Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary.

Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.

Altererythrobacter dongtanensis sp. nov., isolated from a tidal flat.

A Gram-negative, rod-shaped and non-spore-forming bacterial strain, JM27(T), was isolated from a tidal flat of Dongtan Wetland, Chongming Island, China. The strain formed smooth yellow colonies on R2A plates. Growth occurred at 10-37 °C (optimum, 30-37 °C), at pH 6.0-10.0 (optimum, pH 7.0-9.0) and in the presence of 0-1 % NaCl (optimum, 0 %). Catalase test was positive and oxidase test was negative. Ubiquinone 10 (Q10) was the major respiratory quinone. C18:0ω7c and C17:1ω6c were the most abundant fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. The DNA G+C content of strain JM27(T) was 66.4 mol%. The 16S rRNA gene sequence of the isolate showed highest similarity to that of Altererythrobacter marinus H32(T) (96.4 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Altererythrobacter of the family Erythrobacteraceae of the class Alphaproteobacteria. On the basis of phylogenetic analysis, whole-cell fatty acids, polar lipid compositions, and biochemical and physiological characteristics, strain JM27(T) is proposed to represent a novel species of the genus Altererythrobacter for which the name Altererythrobacter dongtanensis sp. nov. is proposed. The type strain is JM27(T) ( = KCTC 22672(T)  = CCTCC AB 209199(T)).

Flavobacterium dongtanense sp. nov., isolated from the rhizosphere of a wetland reed.

Two strains of Gram-reaction-negative, rod-shaped, non-spore-forming, non-motile, aerobic bacteria, designated LW30(T) and LW29, were isolated from the rhizosphere of a wetland reed in Dongtan, Chongming Island, China. The strains formed pale-yellow colonies on R2A plates. Growth occurred at 4-37 °C (optimum 30 °C), at pH 6-9 (optimum pH 7-8) and in the presence of 0-3 % (w/v) NaCl (optimum 0-1 %). Oxidase and catalase activities and flexirubin-type pigments were absent. MK-6 was the major respiratory quinone. The major fatty acids were iso-C(15 : 0), C(15 : 0), iso-C(15 : 1) G and iso-C(17 : 1)ω9c. Strains LW30(T) and LW29 could be differentiated from related species by several phenotypic characteristics. Phylogenetic analyses based on 16S rRNA gene sequences placed strains LW30(T) and LW29 in the genus Flavobacterium with high sequence similarity to Flavobacterium cheniae NJ-26(T) (94.0 %) and Flavobacterium indicium GPTSA 100-9(T) (93.9 %). Together with F. indicium GPTSA 100-9(T), strains LW30(T) and LW29 formed a distinct group in the phylogenetic tree. The DNA G+C content was 30 mol%. On the basis of the phylogenetic and phenotypic evidence, strains LW30(T) and LW29 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium dongtanense sp. nov. is proposed. The type strain is LW30(T) (=KCTC 22671(T) =CCTCC AB 209201(T)).

Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor.

Two Gram-negative, rod-shaped, motile, aerobic bacterial strains designated HY-14(T) and HY-24 were isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. The strains could not grow with 5 % (w/v) NaCl, did not produce acid from d-glucose or utilize d-glucose, gluconate or citrate as a sole carbon source. Summed feature 3 and C(16 : 0) were the most abundant fatty acids; hydroxyl fatty acids C(12 : 0) 3-OH and C(10 : 0) 3-OH were also present. Fatty acid C(12 : 0) 2-OH was absent. The DNA G+C contents of strains HY-14(T) and HY-24 were 50.6+/-0.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HY-14(T) and HY-24 formed a monophyletic clade within the genus Pseudomonas. The highest sequence similarities were to Pseudomonas pseudoalcaligenes DSM 50188(T) (95.9 %). On the basis of phenotypic and phylogenetic properties, strains HY-14(T) and HY-24 are proposed as a novel species of the genus Pseudomonas, for which the name Pseudomonas caeni sp. nov. is proposed. The type strain is HY-14(T) (=KCTC 22292(T)=CCTCC AB208156(T)).

Henriciella marina gen. nov., sp. nov., a novel member of the family Hyphomonadaceae isolated from the East Sea.

A bacterial strain, designated Iso4(T), was isolated from the East Sea of Korea and was subjected to a poly-phasic taxonomy study including phenotypic and chemotaxonomic characteristics as well as 16S rRNA gene sequence analysis. Cells of the strain were Gram-negative, motile, non-budding, non-stalked, and strictly aerobic. Strain Iso4(T) grew optimally at 20 degrees C in the presence of 1 approximately 2% (w/v) NaCl and at pH 6.9 approximately 7.6. The major respiratory quinone was Q-10 and the major cellular fatty acids were C(18:1) omega 7c (53.5%), C(17:1) omega 5c (11.7%), C(17:1) omega 6c (8.1%), C(16:0) (7.8%), C(17:0) (4.8%), C(15:0) (2.9%), and C(16:1) omega 5c (2.2%). The DNA G+C content of strain Iso4(T) was 56.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Iso4(T) formed a monophyletic clade in the family Hyphomonadaceae, supported by high bootstrap value and was most closely related to the genus Hyphomonas (92 approximately 94%), a member of marine bacteria in the family. The phenotypic, genotypic, and chemotaxonomic evidences also suggest strain Iso4(T) represents a novel genus and species in the family Hyphomonadaceae, for which the name Henriciella gen. nov., sp. nov. is proposed. The type strain is Iso4(T) (=KCTC 12513(T) =DSM 19595(T) =JCM 15116(T)).

Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea.

A Gram-negative, non-spore-forming, non-motile, yellow-pigmented, strictly aerobic bacterial strain, designated En5(T), was isolated from the East Sea of Korea and was subjected to a polyphasic taxonomy study. Strain En5(T) grew optimally at 30 degrees C, in the presence of 1-3 % (w/v) NaCl and at pH 5.3-7.6. The major respiratory lipoquinone was MK-6 and the major fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and iso-C(17 : 1)omega9c. The DNA G+C content of strain En5(T) was 30.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain En5(T) formed a distinct evolutionary lineage within the family Flavobacteriaceae and shared 93 % sequence similarity with the type strains of both Galbibacter mesophilus and Zhouia amylolytica. On the basis of its phenotypic and phylogenetic properties, strain En5(T) is suggested to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Joostella marina gen. nov., sp. nov. is proposed. The type strain is En5(T) (=KCTC 12518(T)=DSM 19592(T)=CGMCC 1.6973(T)).

Degradation of 2,6-di-tert-butylphenol by an isolated high-efficiency bacterium strain.

An aerobic bacterium strain, F-3-4, capable of effectively degrading 2, 6-ditert-butylphenol (2, 6-DTBP), was isolated and screened out from an acrylic fiber wastewater and the biofilm in the wastewater treatment facilities. This strain was identified as Alcaligenes sp. through morphological, physiological and biochemical examinations. After cultivation, the strain was enhanced by 26.3% in its degradation capacity for 2,6-DTBP. Results indicated that the strain was able to utilize 2,6-DTBP, lysine, lactamine, citrate, n-utenedioic acid and malic acid as the sole carbon and energy source, alkalinize acetamide, asparagine, L-histidine, acetate, citrate and propionate, but failed to utilize glucose, D-fructose, D-seminose, D-xylose, serine and phenylalanine as the sole carbon and energy source. The optimal growth conditions were determined to be: temperature 37 degrees C, pH 7.0, inoculum size 0.1% and shaker rotary speed 250 r/min. Under the optimal conditions, the degradation kinetics of 2,6-DTBP with an initial concentration of 100 mg/L was studied. Results indicated that 62.4% of 2,6-DTBP was removed after 11 d. The degradation kinetics could be expressed by Eckenfelder equation with a half life of 9.38 d. In addition, the initial concentration of 2,6-DTBP played an important role on the degradation ability of the strain. The maximum initial concentration of 2,6-DTBP was determined to be 200 mg/L. Above this level, the strain was overloaded and exhibited significant inhibition.

[The degradation characteristics of degrading bacterium of 2,6-di-tert-butylphenol].

A degrading bacterial strain F-3-4 for 2,6-Di-tert-butylphenol (2,6-DTBP) was isolated from biofilm in acrylic fiber wastewater treatment structures. By acclimation, its capacity for degradation of 2,6-DTBP was enhanced by 26%. It was identified as Alcaligenes sp. according to morphological, physiological and biochemical characters. By tests in shaking flasks, the effects of the conditions of growth was studied, and it was determined that the optimum conditions of growth for the strain was 37 degrees C, pH 7.0 and inoculum amount 0.1%. Under these conditions, the kinetics of degradation for 2,6-DTBP of initial concentration 100 mg/L was studied, and the result indicated that the removal rate of 2,6-DTBP within 11 days was 62.4%, and the degradation process followed Eckenfelder kinetics. The half life of 2,6-DTBP was 9.38 days. The effect of initial concentration on degradation ability of the strain also was investigated. The results showed that the optimum initial concentration was 200 mg/L. When the initial concentrations were below it, the growth of strain and removal of 2,6-DTBP increased with the increase of initial concentration, while when above the value, they were inhibited.