Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T.

Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.

Genome analysis of Thauera chlorobenzoica strain 3CB-1T, a halobenzoate-degrading bacterium isolated from aquatic sediment.

The genus Thauera is characterized by several species and strains with the ability to degrade a variety of aromatic compounds under denitrifying conditions. Thauera chlorobenzoica strain 3CB-1T, isolated from river sediment, has the unique ability to degrade a variety of halobenzoates, such as 3-chlorobenzoate, 3-bromobenzoate, 3-iodobenzoate, and 2-fluorobenzoate, coupled to nitrate reduction. The genome of T. chlorobenzoica strain 3CB-1T has been sequenced, allowing us to gain insights into the molecular basis for the anaerobic degradation of (halo)aromatic compounds. The 3.77-Mb genome contains 3584 genes; 3514 are protein-coding genes of which 198 are likely associated with degradation of aromatic compounds. It has a G + C content of 67.25%. The genome contains two sets of CoA reductase gene clusters, both belonging to class I benzoate-CoA reductases (BCRs). The genes in one of the two clusters differ from the typical BCRs, with low sequence identities, suggesting they might have different substrate specificities. The genome also contains four benzoate-CoA ligase genes. One likely encodes a 3-hydroxybenzoate-CoA ligase, and two others group together with benzoate-CoA ligases from Thauera aromatica. The fourth has a 77% identity to the mbdA gene from Azoarcus sp. CIB, is absent in the T. aromatica genome, and potentially encodes a halobenzoate-CoA ligase. 3-Chlorobenzoate is reductively dechlorinated in T. chlorobenzoica by a benzoyl-CoA reductase.

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment.

Sedimenticola selenatireducens strain AK4OH1T (= DSM 17993T = ATCC BAA-1233T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. The draft genome comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report the main features of the genome of S. selenatireducens strain AK4OH1T.

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples.

The shift of microbial communities during a transition from mesophilic anaerobic digestion (MAD) to thermophilic anaerobic digestion (TAD) was characterized in two treatments. One treatment was inoculated with sludge and the other was inoculated with manure. In this study, methane was produced both in MAD and TAD, but TAD has slightly more methane produced than MAD. A broad phylogenetic spectrum of bacterial, archaeal, and fungal taxa at thermophilic conditions was detected. Coprothermobacter, Bacillus, Haloplasma, Clostridiisalibacter, Methanobacterium, Methanothermobacter, Saccharomycetales, Candida, Alternaria, Cladosporium, and Penicillium were found almost exclusively in TAD, suggesting their adaptation to thermophilic conditions and ecological roles in digesting the organic compounds. The characterization of the lesser-known fungal community revealed that fungi probably constituted an important portion of the overall community within TAD and contributed to this process by degrading complex organic compounds. The shift of the microbial communities between MAD and TAD implied that temperature drastically affected the microbial diversity in anaerobic digestion. In addition, the difference in microbial communities between sludge and manure indicated that different source of inoculum also affected the microbial diversity and community.

Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation.

Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.

Clinical assessment of early tooth demineralization using polarization sensitive optical coherence tomography.

INTRODUCTION: The aims of this study were to test the hypothesis that polarization sensitive-optical coherence tomography (PS-OCT) can be used to non-destructively measure and quantify the severity of the early demineralization of enamel on buccal and occlusal surfaces and assess the inhibitory effect of fluoride varnish in vivo. METHODS: A split mouth design was used to assess the effects of fluoride varnish on inhibiting dissolution on 20 test subjects. Orthodontic bands with a buccal window were cemented on the premolars and small incisions were produced on occlusal surfaces to serve as sites for plaque retention for enhanced demineralization. Bands were removed after 30 days and PS-OCT scans were acquired in vivo of occlusal and buccal areas. Teeth were extracted, sectioned, and analyzed using polarized light microscopy (PLM) and transverse microradiography (TMR) for comparison with the PS-OCT images. RESULTS: High contrast PS-OCT images were acquired of both occlusal and buccal surfaces in vivo. Both occlusal and buccal surfaces, showed a significant difference (P < 0.05) in the integrated reflectivity (ΔR) between the "sound" and "carious" enamel groups. Although the mineral loss (ΔZ) and ΔR measured using TMR and PS-OCT were less for the fluoride varnish-treated buccal surfaces the difference was not statistically significant (P > 0.05). CONCLUSIONS: Our results indicate that PS-OCT can non-destructively measure early enamel demineralization on the buccal and occulsal surfaces in vivo.

Selective removal of composite sealants with near-ultraviolet laser pulses of nanosecond duration.

It is often necessary to replace pit and fissure sealants and composite restorations. This task is complicated by the necessity for complete removal of the remaining composite to enable suitable adhesion of new composite. Previous studies have shown that 355-nm laser pulses from a frequency-tripled Nd:YAG laser can selectively remove residual composite after orthodontic bracket removal on enamel surfaces. Our objective is to determine if such laser pulses are suitable for selective removal of composite pit and fissure sealants and restorations. Optical coherence tomography is used to acquire optical cross sections of the occlusal topography nondestructively before sealant application, after sealant application, and after sealant removal. Thermocouples are used to monitor the temperature in the pulp chamber during composite removal under clinically relevant ablation rates, i.e., 30 Hz and 30 mJ/pulse. At an irradiation intensity of 1.3 J/cm2, pit and fissure sealants are completely removed without visible damage to the underlying enamel. At intensities above 1.5 J/cm2, incident laser pulses remove the resin layer while at the same time preferentially etching the surface of the enamel. Temperature excursions in the pulp chamber of extracted teeth are limited to less than 5 degrees C if air-cooling is used during the rapid removal (1 to 2 min) of sealants, water-cooling is not necessary. Selective removal of composite restorative materials is possible without damage to the underlying sound tooth structure.