Microbacterium Sulfonylureivorans Sp. Nov., Isolated From A Sulfonylurea Herbicides Degrading Consortium

A novel Gram-stain positive, aerobic, motile, rod-shaped bacterium, designated strain LAM7116T, was isolated from a sulfonylurea herbicides degrading consortium enriched with the birch forest soil from Xinjiang. The optimal temperature and pH for the growth of strain LAM7116T were 35 °C and 7.0, respectively. Strain LAM7116T could grow in the presence of NaCl up to 4% (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain LAM7116T was closely related to the members of the genus Microbacterium, with the highest similarity to Microbacterium flavescens DSM 20643T (98.1%) and Microbacterium kitamiense Kitami C2T (98.1 %). Strain LAM7116T formed a distinct subclade with M. flavescens DSM 20643T within the genus Microbacterium in the 16S rRNA gene phylogenetic trees. The genomic DNA G+C content of LAM7116T was 69.9 mol%. The DNA-DNA hybridization (DDH) value between strain LAM7116T and M. flavescens DSM 20643T was 27.20 %. The average nucleotide identity (ANI) value was 83.96 % by comparing the draft genome sequences of strain LAM7116T and M. flavescens DSM 20643T. The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C17:0 and iso-C16:0. The respiratory quinones of strain LAM7116T were MK-13 and MK-14. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified lipid and an unidentified glycolipid. Based on the phenotypic characteristics and genotypic analyses, we propose that strain LAM7116T represents a novel species, for which the name Microbacterium sulfonylureivorans sp. nov. was proposed. The type strain is LAM7116T (=CGMCC 1.16620T =JCM 32823T). Strain LAM7116T secreted auxin IAA and grew well in Ashby nitrogen-free culture medium. Genomic results showed that strain LAM7116T carried the nitrogenase iron protein (nifU and nifR3) gene, which indicated that strain LAM7116T has the potential to fix nitrogen and promote plant growth. At the same time, the strain LAM7116T can degrade nicosulfuron (a kind of sulfonylurea herbicides) by using glucose as carbon source, microbial degradation of nicosulfuron is the primary process of removing nicosulfuron from environments, and biodegradation is the most effective and environmentally friendly. Microbacterium sulfonylureivorans sp. nov. LAM7116T is a potential candidate for the biofertilizers of organic agriculture areas, having broad prospects for using, and may possess potential to be used in bioremediation of nicosulfuron-contaminated environments.

Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO2 Capture by a Surface-Exposed [Fe4S4] Cluster

ABSTRACT Nitrogenase iron (Fe) proteins reduce CO2 to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-Å crystal structure of the Fe protein from Methanosarcina acetivorans (MaNifH), which is generated in the presence of a reductant, dithionite, and an alternative CO2 source, bicarbonate. Structural analysis of this methanogen Fe protein species suggests that CO2 is possibly captured in an unactivated, linear conformation near the [Fe4S4] cluster of MaNifH by a conserved arginine (Arg) pair in a concerted and, possibly, asymmetric manner. Density functional theory calculations and mutational analyses provide further support for the capture of CO2 on MaNifH while suggesting a possible role of Arg in the initial coordination of CO2 via hydrogen bonding and electrostatic interactions. These results provide a useful framework for further mechanistic investigations of CO2 activation by a surface-exposed [Fe4S4] cluster, which may facilitate future development of FeS catalysts for ambient conversion of CO2 into valuable chemical commodities. IMPORTANCE This work reports the crystal structure of a previously uncharacterized Fe protein from a methanogenic organism, which provides important insights into the structural properties of the less-characterized, yet highly interesting archaeal nitrogenase enzymes. Moreover, the structure-derived implications for CO2 capture by a surface-exposed [Fe4S4] cluster point to the possibility of developing novel strategies for CO2 sequestration while providing the initial insights into the unique mechanism of FeS-based CO2 activation.

Nitrogen Fixation by Vibrio parahaemolyticus and Its Implications for a New Ecological Niche

ABSTRACT A Vibrio parahaemolyticus strain isolated from the rhizosphere of the ecosystem dominant estuarine grass, Spartina alterniflora, was characterized and shown to carry nifH, the gene encoding the nitrogenase iron protein, and to fix N2. Nitrogen fixation may contribute substantially to the adaptability, niche breadth, and ecological significance of V. parahaemolyticus.