Publications

cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments.	three heterotrophic bacterial strains were isolated from different locations in puget sound, washington, by using biphenyl as the principal carbon source. these strains grow by using a limited number of organic compounds, including the aromatic hydrocarbons naphthalene, phenanthrene, anthracene, and toluene, as sole carbon sources. these aerobic, gram-negative rods are motile by means of single polar flagella. their 16s rrna sequences indicate that they are all members of the gamma subdivision o ...	1995	7857792
a marine oligobacterium harboring genes known to be part of aromatic hydrocarbon degradation pathways of soil pseudomonads.	the far-ranging distribution of genes for aromatic hydrocarbon catabolism, predominantly studied in soil pseudomonads, is extended to a marine oligobacterium by finding five homologous sequences in a 5.7-kb chromosomal dna from a new isolate, cycloclasticus oligotrophus rb1. rb1 is capable of growth in unamended seawater or mineral salts media supplemented with a variety of aromatic compounds, including toluene, o-, m-, or p-xylenes, as sole carbon sources. the five open reading frames, designat ...	1996	8787414
enumeration and phylogenetic analysis of polycyclic aromatic hydrocarbon-degrading marine bacteria from puget sound sediments.	naphthalene- and phenanthrene-degrading bacteria in puget sound sediments were enumerated by most-probable-number enumeration procedures. sediments from a creosote-contaminated environmental protection agency superfund site (eagle harbor) contained from 10(4) to 10(7) polycyclic aromatic hydrocarbon (pah)-degrading bacteria g (dry weight) of sediment-1, whereas the concentration at an uncontaminated site ranged from 10(3) to 10(4) g of sediment(-1). isolates of pah-degrading bacteria were obtain ...	1996	8795224
novel organization of catechol meta-pathway genes in sphingomonas sp. hv3 psky4 plasmid.	sphingomonas sp. strain hv3 (formerly pseudomonas sp. hv3), which degrades aromatics and chloroaromatics, harbors a mega-plasmid, psky4. a sequenced 4 kb fragment of the plasmid reveals a novel gene organization for catechol meta-pathway genes. the putative meta operon starts with the cmpf gene encoding a 2-hydroxymuconic semialdehyde hydrolase. the gene has a 6 bp overlap with the previously characterized ring-cleavage gene, catechol 2,3-dioxygenase, cmpe. downstream of cmpe is a 429 bp open re ...	1997	9311141
determination of the biomasses of small bacteria at low concentrations in a mixture of species with forward light scatter measurements by flow cytometry	the forward light scatter intensity of bacteria analyzed by flow cytometry varied with their dry mass, in accordance with theory. a standard curve was formulated with rayleigh-gans theory to accommodate cell shape and alignment. it was calibrated with an extinction-culture isolate of the small marine organism cycloclasticus oligotrophus, for which dry weight was determined by chn analysis and 14c-acetate incorporation. increased light scatter intensity due to formaldehyde accumulation in preserv ...	1998	9758817
a small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater.	dilutions of raw seawater produced a bacterial isolate capable of extended growth in unamended seawater. its 2.9-mb genome size and 40-fg dry mass were similar to values for many naturally occurring aquatic organotrophs, but water and dna comprised a large portion of this small chemoheterotroph, as compared to escherichia coli. the isolate used only a few aromatic hydrocarbons and acetate, and glucose and amino acid incorporation were entirely absent, although many membrane and cytoplasmic prote ...	1998	9797308
isolation of marine polycyclic aromatic hydrocarbon (pah)-degrading cycloclasticus strains from the gulf of mexico and comparison of their pah degradation ability with that of puget sound cycloclasticus strains.	phenanthrene- and naphthalene-degrading bacteria were isolated from four offshore and nearshore locations in the gulf of mexico by using a modified most-probable-number technique. the concentrations of these bacteria ranged from 10(2) to 10(6) cells per ml of wet surficial sediment in mildly contaminated and noncontaminated sediments. a total of 23 strains of polycyclic aromatic hydrocarbon (pah)-degrading bacteria were obtained. based on partial 16s ribosomal dna sequences and phenotypic charac ...	1998	9835552
isolation, characterization, and polyaromatic hydrocarbon degradation potential of aerobic bacteria from marine macrofaunal burrow sediments and description of lutibacterium anuloederans gen. nov., sp. nov., and cycloclasticus spirillensus sp. nov.	two new polyaromatic hydrocarbon-degrading marine bacteria have been isolated from burrow wall sediments of benthic macrofauna by using enrichments on phenanthrene. strain lc8 (from a polychaete) and strain m4-6 (from a mollusc) are aerobic and gram negative and require sodium chloride (>1%) for growth. both strains can use 2- and 3-ring polycyclic aromatic hydrocarbons as their sole carbon and energy sources, but they are nutritionally versatile. physiological and phylogenetic analyses based on ...	2001	11722910
extracellular polysaccharides of rhodococcus rhodochrous s-2 stimulate the degradation of aromatic components in crude oil by indigenous marine bacteria.	rhodococcus rhodochrous s-2 produces extracellular polysaccharides (s-2 eps) containing d-glucose, d-galactose, d-mannose, d-glucuronic acid, and lipids, which is important to the tolerance of this strain to an aromatic fraction of (af) arabian light crude oil (n. iwabuchi, n. sunairi, h. anzai, m. nakajima, and s. harayama, appl. environ. microbiol. 66:5073-5077, 2000). in the present study, we examined the effects of s-2 eps on the growth of indigenous marine bacteria on af. indigenous bacteri ...	2002	11976106
impact of irradiation and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies.	experiments were carried out to develop methods to generate well-characterized, polycyclic aromatic hydrocarbon (pah)-spiked, aged but minimally altered sediments for fate, biodegradation, and bioavailability experiments. changes in indigenous bacterial populations were monitored in mesocosms constructed of relatively clean san diego bay sediments, with and without exposure to gamma radiation, and then spiked with five different pahs and hexadecane. while phenanthrene and chrysene degraders were ...	2002	12039743
bacteria belonging to the genus cycloclasticus play a primary role in the degradation of aromatic hydrocarbons released in a marine environment.	to identify the bacteria that play a major role in the aerobic degradation of petroleum polynuclear aromatic hydrocarbons (pahs) in a marine environment, bacteria were enriched from seawater by using 2-methylnaphthalene, phenanthrene, or anthracene as a carbon and energy source. we found that members of the genus cycloclasticus became predominant in the enrichment cultures. the cycloclasticus strains isolated in this study could grow on crude oil and degraded pah components of crude oil, includi ...	2002	12406758
degradation of chlorinated biphenyl, dibenzofuran, and dibenzo-p-dioxin by marine bacteria that degrade biphenyl, carbazole, or dibenzofuran.	marine bacterial strains (bp-ph, car-sf, and dbf-mak) were isolated using biphenyl, carbazole (car), or dibenzofuran (df) respectively as substrates for growth. their 16s ribosomal dna sequences showed that the species closest to strain bp-ph, strain car-sf, and strain dbf-mak are alteromonas macleodii (96.3% identity), neptunomonas naphthovorans (93.1% identity), and cycloclasticus pugetii (97.3% identity), respectively. the metabolites produced suggested that strain car-sf degrades car via dio ...	2003	12834291
dynamics of microbial populations and strong selection for cycloclasticus pugetii following the nakhodka oil spill.	microbial population changes were monitored immediately after the nakhodka oil spill accident in january 1997 at the heavily oil-contaminated mikuni coast along the sea of japan. the total cell number was almost stable for one year at 2-5 x 10(5) cells ml(-1), while the relative occurrence of culturable heterotrophs and degraders of oil components such as c-heavy oil, kerosene, and n-tetradecane varied, showing a maximum (>50% of the total) immediately following the accident. gene amplification ...	2003	12904913
molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from cycloclasticus sp. strain a5.	cycloclasticus sp. strain a5 is able to grow with petroleum polycyclic aromatic hydrocarbons (pahs), including unsubstituted and substituted naphthalenes, dibenzothiophenes, phenanthrenes, and fluorenes. a set of genes responsible for the degradation of petroleum pahs was isolated by using the ability of the organism to oxidize indole to indigo. this 10.5-kb dna fragment was sequenced and found to contain 10 open reading frames (orfs). seven orfs showed homology to previously characterized genes ...	2003	14602629
microbial communities in oil-contaminated seawater.	although diverse bacteria capable of degrading petroleum hydrocarbons have been isolated and characterized, the vast majority of hydrocarbon-degrading bacteria, including anaerobes, could remain undiscovered, as a large fraction of bacteria inhabiting marine environments are uncultivable. using culture-independent rrna approaches, changes in the structure of microbial communities have been analyzed in marine environments contaminated by a real oil spill and in micro- or mesocosms that mimic such ...	2004	15193328
natural microbial diversity in superficial sediments of milazzo harbor (sicily) and community successions during microcosm enrichment with various hydrocarbons.	hydrocarbon-contaminated superficial sediments collected from the harbor of milazzo (tirrenean sea, northern sicily), a zone strongly affected by anthropogenic activities, were examined for in situ biodegradative capacities. a culture-independent molecular phylogenetic approach was used to study the influence of hydrocarbon and nutrient addition on the activity and diversity of the indigenous microbiota during a microcosm evaluation. the autochthonous microbial community in non-polluted sediment ...	2005	16104865
impacts of bioremediation schemes on bacterial population in naphthalene-contaminated marine sediments.	microcosm experiments were conduced in which the surface of marine sediment was contaminated with naphthalene and subjected to either of three different bioremediation schemes, i.e., biostimulation (bs) by supplementing with slow-release nitrogen and phosphorus fertilizers, bioaugmentation (ba) by inoculating with cycloclasticus sp. e2, an aromatics-degrading bacterium identified to play an important role for aromatic-hydrocarbon degradation in marine environments and combination (cb) of bs and ...	2006	16715402
determining the identity and roles of oil-metabolizing marine bacteria from the thames estuary, uk.	crude oil is a complex mixture of different hydrocarbons. while diverse bacterial communities can degrade oil, the specific roles of individual members within such communities remain unclear. to identify the key bacterial taxa involved in aerobic degradation of specific hydrocarbons, microcosm experiments were established using seawater from stanford le hope, thames estuary, uk, adjacent to a major oil refinery. in all microcosms, hydrocarbon degradation was significant within 10 weeks, ranging ...	2007	17227421
effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters.	improved strategies for oil-spill remediation will follow a better understanding of the nature, activities and regulating parameters of petroleum hydrocarbon-degrading microbial communities in temperate marine environments. the addition of crude oil to estuarine water resulted in an immediate change in bacterial community structure, increased abundance of hydrocarbon-degrading microorganisms and a rapid rate of oil degradation, suggesting the presence of a pre-adapted oil-degrading microbial com ...	2007	17227422
obligate oil-degrading marine bacteria.	over the past few years, a new and ecophysiologically unusual group of marine hydrocarbon-degrading bacteria - the obligate hydrocarbonoclastic bacteria (ohcb) - has been recognized and shown to play a significant role in the biological removal of petroleum hydrocarbons from polluted marine waters. the introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited number of indigenous marine bacterial genera--alcanivorax, marinobacter, thallassolituus, c ...	2007	17493798
dynamics of the hydrocarbon-degrading cycloclasticus bacteria during mesocosm-simulated oil spills.	we used catalysed reported deposition - fluorescence in situ hybridization (card-fish) to analyse changes in the abundance of the bacterial groups alphaproteobacteria, gammaproteobacteria and bacteroidetes, and of hydrocarbon-degrading cycloclasticus bacteria in mesocosms that had received polycyclic aromatic hydrocarbons (pahs) additions. the effects of pahs were assessed under four contrasting hydrographic conditions in the coastal upwelling system of the rías baixas: winter mixing, spring blo ...	2007	17803779
novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia.	polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ...	2008	18366740
a pyrene-degrading consortium from deep-sea sediment of the west pacific and its key member cycloclasticus sp. p1.	a pyrene-degrading bacterial consortium was obtained from deep-sea sediments of the pacific ocean. the consortium degraded many kinds of polycyclic aromatic hydrocarbons (pahs), including naphthalene, phenanthrene, pyrene, acenaphthene, fluorene, anthracene, fluoranthene, 2-methylnaphthalene and 2,6-dimethylnaphthalene, but it did not grow with chrysene and benzo[alpha]pyrene. with methods of plate cultivation and polymerase chain reaction-denaturing gradient gel electrophoresis (pcr-dgge), 72 b ...	2008	18430013
biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the middle atlantic ridge.	the bacteria involved in the biodegradation of polycyclic aromatic hydrocarbons (pahs) in deep sea subsurface environments are largely unknown. in order to reveal their biodiversity, sediments from 2.2 m under the bottom surface at a water depth of 3542 m were sampled on the middle atlantic ridge with a gravity column sampler. the sediments were promptly enriched with either crude oil or a mixture of pahs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and further enriched with ...	2008	18445026
both cycloclasticus spp. and pseudomonas spp. as pah-degrading bacteria in the seine estuary (france).	like other highly urbanized and industrialized estuaries, the seine estuary (france) has, for decades, received high inputs of polycyclic aromatic hydrocarbons (pahs). in order to estimate the bioremediation potentials and to identify the bacterial species involved in hydrocarbon degradation, we used microcosms containing seawater from the seine estuary supplemented with either naphthalene, phenanthrene, fluorene or pyrene. in the microcosms enriched with naphthalene or phenanthrene, hydrocarbon ...	2010	19817864
the potential of cycloclasticus and altererythrobacter strains for use in bioremediation of petroleum-aromatic-contaminated tropical marine environments.	cycloclasticus sp. a5, which has been suggested to be a major degrader of petroleum aromatics spilled in temperate seas, showed higher degrading activities for petroleum aromatics, at both 25 degrees c and tropical sea temperature 30 degrees c, than the novel aromatic-degrading isolates, related to altererythrobacter epoxidivorans (97.5% similarity in the almost full-length 16s rrna gene sequence) and rhodovulum iodosum (96.3% similarity), obtained after enrichment on crude oil in a continuous s ...	2010	20541115
[in situ enrichment and diversity analysis of polycyclic aromatic carbon degrading bacteria in the coastal seawater of xiamen island].	the aim of this study is to assess the diversity of polycyclic aromatic carbon (pah)-degrading bacteria in the coastal seawater of xiamen island.	2010	21141476
bioconversion of substituted naphthalenes and β-eudesmol with the cytochrome p450 bm3 variant f87v.	bioconversion of various substituted naphthalenes that contain 1-methoxy- and 1-ethoxy-naphthalenes, methylnaphthalenes, dimethylnaphthalenes, and naphthalenecarboxylic acid methyl esters were performed using recombinant escherichia coli cells, which expressed the gene coding for a cytochrome p450 bm3 variant f87v (p450 bm3 (f87v)) that was n-terminally fused to an archaeal peptidyl-prolyl cis-trans isomerase. in addition, bioconversion experiments with the same substrates were carried out using ...	2010	21184059
production of novel antioxidative prenyl naphthalen-ols by combinational bioconversion with dioxygenase phna1a2a3a4 and prenyltransferase nphb or sco7190.	we performed combinational bioconversion of substituted naphthalenes with phna1a2a3a4 (an aromatic dihydroxylating dioxygenase from marine bacterium cycloclasticus sp. strain a5) and prenyltransferase nphb (geranyltransferase from streptomyces sp. strain cl190) or sco7190 (dimethylallyltransferase from streptomyces coelicolor a3(2)) to produce prenyl naphthalen-ols. using 2-methylnaphthalene, 1-methoxynaphthalene, and 1-ethoxynaphthalene as the starting substrates, 10 novel prenyl naphthalen-ols ...	2011	21389612
mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution.	mangroves are transitional coastal ecosystems in tropical and sub-tropical regions and represent biologically important and productive ecosystems. despite their great ecological and economic importance, mangroves are often situated in areas of high anthropogenic influence, being exposed to pollutants, such as those released by oil spills.	2011	21399677
Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill.	Microbial communities present in the Gulf of Mexico rapidly responded to the Deepwater Horizon oil spill. In deep water plumes, these communities were initially dominated by members of Oceanospirillales, Colwellia, and Cycloclasticus. None of these groups were abundant in surface oil slick samples, and Colwellia was much more abundant in oil-degrading enrichment cultures incubated at 4 °C than at room temperature, suggesting that the colder temperatures at plume depth favored the development of ...	2011	21969552