Lianghui Ji

Disruption of Putrescine Biosynthesis in Shewanella oneidensis Enhances Biofilm Cohesiveness and Performance in Cr(VI) Immobilization

ABSTRACT Although biofilm-based bioprocesses have been increasingly used in various applications, the long-term robust and efficient biofilm performance remains one of the main bottlenecks. In this study, we demonstrated that biofilm cohesiveness and performance of Shewanella oneidensis can be enhanced through disrupting putrescine biosynthesis. Through random transposon mutagenesis library screening, one hyperadherent mutant strain, CP2-1-S1, exhibiting an enhanced capability in biofilm formation, was obtained. Comparative analysis of the performance of biofilms formed by S. oneidensis MR-1 wild type (WT) and CP2-1-S1 in removing dichromate (Cr2O7 2−), i.e., Cr(VI), from the aqueous phase showed that, compared with the WT biofilms, CP2-1-S1 biofilms displayed a substantially lower rate of cell detachment upon exposure to Cr(VI), suggesting a higher cohesiveness of the mutant biofilms. In addition, the amount of Cr(III) immobilized by CP2-1-S1 biofilms was much larger, indicating an enhanced performance in Cr(VI) bioremediation. We further showed that speF, a putrescine biosynthesis gene, was disrupted in CP2-1-S1 and that the biofilm phenotypes could be restored by both genetic and chemical complementations. Our results also demonstrated an important role of putrescine in mediating matrix disassembly in S. oneidensis biofilms.

Influence of outer membrane c-type cytochromes on particle size and activity of extracellular nanoparticles produced by Shewanella oneidensis

The metal‐reducing bacterium Shewanella oneidensis is capable of reducing various metal(loid)s and produces nanoparticles (NPs) extracellularly, in which outer membrane c‐type cytochromes (OMCs) have been suggested to play important roles. The objective of this study was to investigate the influence of the OMCs, that is, MtrC and OmcA, on the size and activity of the extracellular silver NPs (AgNPs) and silver sulfide NPs (Ag2S NPs) produced by S. oneidensis MR‐1. We found that (i) the lack of OMCs on S. oneidensis cell surface decreased the particle size of the extracellular biogenic AgNPs and Ag2S NPs; (ii) the biogenic AgNPs from the mutant lacking OMCs showed higher antibacterial activity; and (iii) the biogenic Ag2S NPs from the mutant lacking OMCs exhibited higher catalytic activity in methylviologen reduction. The results suggest that it may be possible to control particle size and activity of the extracellular biogenic NPs via controlled expression of the genes encoding surface proteins. In addition, we also reveal that in extracellular biosynthesis of NPs the usually neglected non‐cell‐associated NPs could have high catalytic activity, highlighting the need of novel methods that can efficiently retain extracellular NPs in the biosynthesis processes. Biotechnol. Bioeng. 2013; 110: 1831–1837.

Pleomorphomonas diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L.

A novel aerobic, non-motile, pleomorphic, Gram-negative and nitrogen-fixing bacterial strain, designated R5-392(T), was isolated from surface-sterilized root tissue of Jatropha curcas. The organism grew optimally at 30 °C in media containing 1 % (w/v) NaCl and at pH 6.0-8.0. The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 63.2 mol%. Analysis of the 16S rRNA gene sequence suggested that strain R5-392(T) is affiliated with the order Rhizobiales within the class Alphaproteobacteria and is most closely related to Pleomorphomonas oryzae F-7(T) (98.8 % similarity) and Pleomorphomonas koreensis Y9(T) (98.3 % similarity). Analysis of partial nifH gene sequences also revealed a monophyletic lineage within the class Alphaproteobacteria, and strain R5-392(T) was most closely related to P. oryzae F-7(T) (98 %). Highest nitrogenase activity was detected in the presence of low-level organic nitrogen or in the presence of nitrogenase co-factors (Fe/Mo) in N-free media. Phenotypic and chemotaxonomic data suggest that strain R5-392(T) represents a novel species within the genus Pleomorphomonas, for which the name Pleomorphomonas diazotrophica sp. nov. is proposed. The type strain is R5-392(T) ( = KACC 16233(T) = DSM 25022(T)).

Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L.

A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae) and Acidothermus (family Acidothermaceae) and the other by members of the genera Geodermatophilus, Blastococcus and Modestobacter (family Geodermatophilaceae). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C18 : 1ω9c, anteiso-C17 : 0 and C17 : 1ω8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650(T) represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650(T) ( = DSM 45627(T) = KACC 16232(T)).

Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov., leaf-associated bacteria isolated from Jatropha curcas L.

Four orange-pigmented isolates, L7-456, L7-484(T), L9-479 and L9-753(T), originating from surface-sterilized leaf tissues of Jatropha curcas L. cultivars were characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all four isolates belong to the genus Aureimonas. In these analyses, strain L7-484(T) appeared to be most closely related to Aureimonas ureilytica 5715S-12(T) (95.7 % sequence identity). The 16S rRNA gene sequences of strains L7-456, L9-479 and L9-753(T) were found to be identical and also shared the highest similarity with A. ureilytica 5715S-12(T) (97.5 %). Both L7-484(T) and L9-753(T) contained Q-10 and Q-9 as predominant ubiquinones and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, sulfoquinovosyldiacylglycerol and an aminophospholipid as the major polar lipids. C18 : 1ω7c and C16 : 0 were the major fatty acids. Similar to other species in the genus Aureimonas, hydroxylated fatty acids (e.g. C18 : 1 2-OH) and cyclic fatty acids (C19 : 0 cyclo ω8c) were also present. The DNA G+C contents of L7-484(T) and L9-753(T) were 66.1 and 69.4 mol%, respectively. Strains L7-484(T) and L9-753(T) exhibited less than 40 % DNA-DNA hybridization both between themselves and to A. ureilytica KACC 11607(T). Our results support the proposal that strain L7-484(T) represents a novel species within the genus Aureimonas, for which the name Aureimonas jatrophae sp. nov. is proposed, and that strains L9-753(T), L7-456 ( = KACC 16229  = DSM 25023) and L9-479 ( = KACC 16228  = DSM 25024) represent a second novel species within the genus, for which the name Aureimonas phyllosphaerae sp. nov. is proposed. The type strains of Aureimonas jatrophae sp. nov. and Aureimonas phyllosphaerae sp. nov. are respectively L7-484(T) ( = KACC 16230(T)  = DSM 25025(T)) and L9-753(T) ( = KACC 16231(T)  = DSM 25026(T)).

Complete Genome Sequence of Enterobacter sp. Strain R4-368, an Endophytic N-Fixing Gammaproteobacterium Isolated from Surface-Sterilized Roots of Jatropha curcas L.

ABSTRACT Enterobacter sp. strain R4-368 is one of the few characterized Jatropha endophytic diazotrophic bacteria and was isolated from surface-sterilized roots. This bacterium shows strong growth-promoting effects, being able to increase plant biomass and seed yields. Enterobacter sp. R4-368 is the second fully sequenced diazotrophic Enterobacter species. The sequence information shall facilitate the elucidation of the molecular mechanisms of plant growth promotion, nitrogen fixation in nonlegume plant species, and evolution of biological nitrogen fixation systems.

Draft Genome Sequences of Rhodosporidium toruloides Strains ATCC 10788 and ATCC 10657 with Compatible Mating Types

ABSTRACT Rhodosporidium toruloides ATCC 10788 (haploid, A1 mating type) and ATCC 10657 (haploid, A2 mating type) were derived from the same diploid parent strain Rhodotorula glutinis ATCC 90781 and are important strains for metabolic engineering. Draft genome sequences of both strains are reported here. The current assembly of strain ATCC 10788 comprises 61 scaffolds with a total size of 20.75 Mbp and a GC content of 62.01%, while that of strain ATCC 10657 comprises 137 scaffolds with a total size of 21.49 Mbp and a GC content of 61.81%. Genome annotation predicts 7,730 and 7,800 protein encoding genes for strain ATCC 10788 and strain ATCC 10657, respectively.

Draft Genome Sequence of Methylobacterium sp. Strain L2-4, a Leaf-Associated Endophytic N-Fixing Bacterium Isolated from Jatropha curcas L.

ABSTRACT Methylobacterium sp. strain L2-4 is an efficient nitrogen-fixing leaf colonizer of biofuel crop Jatropha curcas. This strain is able to greatly improve the growth and seed yield of Jatropha curcas and is the second reported genome sequence of plant growth-promoting bacteria isolated from Jatropha curcas.

Chania multitudinisentens gen. nov., sp. nov., an N-acyl-homoserine-lactone-producing bacterium in the family Enterobacteriaceae isolated from landfill site soil.

Phylogenetic and taxonomic characterization was performed for bacterium RB-25T, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20-37 °C at pH 5-8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25T formed a distinct lineage within the family Enterobacteriaceae of the class Gammaproteobacteria. It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pantoea rwandensis LMG 26275T (96.6 %), Rahnella aquatilis CIP 78.65T (96.5 %), Pectobacterium betavasculorum ATCC 43762T (96.4 %), Pantoea rodasii LMG 26273T (96.3 %), Gibbsiella dentisursi NUM 1720T (96.3 %) and Serratia glossinae C1T (96.2 %). Multilocus sequence analyses based on fusA, pyrG, rplB, rpoB and sucA sequences showed a clear distinction of strain RB-25T from the most closely related genera. Isolate RB-25T could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25T represents a novel species of a new genus, for which the name Chaniamultitudinisentens gen. nov., sp. nov. is proposed. The type strain is RB-25T (=DSM 28811T=LMG 28304T).

Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.

Two yellow-pigmented isolates, S5-249T and L9-754T, originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249T and L9-754T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6-97.2 % sequence similarity with those of other species in the genus Sphingomonas, suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249T and L9-754T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249T and L9-754T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249T and L9-754T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937T and the two type strains (S5-249T and L9-754T) were 72.31 and 77.73 %, respectively. Digital DNA-DNA hybridization (dDDH) studies between the novel strains (S5-249T and L9-754T) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249T=DSM 27345T=KACC 17593T) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754T=DSM 27347T=KACC 17595T).