PCR-amplified 16S rRNA Gene Fragments Research Articles

Response of Gut Microbiota to Fasting and Hibernation in Syrian Hamsters

Although hibernating mammals wake occasionally to eat during torpor, this period represents a state of fasting. Fasting is known to alter the gut microbiota in nonhibernating mammals; therefore, hibernation may also affect the gut microbiota. However, there are few reports of gut microbiota in hibernating mammals. The present study aimed to compare the gut microbiota in hibernating torpid Syrian hamsters with that in active counterparts by using culture-independent analyses. Hamsters were allocated to either torpid, fed active, or fasted active groups. Hibernation was successfully induced by maintaining darkness at 4 degrees C. Flow cytometry analysis of cecal bacteria showed that 96-h fasting reduced the total gut bacteria. This period of fasting also reduced the concentrations of short chain fatty acids in the cecal contents. In contrast, total bacterial numbers and concentrations of short chain fatty acids were unaffected by hibernation. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments indicated that fasting and hibernation modulated the cecal microbiota. Analysis of 16S rRNA clone library and species-specific real-time quantitative PCR showed that the class Clostridia predominated in both active and torpid hamsters and that populations of Akkermansia muciniphila, a mucin degrader, were increased by fasting but not by hibernation. From these results, we conclude that the gut microbiota responds differently to fasting and hibernation in Syrian hamsters.

Growth of phototrophic biofilms from limestone monuments under laboratory conditions

In the current study, five phototrophic biofilms from different Southern Europe limestone monuments were characterised by molecular techniques and cultivated under laboratory conditions. Phototrophic biofilms were collected from Orologio Tower in Martano (Italy), Santa Clara-a-Velha Monastery and Ajuda National Palace, both in Portugal, and Seville and Granada Cathedrals from Spain. The biofilms were grown under laboratory conditions and periodically sampled in order to monitor their evolution over a three-month period. Prokaryotic communities from natural samples and cultivated biofilms were monitored using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments in conjunction with clone sequencing and phylogenetic analysis. DNA-based molecular analysis of 16S rRNA gene fragments from the natural green biofilms revealed complex and different communities composition with respect to phototrophic microorganisms. The biofilms from Orologio Tower (Martano, Italy) and Santa Clara-a-Velha Monastery (Coimbra, Portugal) were dominated by the microalga Chlorella. The cyanobacterium Chroococcidiopsis was the dominating genus from Ajuda National Palace biofilm (Lisbon, Portugal). The biofilms from Seville and Granada Cathedrals (Spain) were both dominated by the cyanobacterium Pleurocapsa. The DGGE analysis of the cultivated biofilms showed that the communities developed differently in terms of species establishment and community composition during the three-month incubation period. The biofilm culture from Coimbra (Portugal) showed a remarkable stability of the microbial components of the natural community in laboratory conditions. With this work, a multiple-species community assemblage was obtained for further stone colonisation experiments.

Phylogenetic Analyses of Bacterial Communities Developed in a Cassette-Electrode Microbial Fuel Cell

Quantitative and qualitative differences were analyzed between planktonic and anode-biofilm bacterial communities developed in a cassette-electrode microbial fuel cell treating starch, peptone, and fish extract. Quantitative analyses based on protein contents and rRNA-gene copy numbers indicated that planktonic microbes were over eight-times more abundant than anode-biofilm microbes. Clone-library analyses of PCR-amplified 16S rRNA gene fragments revealed the presence of bacteria affiliated with the phyla Bacteroidetes, Firmicutes, and Proteobacteria in these two communities. The most abundant sequence was affiliated with the family Porphyromonadaceae, and accounted for over 50% and 20% of all the sequences in the planktonic- and biofilm-microbe libraries, respectively.

Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production

In full-scale drinking water production from groundwater, subsurface aeration is an effective means of enhancing the often troublesome process of nitrification. Until now the exact mechanism, however, has been unknown. By studying the microbial population we can improve the understanding of this process. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments of bacteria, archaea and ammonia-oxidizing bacteria was used to characterize the microbial populations in raw groundwater and trickling filters of an active nitrifying surface aerated system and an inactive non-surface aerated system. Only in the active filter were nitrifying microorganisms found above the detection limit of the method. In ammonia oxidation in this groundwater filter both bacteria and archaea played a role, while members belonging to the genus Nitrospira were the only nitrite-oxidizing species found. The subsurface aerated groundwater did not contain any of the nitrifying organisms active in the filter above the detection limit, but did contain Gallionella species that might play a major role in iron oxidation in the filter.

Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway

Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 micromol 13CH4 g(-1) wet weight occurred. Extracted DNA was separated into 'light' and 'heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs.

Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary

The diversity and spatio-temporal distribution of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) were investigated along a salinity gradient in sediments of the Westerschelde estuary. Sediment samples were collected from three sites with different salinities, and at six time points over the year. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA and amoA gene fragments was used to identify the AOA and AOB present. Members of the AOA were mainly belonging to the Crenarchaeota Group 1, which were found at all sites, while members of the genus Nitrosomonas, which were abundant at the brackish sites, and of the genus Nitrosospira, which were present in early spring at the marine sites, were found to be the dominant AOB. Statistical analysis indicated that salinity and temperature were the main factors controlling the diversity and distribution of both AOA and AOB. Variability in net primary production rates was also correlated with species composition of both groups, but changes in the nitrite concentration only to the distribution of the AOA.

Seasonal and Spatial Variation of Bacterial Community Structure in River-Mouth Areas of Gokasho Bay, Japan

This study investigated seasonal and spatial dynamics of the bacterial community in Gokasho bay with denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA gene fragments. The community structure was related to physico-chemical water conditions in the area examined. The bacterial community clustered into three groups: bacteria collected during January-May; those collected from water at the surface in July and September; and those collected from water at the bottom in July and September and from both depths in November. Canonical correspondence analyses indicated that the seasonal variability in bacterial community was associated with water temperature succession. On the other hand, concentrations of particulate organic matter and nitrite plus nitrate were related to the vertical change in community structure in summer and autumn as well as HNF abundance, suggesting that both top-down and bottom-up control affected the community. The influence of salinity was insignificant though bacterial production was related to salinity. No relationship was observed between the variation in community structure and that in hydrolytic enzyme activity. The results indicate that changes in bacterial activity are not coupled with variation in community structure.

Covariation between zooplankton community composition and cyanobacterial community dynamics in Lake Blaarmeersen (Belgium)

The cyanobacterial community composition in the mesotrophic Lake Blaarmeersen was determined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments during two consecutive years to assess the importance of different classes of explanatory variables (bottom-up and top-down factors, physical variables and phytoplankton) in cyanobacterial community dynamics. The most dominant cyanobacteria in Lake Blaarmeersen were Synechococcus (three genotypes), Limnothrix redekei and Anabaena/Aphanizomenon. Analyses of Similarity revealed that the cyanobacterial community in Lake Blaarmeersen differed significantly between the growing season and the winter season as well as between the epilimnion and hypolimnion during the stratified periods. Mantel tests revealed significant correlations between the DGGE data and bottom-up factors, physical variables, the phytoplankton community composition and, interestingly, the zooplankton community composition. In general, the zooplankton community composition (especially the cladoceran community) was more important in structuring the cyanobacterial community than the total zooplankton biomass. This study shows that grazing zooplankton communities can have a relatively strong impact on the cyanobacterial community dynamics and that this impact can be equally important as bottom-up processes regulated by nutrient concentrations and/or physical variables.

Enrichment of dense nitrifying bacterial communities in membrane-coupled bioreactors

In this study, membrane-coupled bioreactors (MBRs) were used to enrich for dense cultures of nitrifying bacteria. MBRs were initially fed a solution containing 500 mg L −1 of ammonia (as N) until biomass accumulation stopped (>90 days), after which ammonia was eliminated from the feed solution and replaced with 500 mg L −1 of nitrite (as N). These experiments demonstrated that MBRs could successfully enrich for dense (as high as 1000 mg L −1 of cell protein) communities of nitrifying bacteria. Analysis of the bacterial community structures of these MBRs via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments (PCR–DGGE) revealed that the bacterial communities were dominated by several species of Nitrosomonas, Nitrosospira, and Nitrobacter, as well as numerous other populations of unknown function. A curious result occurred, however, when the feed solution was switched from ammonia to nitrite. Following this transition, a Nitrosomonas sp. became especially prominent (∼60% of the total PCR–DGGE band intensity), while the Nitrobacter sp. failed to have a substantial response. This result suggests that our MBRs possibly enriched for a single bacterial population capable of the complete oxidation of ammonia to nitrate, although additional research is needed to confirm or refute this conclusion.

Degradative Capacities and Bioaugmentation Potential of an Anaerobic Benzene-degrading Bacterium Strain DN11

Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 microM, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations.

Intra-habitat heterogeneity of environmental factors regulating bacterioplankton community composition in Lake Taihu, China

To investigate the intra-habitat heterogeneity of environmental factors that may have an impact on the bacterioplankton community composition (BCC), a 1 yr observation was done at 2 study sites in Lake Taihu, a large shallow eutrophic lake in China. One site was located at the center of Meiliang Bay, the other site was near the central region of the lake. Denaturing gradient gel elec- trophoresis (DGGE) of PCR-amplified partial 16S rRNA gene fragments was applied to analyze BCC. The unweighted pair group method with arithmetic mean (UPGMA) was used to investigate differ- ences among BCC. Redundancy analyses (RDA) of the gel patterns, in relation to the physical, chem- ical, and biological factors of the 2 sites, were performed. Differences between the samples in Mei- liang Bay and the lake center were evident during all periods. Four variables (the biomass of Microcystis spp., chl a, dissolved inorganic phosphorus (DIP), and water turbidity) were most strongly correlated with the bacterioplankton DGGE patterns. Particularly, significant intra-habitat hetero- geneity of the environmental factors was detected. In Meiliang Bay, seasonal variations in DIP con- centration had a profound impact on the composition of bacterioplankton communities, while in the lake center, wind-induced frequent sediment resuspension was an important reason for the varia- tions in BCC. The inherent intra-habitat heterogeneity of environmental conditions is essential to maintain the heterogeneity of BCC at the 2 study sites.

Effects of phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 48:47-60 (2007) - doi:10.3354/ame048047 Effects of phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities Beate Rink1, Susanne Seeberger1, Torben Martens1, Claus-Dieter Duerselen2, Meinhard Simon1, Thorsten Brinkhoff1,* 1Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, PO Box 2503, 26111 Oldenburg, Germany 2AquaEcology, Marie-Curie-Straße 1, 26129 Oldenburg, Germany *Corresponding author. Email: thorsten.brinkhoff@icbm.de ABSTRACT: We studied the composition of free-living and particle-associated bacterial communities during the course of the phytoplankton succession in spring and early summer in the Wadden Sea, a tidal flat ecosystem in the southern North Sea. We applied the denaturing gradient gel electrophoresis (DGGE) approach based on PCR-amplified 16S rRNA gene fragments and, in addition to Bacteria-specific primers, used primer sets targeting Alphaproteobacteria, the Roseobacter-clade and the Bacteroidetes phylum. Even though the application of the primer sets targeting Bacteria and Alphaproteobacteria detected some changes, they were most pronounced with those targeting the Roseobacter-clade and Bacteroidetes. The changes were supported by a correspondence analysis, which showed a statistically significant correlation of the DGGE banding patterns of the Roseobacter-specific PCR with the composition of the phytoplankton (p = 0.03). This indicates that changes in the phytoplankton composition in this habitat are not reflected by changes in the most abundant or most readily amplifiable phylotypes. The findings rather suggest that few, specialized, heterotrophic bacteria are most responsive to the organic matter supplied by distinct phytoplankton communities and that the main part of organic matter in the Wadden Sea is utilized by generalists. Sequence analyses of excised bands revealed a high diversity for the Bacteria- and Bacteroidetes-targeted approaches. The bacterial community detected by the primer set targeting Alphaproteobacteria, however, was mainly composed of bacteria affiliated to the Roseobacter-clade. KEY WORDS: Free-living bacteria · Particle-attached bacteria · Bacteroidetes · Roseobacter · Phytoplankton · Denaturing gradient gel electrophoresis · Wadden Sea Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 48, No. 1. Online publication date: June 20, 2007 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2007 Inter-Research.

Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

Parenteral long-acting amoxicillin reduces intestinal bacterial community diversity in piglets even 5 weeks after the administration

We investigated the long-term effects of a single intramuscular administration of amoxicillin (15 mg kg(-1)) 1 day after birth, on piglet intestinal microbiota. Animals received no creep feed before weaning on day 28 of age. For the next 11 days, the piglets received a wheat-barley-based diet. Colon digesta samples were collected on day 39 and subjected to denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. DGGE fingerprint diversity indices differed between the group treated with amoxicillin and the untreated group (0.8+/-0.19 and 1.03+/-0.17, respectively, P=0.012). Reamplification and sequencing of two bands present in all samples revealed that a Roseburia faecalis-related population was strongly reduced in relative abundance (98% identity) in the treated group, while an enterobacterial population with 100% identity to Shigella spp., Escherichia coli and Salmonella enterica serovar Typhi was enriched. A band corresponding to Lactobacillus sobrius was present only in the control group. The protective effect of prophylactic antibiotic administration may be outweighed by the long-lasting disturbance of the gut ecosystem.

Molecular characterization of mesophilic and thermophilic sulfate reducing microbial communities in expanded granular sludge bed (EGSB) reactors

The microbial communities established in mesophilic and thermophilic expanded granular sludge bed reactors operated with sulfate as the electron acceptor were analyzed using 16S rRNA targeted molecular methods, including denaturing gradient gel electrophoresis, cloning, and phylogenetic analysis. Bacterial and archaeal communities were examined over 450 days of operation treating ethanol (thermophilic reactor) or ethanol and later a simulated semiconductor manufacturing wastewater containing citrate, isopropanol, and polyethylene glycol 300 (mesophilic reactor), with and without the addition of copper(II). Analysis, of PCR-amplified 16S rRNA gene fragments using denaturing gradient gel electrophoresis revealed a defined shift in microbial diversity in both reactors following a change in substrate composition (mesophilic reactor) and in temperature of operation from 30 degrees C to 55 degrees C (thermophilic reactor). The addition of copper(II) to the influent of both reactors did not noticeably affect the composition of the bacterial or archaeal communities, which is in agreement with the very low soluble copper concentrations (3-310 microg l(-1)) present in the reactor contents as a consequence of extensive precipitation of copper with biogenic sulfides. Furthermore, clone library analysis confirmed the phylogenetic diversity of sulfate-reducing consortia in mesophilic and thermophilic sulfidogenic reactors operated with simple substrates.

Molecular assessment of complex microbial communities degrading long chain fatty acids in methanogenic bioreactors

Microbial diversity of anaerobic sludge after extended contact with long chain fatty acids (LCFA) was studied using molecular approaches. Samples containing high amounts of accumulated LCFA were obtained after continuous loading of two bioreactors with oleate or with palmitate. These sludge samples were then incubated in batch assays to allow degradation of the biomass-associated LCFA. In addition, sludge used as inoculum for the reactors was also characterized. Predominant phylotypes of the different samples were monitored using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. Fingerprinting analysis showed changes in bacterial and archaeal communities during LCFA accumulation and degradation. Full-length 16S rRNA gene sequences of 22 clones, representing the predominant bacteria and archaea, were determined. Most bacterial clones (80%) clustered within the Clostridiaceae. Two major groups of methanogens were identified: hydrogen- and formate-utilizing organisms, closely related to Methanobacterium, and acetoclastic organisms closely related to Methanosaeta and Methanosarcina. Quantification by FISH and real-time PCR showed that the relative abundance of archaea increased during degradation of biomass-accumulated LCFA. These results provide insight into the importance and dynamics of balanced communities of bacteria and methanogens in LCFA-accumulation/degradation cycles.

Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results?

Bacterial communities of four arable soils – pelosol, gley, para brown soil, and podsol brown soil – were analysed by fingerprinting of 16S rRNA gene fragments amplified from total DNA of four replicate samples for each soil type. Fingerprints were generated in parallel by denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and single strand conformation polymorphism (SSCP) to test whether these commonly applied techniques are interchangeable. PCR amplicons could be separated with all three methods resulting in complex ribotype patterns. Although the fragments amplified comprised different variable regions and lengths, DGGE, T-RFLP and SSCP analyses led to similar findings: (a) a clustering of fingerprints which correlated with soil physico-chemical properties, (b) little variability between the four replicates of the same soil, (c) the patterns of the two brown soils were more similar to each other than to those of the other two soils, and (d) the fingerprints of the different soil types revealed significant differences in a permutation test, which was recently developed for this purpose.

Comparative phylogenetic analysis of microbial communities in pristine and hydrocarbon-contaminated Alpine soils

A molecular characterization of pristine and petroleum hydrocarbon-contaminated Alpine soils sampled in Tyrol (Austria) was performed. To identify predominant bacteria, PCR-amplified 16S rRNA gene fragments from five pristine and nine contaminated soils were analysed using denaturing gradient gel electrophoresis (DGGE). Sequencing and phylogenetic analyses demonstrated that the majority of the DGGE bands represented bacteria in the Actinobacteria and Proteobacteria phyla: 18 and 73%, respectively, in pristine soils, compared with 20 and 76%, respectively, in contaminated soils. A different distribution pattern of bacterial classes in the Proteobacteria was observed between pristine and contaminated soils. The relative proportion of microorganisms belonging to the Alphaproteobacteria was larger in pristine (46%) than in contaminated (24%) soils, while Betaproteobacteria and Gammaproteobacteria were detected only in the hydrocarbon-contaminated soils. This result compared favourably with earlier work in which hydrocarbon-degradation genotypes, largely pseudomonads and Acinetobacter, belonging to the Gammaproteobacteria, were enriched following oil hydrocarbon contamination. In contrast, members of the Actinobacteria phylum, represented by Rhodococcus and Mycobacterium, were found in pristine soils where contamination events had not occurred. The results demonstrate a significant shift in the microbial community structure in Alpine soils following contamination. Furthermore, more potentially novel phylotypes were found in the pristine soils than in the contaminated soils.

Microbial Communities Involved in Anaerobic Degradation of Unsaturated or Saturated Long-Chain Fatty Acids

Anaerobic long-chain fatty acid (LCFA)-degrading bacteria were identified by combining selective enrichment studies with molecular approaches. Two distinct enrichment cultures growing on unsaturated and saturated LCFAs were obtained by successive transfers in medium containing oleate and palmitate, respectively, as the sole carbon and energy sources. Changes in the microbial composition during enrichment were analyzed by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Prominent DGGE bands of the enrichment cultures were identified by 16S rRNA gene sequencing. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. Bacteria corresponding to predominant DGGE bands in oleate and palmitate enrichment cultures clustered with fatty acid-oxidizing bacteria within Syntrophomonadaceae and Syntrophobacteraceae families. A low methane yield, corresponding to 9 to 18% of the theoretical value, was observed in the oleate enrichment, and acetate, produced according to the expected stoichiometry, was not further converted to methane. In the palmitate enrichment culture, the acetate produced was completely mineralized and a methane yield of 48 to 70% was achieved from palmitate degradation. Furthermore, the oleate enrichment culture was able to use palmitate without detectable changes in the DGGE profile. However, the palmitate-specialized consortia degraded oleate only after a lag phase of 3 months, after which the DGGE profile had changed. Two predominant bands appeared, and sequence analysis showed affiliation with the Syntrophomonas genus. These bands were also present in the oleate enrichment culture, suggesting that these bacteria are directly involved in oleate degradation, emphasizing possible differences between the degradation of unsaturated and saturated LCFAs.

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 BA. These three schemes were found to be similarly effective for removing naphthalene, while naphthalene disappearance in sediment without any treatment (WT) was slower than those in the treated sediments. Shifts in bacterial populations during and after bioremediation were analyzed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. It was found that the Cycloclasticus rRNA type occurred as the strongest bands in the course of naphthalene degradation. Clustering analysis of DGGE profiles showed that bacterial populations in the WT, BS and CB sediments differed consistently from those in the uncontaminated control, while the profile for the BA sediment was finally included in the cluster for uncontaminated control sediments after a 150-day treatment. The results suggest that bioaugmentation with ecologically competent pollutant-degrading bacteria is an ecologically promising bioremediation scheme.