aerated lagoons from a wastewater treatment plant receiving urban and industrial effluents. Pronounced shifts between bacterial communities collected in winter–spring and summer–autumn months were detected. Temperature, dissolved oxygen (DO) and pH were the variables that most influenced the bacterial communities. Phylogenetic affiliation of predominant members was assessed by the determination of the 16S rDNA sequence of correspondent bands. Affiliations to Cytophaga – Flexibacter – Bacteroides (CFB) group, Firmicutes, and β - and e -proteobacteria were found.

We report, for the first time, on the production of an emulsifying polymer produced by a Flexibacter species (designated strain TG382). This polymer, E-382, was produced extracellularly during growth of the organism in a marine broth amended with glucose. After cold ethanol precipitation, extensive dialysis and lyophilization, a chemical analysis of the resultant dried polymer revealed it to be a glycoprotein composed of 10.9% protein, 23.3% carbohydrate and a 5.5% uronic acid content. At relatively low concentrations (0.02%, w/v), E-382 was found to form oil-in-water emulsions against hydrocarbon and food oils under neutral pH and acidic conditions. The most stable emulsions were formed against the oils sunflower, vegetable and ground nut under neutral pH conditions. Aqueous solutions of the polymer were viscous, and its reduced viscosity ( η red ) was determined to be 0.54 m 3 /kg. Although proteins and uronic acids may possess surface-active properties, the viscosifying effect of this polymer, which is a typical feature of some commercial hydrocolloids, is more likely to confer its high emulsion-stabilizing qualities.

A Gram-negative, rod-shaped, non-spore-forming bacterium, designated strain R2A36-4T, was isolated from greenhouse soil and subjected to a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Sphingobacteriaceae. Its nearest phylogenetic neighbour was the type strain of [Flexibacter] canadensis CIP 104802T (93.2 % 16S rRNA gene sequence similarity). Strain R2A36-4T and [F.] canadensis CIP 104802T fell in a distinct cluster within the family Sphingobacteriaceae. Strain R2A36-4T contained MK-7 as the predominant quinone. Strain R2A36-4T and [F.] canadensis CIP 104802T had iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 and C15 : 1 ω6c as the major fatty acids. Strain R2A36-4T could be distinguished from [F.] canadensis on the basis of several physiological properties and fatty acid compositions. Based on phenotypic characterization and 16S rRNA gene sequence analysis, strain R2A36-4T represents a novel species within a new genus, for which the name Solitalea koreensis gen. nov., sp. nov. is proposed. The type strain of Solitalea koreensis is strain R2A36-4T (=KACC 12953T=DSM 21342T). It is also proposed that [F.] canadensis be transferred to this genus as Solitalea canadensis comb. nov. (type strain UASM 9DT=ATCC 29591T=CIP 104802T=DSM 3403T=NBRC 15130T=JCM 21819T=KACC 13276T=LMG 8368T).

The bacterial phylogenetic diversities of the bacterial communities in the salt marsh colonized by Spartina alterniflora (SA) and uncultured marsh (UM) along the Yellow Sea of China were analyzed based on the 16S rDNA PCR techniques. Two libraries containing 251 clones of 16S rRNA genes from the Spartina colonized marsh and 283 from UM were constructed by PCR using a bacteria-specific primer 8f and the common primer 1542r. Forty-seven clones from SA and 55 from UM were selected for partial sequencing. A phylogenetic tree was constructed by the alignment analysis of the total environmental DNA sequences. Clones were clustered into 8 divisions of bacteria: (1) Proteobacteria containing 12 genera in beta, gamma, delta and epsilon subdivision; (2) Bacteroidetes containing 7 genera; (3) Planctomycetes containing 2 genera; (4) Firmicutes containing 1 genus; (5) Spirochaetes containing 1 genus; (6) Acidobacteria containing 1 genus; (7) Actinobacteria containing 1 genus; and (8) BRC1 containing 1 genus, as well as 3 groups of bacteria that could not be clustered into any recognized bacterial divisions or candidate divisions. BLAST searches of the GenBank database confirmed that 79.7% of the clones in the two libraries were closely related to the 16S rDNA sequences of the uncultured bacteria with the similarity ≥90%. Among them, Proteobacteria (36.7% and 54.4% of the total clones from the SA and UM libraries, respectively) and Bacteroidetes (30.0% and 18.3%, respectively) are two dominant groups in both the sites. However, some phyla, such as Firmicutes and Actinobacteria , were found at SA site but not at UM site, and vice versa, some phyla, such as Spirochaetes and BRC1, were found at UM, but not at SA. Moreover, the dominant species in each phylum were varied, dependent on whether or not the marsh was colonized by Spartina . For instance, in Bacteroidete , 44.4% clones at SA library were affiliated to Gelidibacter , but 32.7% clones were affiliated to Flexibacter at UM library. In Proteobacteria , the clones at UM library affiliated to δ, γ, ɛ and β-subdivisions were 38.8%, 34.7%, 23.5% and 3.1%, respectively, but at SA library were 30.3%, 47.0%, 13.6% and 9.1%, correspondingly. These results indicated that the bacterial diversity in the salt marsh along the Yellow Sea of China was greatly changed after Spartina colonization.

Fungistasis is one of the important approaches to control soil-borne plant pathogens. Some hypotheses about the mechanisms for soil fungistasis had been established, which mainly focused on the soil bacterial community composition, structure, diversity as well as function. In this study, the bacterial community composition and diversity of a series of soils treated by autoclaving, which coming from the same original soil sample and showing gradient fungistasis to the target soil-borne pathogen fungi Fusarium graminearum, was investigated by soil bacterial 16S rDNA-PCR (polymerase chain reaction) cloning, restriction fragment length polymorphism (RFLP), and sequencing. The results showed that the soil fungistasis capacity was closely correlated with soil bacterial community composition and diversity, such as soil fungistasis declined with the decrease of soil bacterial diversity. Meanwhile, the bacterial community composition and structure were significantly different along the gradient of soil fungistasis tested. alpha-Proteobacteria, beta-Proteobacteria, Flexibacter, and some uncultured soil bacteria were contributed to soil fungistasis in combination with some other special bacteria (Pseudomonas and Acidobacteria) which were know to be key species in suppression of fungal growth.

Bacterial community structure and diversity of Tunisian agricultural soil treated with different amounts of municipal solid waste compost (MSWC) and other fertilizers were studied using DGGE and ARISA fingerprinting methods. Sequence analysis of dominant DGGE bands revealed the presence of three major clusters, Cytophaga/Flexibacter/Bacteroides (CFB) group, Proteobacteria and Acidobacteria group. Using ARISA profiles, dominant populations were assigned to low and high GC Gram positive bacteria, Cyanobacteria, Spirochetes and Cytophagales. The two methods revealed the absence of significant bacterial community shifts related to the different MSWC applications. Moreover, indigenous bacterial population of the used loam-clayey soil was observed to limit proliferation and survival of Proteobacteria, initially dominant in MSWC and farmyard manure. Effectiveness of the two methods for soil bacterial community studying was shown. While DGGE was more accurate for bacterial identification, ARISA was more practical for handling and rapid estimation of dominant bacteria.

The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f-1492r) was selected to specifically amplify bacterial 16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs (Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in rice roots.

A novel, strictly aerobic, heterotrophic, gliding, Gram-negative, oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6220T, was isolated from seawater and studied by using a polyphasic taxonomic approach. The DNA G+C content of strain KMM 6220T was 59.9 mol%. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 1 ω7/iso-C15 : 0 2-OH. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain KMM 6220T formed a cluster with the misclassified strains [Flexibacter] aggregans NBRC 15974 and [Flexibacter] tractuosus NBRC 16035 and with the type strains of Reichenbachiella agariperforans and Roseivirga ehrenbergii with levels of similarity of 95.9, 94.4, 92.0 and 91.8 %, respectively. On the basis of its phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain KMM 6220T is considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Fulvivirga kasyanovii gen. nov., sp. nov. is proposed. The type strain of the type species is KMM 6220T (=CCTCC AB 206119T=KCTC 12832T).

We used a clone library method to investigate changes in the biofilm microflora associated with the conditioning of filter materials in a recirculating water system for the culture of goldfish Carassius auratus . The microbial density was higher in the outer layer of biofilm from filter materials (1.7 × 10 10 –3.0 × 10 10 cells/g) than in the inner layer (1.5 × 10 9 –2.4 × 10 9 cells/g) throughout the experimental period. The clone library method using bacterial 16S rRNA genes collected from the outer layer of filter material yielded sequences from four (day 8), nine (day 15), twelve (day 22) and nine (day 64) taxonomic categories of bacteria including Acidobacteria, Actinobacteria, Bacilli, Bacteroidetes, Flavobacteria, Fusobacteria, Nitrospira, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Sphingobacteria, Verrucomicrobia and unclassified bacteria. The inner layer yielded sequences from six (day 8), eight (day 15), five (day 22) and five (day 64) taxonomic categories of bacteria including Acidobacteria, Actinobacteria, Bacilli, Flavobacteria, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Sphingobacteria, Verrucomicrobia and unclassified bacteria. Bacteria in the outer layer of biofilm belonged predominantly to the genera Acinetobacter , Cetobacterium , Comamonas , Flectobacillus , Flavobacterium , Ideonella and Pseudomonas , whereas those in the inner layer were predominantly members of the genera Flavobacterium , Flexibacter , Ideonella , Janthinobacterium , Pedobacter and Pseudomonas . As the filter materials became conditioned, the population of nitrite-oxidizing bacteria related to Nitrospira was restricted to the outer layer of the biofilm. In addition, phylogenetic analysis indicated the presence of both an indigenous Nitrospira and a distinct type of Nitrospira that appeared after conditioning had begun.

Summary The aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, Cape Evans, McMurdo, Antarctica by an SSU rDNA gene library approach. Our study by sequencing of clones from SSU rDNA gene library approach revealed high diversity in the soil sample from Antarctica. More than 50% of clones showed homology to Cytophaga—Flavobacterium–Bacteroides group; sequences also belonged to α , β , γ proteobacteria , Thermus–Deinococcus and high GC gram-positive group; Phylogenetic analysis of the SSU rDNA clones showed the presence of species belonging to Cytophaga spp., Vitellibacter vladivostokensis, Aequorivita lipolytica, Aequorivita crocea, Flavobacterium spp., Flexibacter sp., Subsaxibacter broadyi, Bacteroidetes, Roseobacter sp., Sphingomonas baekryungensis, Nitrosospira sp., Nitrosomonas cryotolerans, Psychrobacter spp., Chromohalobacter sp., Psychrobacter okhotskensis, Psychrobacter fozii, Psychrobacter urativorans, Rubrobacter radiotolerans, Marinobacter sp., Rubrobacteridae , Desulfotomaculum aeronauticum and Deinococcus sp. The presence of ammonia oxidizing bacteria in Antarctica soil was confirmed by the presence of the amoA gene. Phylogenetic analysis revealed grouping of clones with their respective groups.

A total of 350 tetracycline-resistant (Tcr) bacteria were isolated from livestock feces, farmyard manure (FYM), and soil in Japan. The isolates were classified into 28 established genera of the phyla Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria by studying partial 16S rRNA gene sequences. PCR analysis revealed that 249 of the 350 Tcr isolates contained at least 1 of 15 Tcr genes (tet genes): 140 isolates contained an efflux pump gene and 109 isolates contained a ribosomal protection protein (RPP) gene. The predominant fecal isolates were identified as members of the genera Enterococcus and Escherichia, carrying tet (M) and tet (H), respectively. The predominant soil isolates were identified as members of the genera Burkholderia and Afipia, carrying tet (Z) and tet (B), respectively. This study is the first to describe the presence of tet genes in members of the genera Bordetella, Bradyrhizobium, Burkholderia, Dyella, Flexibacter, Kurthia, Luteibacter, Lysobacter, "Nordella", Ochrobactrum, Pediococcus, Rhodopseudomonas, and Vagococcus. It has revealed that tet genes are distributed in much more diverse phylogenetic groups of bacteria in the environment than has been reported previously.

Nephridial (excretory organ) symbionts are widespread in lumbricid earthworms and the complexity of the nephridial symbiont communities varies greatly between earthworm species. The two most common symbionts are the well-described Verminephrobacter and less well-known Flexibacter-like bacteria. Verminephrobacter are present in almost all lumbricid earthworms, they are species-specific, vertically transmitted, and have presumably been associated with their hosts since the origin of lumbricids. Flexibacter-like symbionts have been reported from about half the investigated earthworms; they are also vertically transmitted. To investigate the evolution of this tri-partite symbiosis, phylogenies for 18 lumbricid earthworm species were constructed based on two mitochondrial genes, NADH dehydrogenase subunit 2 (ND2) and cytochrome c oxidase subunit I (COI), and compared to their symbiont phylogenies based on RNA polymerase subunit B (rpoB) and 16S rRNA genes. The two nephridial symbionts showed markedly different evolutionary histories with their hosts. For Verminephrobacter, clear signs of long-term host-symbiont co-evolution with rare host switching events confirmed its ancient association with lumbricid earthworms, likely dating back to their last common ancestor about 100 million years (MY) ago. In contrast, phylogenies for the Flexibacter-like symbionts suggested an ability to switch to new hosts, to which they adapted and subsequently became species-specific. Putative co-speciation events were only observed with closely related host species; on that basis, this secondary symbiosis was estimated to be minimum 45 MY old. Based on the monophyletic clustering of the Flexibacter-like symbionts, the low 16S rRNA gene sequence similarity to the nearest described species (

Alkaline phosphatase activity was assayed in Flexibacter chinensis to determine the effects of long term starvation stress and the effect of different nutrient amendments to starvation medium on the reactivation of this enzyme. Alkaline phosphatase activity increased at all temperature in starvation medium showing that reactivation could occur in cells previously grown in a high phosphate medium even under conditions where cell viability was declining, suggesting that in Flexibacter, de novo synthesis of enzyme occurs under starvation conditions. Addition of glucose and urea led to reactivation of alkaline phosphatase while the addition of inorganic phosphate had no effect on alkaline phosphatase activity.