Qing X. Li

Bacterial Degradation of Aromatic Compounds

Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

We report the complete genome sequence of the deep-sea γ-proteobacterium, Idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the Lōihi submarine volcano, Hawaii. The I. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A comparison of I. loihiensis to the genomes of other γ-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of sugar transport systems and certain enzymes of sugar metabolism. This finding suggests that I. loihiensis relies primarily on amino acid catabolism, rather than on sugar fermentation, for carbon and energy. Enzymes for biosynthesis of purines, pyrimidines, the majority of amino acids, and coenzymes are encoded in the genome, but biosynthetic pathways for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr was confirmed by in vivo experiments. The I. loihiensis genome contains a cluster of 32 genes encoding enzymes for exopolysaccharide and capsular polysaccharide synthesis. It also encodes diverse peptidases, a variety of peptide and amino acid uptake systems, and versatile signal transduction machinery. We propose that the source of amino acids for I. loihiensis growth are the proteinaceous particles present in the deep sea hydrothermal vent waters. I. loihiensis would colonize these particles by using the secreted exopolysaccharide, digest these proteins, and metabolize the resulting peptides and amino acids. In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem.

Simultaneous heterotrophic nitrification and aerobic denitrification by bacterium Rhodococcus sp. CPZ24.

Rhodococcus sp. CPZ24 was isolated from swine wastewater and identified. Batch (0.25 L flask) experiments of nitrogen removal under aerobic growth conditions showed complete removal of 50 mg L(-1) ammonium nitrogen within 20 h, while nitrate nitrogen removal reached 67%. A bioreactor (50 L) was used to further assess the heterotrophic nitrification and aerobic denitrification abilities of Rhodococcus sp. CPZ24. The results showed that 85% of the ammonium nitrogen (100 mg L(-1)) was transformed to nitrification products (NO(3)(-)-N and NO(2)(-)-N) (13%), intracellular nitrogen (24%), and gaseous denitrification products (48%) within 25 h. The ammonium nitrogen removal rate was 3.4 mg L(-1)h(-1). The results indicate that the strain CPZ24 carries out simultaneous nitrification and denitrification, demonstrating a potential use of the strain for wastewater treatment.

Insecticidal activity of basil oil, trans-anethole, estragole, and linalool to adult fruit flies of Ceratitis capitata, Bactrocera dorsalis, and Bactrocera cucurbitae.

ABSTRACT Basil oil and its three major active constituents (trans-anethole, estragole, and linalool) obtained from basil (Oscimum basilicum L.) were tested on three tephritid fruit fly species [Ceratitis capitata (Wiedemann), Bactrocera dorsalis (Hendel), and Bactrocera cucurbitae (Coquillett)] for insecticidal activity. All test chemicals acted fast and showed a steep dose-response relationship. The lethal times for 90% mortality/knockdown (LT90) of the three fly species to 10% of the test chemicals were between 8 and 38 min. The toxic action of basil oil in C. capitata occurred significantly faster than in B. cucurbitae but slightly faster than in B. dorsalis. Estragole acted faster in B. dorsalis than in C. capitata and B. cucurbitae. Linalool action was faster in B. dorsalis and C. capitata than in B. cucurbitae. trans-Anethole action was similar to all three species. Methyl eugenol acted faster in C. capitata and B. cucurbitae than in B. dorsalis. When linalool was mixed with cuelure (attractant to B. cucurbitae male), its potency to the three fly species decreased as the concentration of cuelure increased. This was due to linalool hydrolysis catalyzed by acetic acid from cuelure degradation, which was confirmed by chemical analysis. When methyl eugenol (B. dorsalis male attractant) was mixed with basil oil, trans-anethole, estragole, or linalool, it did not affect the toxicity of basil oil and linalool to B. dorsalis, but it did significantly decrease the toxicity of trans-anethole and estragole. Structural similarity between methyl eugenol and trans-anethole and estragole suggests that methyl eugenol might act at a site similar to that of trans-anethole and estragole and serve as an antagonist if an action site exists. Methyl eugenol also may play a physiological role on the toxicity reduction.

Degradation pathways of phenanthrene by Sinorhizobium sp. C4.

Sinorhizobium sp. C4 was isolated from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Hilo, HI, USA. This isolate can utilize phenanthrene as a sole carbon source. Sixteen metabolites of phenanthrene were isolated and identified, and the metabolic map was proposed. Degradation of phenanthrene was initiated by dioxygenation on 1,2- and 3,4-C, where the 3,4-dioxygenation was dominant. Subsequent accumulation of 5,6- and 7,8-benzocoumarins confirmed dioxygenation on multiple positions and extradiol cleavage of corresponding diols. The products were further transformed to 1-hydroxy-2-naphthoic acid and 2-hydroxy-1-naphthoic acid then to naphthalene-1,2-diol. In addition to the typical degradation pathways, intradiol cleavage of phenanthrene-3,4-diol was proposed based on the observation of naphthalene-1,2-dicarboxylic acid. Degradation of naphthalene-1,2-diol proceeded through intradiol cleavage to produce trans-2-carboxycinnamic acid. Phthalic acid, 4,5-dihydroxyphthalic acid, and protocatechuic acid were identified as probable metabolites of trans-2-carboxycinnamic acid, but no trace salicylic acid or its metabolites were found. This is the first detailed study of PAH metabolism by a Sinorhizobium species. The results give a new insight into microbial degradation of PAHs.

Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov.

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants. In this study, both pristine and contaminated soils were sampled as a source of PAH-degrading organisms. Nine strains isolated from these soils were identified as rapidly growing members of the genus Mycobacterium through basic phenotypic characteristics and through sequence similarity of three genes. Because the sequence similarity of the 16S rRNA gene is relatively high among members of this genus, additional conserved genes encoding the beta subunit of RNA polymerase (rpoB) and a heat-shock protein (hsp65) were sequenced. Several analyses were completed to differentiate the strains from one another and to determine their species-level taxonomy, including fatty acid methyl ester analysis, biochemical tests and substrate-utilization profiling. A phylogenetic tree incorporating sequences for all three genes was constructed with the isolates and their close described relatives. Results for biochemical tests, substrate-utilization tests and DNA sequencing were compared with those of the phylogenetically similar organisms to establish the isolated strains as representatives of novel species with characteristics unlike those of previously described species of Mycobacterium. Finally, DNA-DNA hybridization was performed between strains and their close relatives to confirm their position within novel species. Our results demonstrated that the isolates represent five novel species, which were named Mycobacterium crocinum sp. nov. (type strain czh-42(T) =ATCC BAA-1373(T) =CIP 109262(T); reference strains czh-1A =ATCC BAA-1370 =CIP 109266 and czh-3 =ATCC BAA-1371=CIP 109267), Mycobacterium pallens sp. nov. (type strain czh-8(T) =ATCC BAA-1372(T) =CIP 109268(T)), Mycobacterium rutilum sp. nov. (type strain czh-117(T) =ATCC BAA-1375(T) =CIP 109271(T); reference strains czh-107 =ATCC BAA-1374 =CIP 109270 and czh-132 =ATCC BAA-1376 =CIP 109272), Mycobacterium rufum sp. nov. (type strain JS14(T) =ATCC BAA-1377(T) =CIP 109273(T)) and Mycobacterium aromaticivorans sp. nov. (type strain JS19b1(T) =ATCC BAA-1378(T) =CIP 109274(T)).

Chemical Composition, Characterization, and Differentiation of Honey Botanical and Geographical Origins

Botanical and biographical origins of honey are an important issue in food quality and safety. This chapter focuses on use of chemical components to determine botanical and geographical origins of honey. The botanical and geographical origins of the nectar are related with the chemical composition of honey. Honey can originate from single and multiplant species. In general, the prices of honey from single plant species are much higher than those of common polyfloral honey because of consumer preferences. Single and multiple chemicals and components can well indicate the botanical and geographical origins of the honey. Marker chemicals and components include flavonoids, pollen, aroma compounds, oligosaccharides, trace elements, amino acids, and proteins. If multiple chemicals are used as markers, patterns of the chemicals are often used to detect the botanical and geographical origins of honey. Modern statistical software in combination with advanced analytical instrumentation provides high potential for the differentiation of the botanical and geographical origins of the honey.

Rapid Determination of the Geographical Origin of Honey Based on Protein Fingerprinting and Barcoding Using MALDI TOF MS

The authentication of foods is an important aspect of quality control and food safety. Honey is one of the most natural and most popular foods in the world. A fast and reliable method to determine the geographical origin of honey was developed based on fingerprinting and barcoding of proteins in honey by using matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS) and MALDI Biotyper 1.1 software, respectively. The protein mass spectra of 16 honey samples of known Hawaii origin were obtained and peak information was extracted to generate protein fingerprints. This information was transformed into a database library of spectral barcodes that were used for differentiation of the geographical origin of honeys based on pattern matching. The differentiation ability of the database library of barcodes was validated by comparing the results of replicate assays of 5 of the 16 honey samples of known Hawaii origin obtained directly from the producers. Validation results showed that the protein fingerprints of honeys have better comparability with those honeys in the library known to be from the same region than with those of honey samples from other regions. The protein fingerprints were used to differentiate the geographical origins of commercially purchased honey samples with labels indicating that they were produced in different countries and various states of the USA, including Hawaii. The results showed that the MALDI TOF MS Biotyper system can be a rapid, simple and practical method for determining the geographical origin of honeys sold in commerce.

The cloned 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene from Sinorhizobium sp. strain BL3 in Rhizobium sp. strain TAL1145 promotes nodulation and growth of Leucaena leucocephala

The objective of this study was to determine the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase of symbionts in nodulation and growth of Leucaena leucocephala. The acdS genes encoding ACC deaminase were cloned from Rhizobium sp. strain TAL1145 and Sinorhizobium sp. BL3 in multicopy plasmids, and transferred to TAL1145. The BL3-acdS gene greatly enhanced ACC deaminase activity in TAL1145 compared to the native acdS gene. The transconjugants of TAL1145 containing the native or BL3 acdS gene could grow in minimal media containing 1.5mM ACC, whereas BL3 could tolerate up to 3mM ACC. The TAL1145 acdS gene was inducible by mimosine and not by ACC, while the BL3 acdS gene was highly inducible by ACC and not by mimosine. The transconjugants of TAL1145 containing the native- and BL3-acdS genes formed nodules with greater number and sizes, and produced higher root mass on L. leucocephala than by TAL1145. This study shows that the introduction of multiple copies of the acdS gene increased ACC deaminase activities of TAL1145 and enhanced its symbiotic efficiency on L. leucocephala.

Distribution of polychlorinated biphenyls in marine species from French Frigate Shoals, North Pacific Ocean

Polychlorinated biphenyls (PCBs) were analyzed in: sediment; coral (Porites evermanni); fish (Stegastes fasciolatus, Neoniphon sammara, Acanthurus triostegus and Mulloidichthys vanicolensis); crab (Grapsus tenuicrustatus); lobster (Panulirus marginatus); and eel (Conger cinereus, Gymnothoraxflavimarginatus, G. undulatus and G. meleagris) samples collected from Tern Island and the corresponding reference samples from Disappearing Island. The two islands are part of French Frigate Shoals, a national wildlife refuge in the North Pacific Ocean. The dominant congeners 118, 138 and 153 represent 22-25, 32-34, 12-39, 37-46 and 30-55% of the sum of PCBs in the coral, sediment, fish, crab and eel, respectively. In general, high trophic species such as eels were found to highly bioaccumulate PCBs. The total average PCB concentrations were as high as 96 and 29 microg/g dry wt. in eels and damselfish, respectively, from Tern Island. The localized behavior and high bioaccumulation potential for PCBs suggest that damselfish are an excellent species for monitoring PCBs in small areas in the ocean. The high average concentrations of the sum of PCBs in different food chain levels suggest that pollution source(s) are around Tern Island and possibly around Disappearing Island. Aroclor 1254 and its analogs are suspected sources responsible for PCBs in the samples.