Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110

Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions

<i>Dehalococcoides mccartyi</i> Strain JNA in Pure Culture Extensively Dechlorinates Aroclor 1260 According to Polychlorinated Biphenyl (PCB) Dechlorination Process N

We isolated <i>Dehalococcoides mccartyi</i> strain JNA from the JN mixed culture which was enriched and maintained using the highly chlorinated commercial PCB mixture Aroclor 1260 for organohalide respiration. For isolation we grew the culture in minimal liquid medium with 2,2′,3,3′,6,6′-hexachlorobiphenyl (236–236-CB)­(20 μM) as respiratory electron acceptor. We repeatedly carried out serial dilutions to extinction and recovered dechlorination activity from transfers of 10^–7 and 10^–8 dilutions. Fluorescence microscopy, DGGE and RFLP analysis of PCR amplified16S rRNA genes, and multilocus sequence typing of three housekeeping genes confirmed culture purity. No growth occurred on complex media. JNA dechlorinated most hexa- and heptachlorobiphenyls in Aroclor 1260 (50 μg/mL) leading to losses of 51% and 20%, respectively. Dechlorination was predominantly from flanked <i>meta</i> positions of <u>3</u>4-, 2<u>3</u>4-, 2<u>3</u>5-, 2<u>3</u>6-, 24<u>5</u>-, 2<u>3</u>45-, 2<u>3</u>46-, and 23<u>5</u>6-chlorophenyl rings, as indicated by the underscores. The major products were 24–24-CB, 24–26-CB, 24–25-CB, and 25–26-CB. We identified 85 distinct PCB dechlorination reactions and 56 different PCB dechlorination pathways catalyzed by JNA. Dechlorination pathways were confirmed by mass balance of substrates and products. This dechlorination pattern matches PCB Dechlorination Process N. JNA is the first pure culture demonstrated to carry out this extensive and environmentally relevant PCB dechlorination pattern

<i>Dehalococcoides mccartyi</i> Strain JNA Dechlorinates Multiple Chlorinated Phenols Including Pentachlorophenol and Harbors at Least 19 Reductive Dehalogenase Homologous Genes

Pentachlorophenol and other chlorinated phenols are highly toxic ubiquitous environmental pollutants. Using gas chromatographic analysis we determined that <i>Dehalococcoides mccartyi</i> strain JNA in pure culture dechlorinated pentachlorophenol to 3,5-dichlorophenol (DCP) via removal of the <i>ortho</i> and <i>para</i> chlorines in all of the three possible pathways. In addition, JNA dechlorinated 2,3,4,6-tetrachlorophenol via 2,4,6-trichlorophenol (TCP) and 2,4,5-TCP to 2,4-DCP and 3,4-DCP, respectively, and dechlorinated 2,3,6-TCP to 3-chlorophenol (CP) via 2,5-DCP. JNA converted 2,3,4-TCP to 3,4-DCP and 2,4-DCP by <i>ortho</i> and <i>meta</i> dechlorination, respectively. 2,3-DCP was dechlorinated to 3-CP, and, because cultures using it could be transferred with a low inoculum (0.5 to 1.5% vol/vol), it may act as an electron acceptor to support growth. Using PCR amplification with targeted and degenerate primers followed by cloning and sequencing, we determined that JNA harbors at least 19 reductive dehalogenase homologous (<i>rdh</i>) genes including orthologs of <i>pcb</i>A4 and <i>pcb</i>A5, <i>pce</i>A, and <i>mbr</i>A, but not <i>tce</i>A or <i>vcr</i>A. Many of these genes are shared with <i>D. mccartyi</i> strains CBDB1, DCMB5, GT, and CG5. Strain JNA has previously been shown to extensively dechlorinate the commercial polychlorinated biphenyl (PCB) mixture Aroclor 1260. Collectively the data suggest that strain JNA may be well adapted to survive in sites contaminated with chlorinated aromatics and may be useful for <i>in situ</i> bioremediation