16S rRNA Gene Libraries Research Articles

An assessment of microbial communities associated with surface mining-disturbed overburden

To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16years and 37years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37years of overburden maturation.

Sterile paper points as a bacterial DNA-contamination source in microbiome profiles of clinical samples

ObjectivesHigh throughput sequencing of bacterial DNA from clinical samples provides untargeted, open-ended information on the entire microbial community. The downside of this approach is the vulnerability to DNA contamination from other sources than the clinical sample. Here we describe contamination from sterile paper points (PPs) used in microbial sample collection. MethodsPeri-implant samples from 48 individuals were collected using sterile PPs. Control samples contained only PPs or DNA extraction blank controls. 16S rRNA gene libraries were sequenced using 454 pyrosequencing. 16S rRNA gene copy numbers were measured by quantitative PCR. ResultsNearly half of the sequencing reads belonged to two OTUs classified as Enterococcus (25% of reads) or Exiguobacterium (21%), which are not typical oral microorganisms. Of 87 peri-implant samples, only 10 samples (11%) contained neither of the two OTUs. The relative abundance of both unusual OTUs correlated with each other (p<0.001; r=0.828, Spearman correlation). The control samples showed that 2 of 4 (50%) of the sterile unused PPs contained bacterial DNA equivalent to 1.2×103 and 1.1×104 cells respectively, which was within the range of DNA in the clinical samples (average 1.8×107, SD 4.8×107, min 4.4×102, max 2.8×108). The microbial profile from these PPs was dominated (>83% of reads) by the two unusual OTUs. ConclusionsSterile PPs can contain contaminating bacterial DNA. The use of PPs as a sampling tool for microbial profiling of clinical samples by open-ended techniques such as sequencing or DGGE should be avoided. Clinical significanceClinicians working with PPs as sampling tools for bacterial DNA should consider using an alternative sampling tool, because sterile unused PPs can be a considerable source of foreign bacterial DNA. We recommend sterile curettes for collecting clinical samples for open-ended techniques, such as sequencing or DGGE.

Microbiological Distribution of Multi-Level-well Samples in the Coast of South China

In this study, the Microbiological communities wereinvestigated by culture-independent molecular approaches. Four 16S rRNA genelibraries from mineral waterand different groundwater of wells collected from Zhuhai of the South China were constructed and analyzed by amplifiedribosomal DNA restriction analysis technique (ARDRA). The clones of dominantARDRA patterns were selected to sequence. The phylogenetic analysis indicatedthat the sequences from dominant ARDRA patterns belonged toProteobacteria, Bacteroidetes，archaea ,Actinobacteria,Planctomycetes,and Candidate division OP3, OP8, OP11et al.Thepercentages ofProteobacteriaisolated from multi-level-well samples D1,D5,D6were respectively 32.3％,34.3%,46.7%;The Bacteroidetes were respectively 5.0％,11.2％,6.5％; and Actinobacteria were respectively 5.4％,6.6％,7.8％. As a background,the seawater clone library, with the majority (32.8%) of the clones clusteringwithin theProteobacteria, the second most abundant group wereBacteroidetesandPlanctomycetes(both 9.3%), The results suggest that microbialcommunity from different vertical layers ofgroundwater in pristine habitats that have been described for the first time inChina.

Highly Heterogeneous Bacterial Communities Associated with the South China Sea Reef Corals Porites lutea, Galaxea fascicularis and Acropora millepora

Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.

Detection and Localization ofRickettsia spin Mealybug

Mealybug, Phenacoccus solenopsis Tinsley, is a sap-sucking hemipteran insect. It is an agricultural pest that is now widely distributed in India. In this study we report the presence of Rickettsia from P. solenopsis. We constructed a 16S rRNA gene library to study the bacterial diversity associated with this insect and we found that all the clones from the library were only of Candidatus Tremblaya phenacola. This study also highlights that the normal protocol adopted to study the bacterial diversity from environmental sample, by preparation of a 16S rRNA gene library, does not work when the bacterial population is highly skewed in favor of one bacteria (primary endosymbiont in this case). Hence, we used bacterial genus specific polymerase chain reaction primers to test the presence of any of the widely known secondary endosymbionts associated with insects. We tested for the presence of Cardinium, Rickettsia, Wolbachia, and Arsenophonus in P. solenopsis collected from 10 different locations across India. Only Rickettsia was detected from four locations while we were not able to find any other bacteria. We confirmed the presence of these bacteria by localizing Rickettsia and the primary endosmbiont, Candidatus Tremblaya sp. to the bacteriocyte of P. solenopsis using fluorescent in situ hybridization.

Molecular characterization of the planktonic microorganisms in water of two mountain brackish lakes

The prokaryotic diversity in two brackish lakes (Sayram Lake and Chaiwopu Lake) was investigated by constructing bacterial and archaeal clone libraries of 16S rRNA genes. Bacterial clones from Sayram Lake were classified into six phyla (Proteobacteria, Verrucomicrobia, Bacteroidetes, Planctomycetes, Acidobacteria, Actinobacteria). Of these, Proteobacteria and Verrucomicrobia were the most dominant, representing 50.4 and 16.8% of the clone library, respectively. Sequences related to Proteobacteria (58.1%), Cyanobacteria (17.2%), Bacteroidetes (15%), Verrucomicrobia (4.3%), Actinobacteria (3.2%) constituted over 97% of the bacterial clone library from Chaiwopu Lake. In addition, 58.8% (Sayram Lake) and 48% (Chaiwopu Lake) of bacterial clones showed high sequence identity to pure cultures. The composition of Archaea was obviously different between the two lakes. Only the Crenarchaeota phylum was found in the Sayram Lake, whereas Archaeal sequences from Chaiwopu Lake were classified into three phyla: Crenarchaeota (5.8%), Thaumarchaeota (81.2%), and Euryarchaeota (13%). Among the archaeal sequences, 94.2% were highly related to cultivable species of the genus Nitrosopumilus, Methanoculleus, and Methanobacterium. These results showed a high diversity of potential cultivable heterotrophic bacteria in Sayram Lake and Chaiwopu Lake. Chaiwopu Lake was a source of potentially novel, cultivable archaea.

A humin-dependent Dehalobacter species is involved in reductive debromination of tetrabromobisphenol A

Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant on the market. It has been detected in various environmental samples, and a growing body of evidence has demonstrated its toxic effects on living organisms. In this study, we report the enrichment and phylogenetic identification of bacteria that debrominate TBBPA to bisphenol A in the presence of humin. Incubation experiments indicated that humin was required for this debromination activity. Of the five compounds examined for inclusion in the TBBPA-debrominating culture, formate was the optimal electron donor. A 16S rRNA gene library showed that the culture was dominated by three known dehalogenator genera: Dehalobacter, Geobacter, and Sulfurospirillum. Further investigation indicated that Dehalobacter was responsible for the debromination of TBBPA. PCR–denaturing gradient gel electrophoresis analysis showed that Dehalobacter grew in the culture by utilizing TBBPA. Moreover, the copy number of the Dehalobacter 16S rRNA genes increased by about two orders of magnitude in the cultures without the addition of TBBPA, whereas it increased by approximately four orders of magnitude when TBBPA was present. The incubation experiments showed that Dehalobacter was reliant on humin for its debromination activity, indicating a new type of metabolism in Dehalobacter that is linked to humin respiration.

Bacterial and Fungal Communities in Tempeh as Reveal by Amplified Ribosomal Intergenic Sequence Analysis

Tempeh is an Indonesian traditional fermented food produced using Rhizopus as a starter culture. In practice, however, the starter culture as well as fermentation processes would yield a polymicrobial fermentation, which generated a unique tempeh flavor and texture. This condition makes Indonesian tempeh as one of the most complex fermented food, while at the same time would make it difficult to scale up tempeh production with uniform quality and consistency. The aim of this study was to compare a number of tempeh microbial communities employing Amplified Ribosomal Intergenic Sequence Analysis (ARISA). Fresh tempeh samples were obtained from tempeh producers in Java and Moluccas. 16S rRNA gene libraries and DNA sequencing were employed to analyze further the nature of bacterial diversity in two selected tempeh samples. The results of our study showed that different tempeh producer possessed different Bacterial ARISA (BARISA) or fungi ARISA (FARISA) profiles. However, BARISA profiles were found to be more discriminative than FARISA, and therefore BARISA would be more useful for tempeh genetic fingerprint or barcoding.

Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China

Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0% for 16S rRNA gene clones and 64.3% for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54% of the total volatile fatty acids and methane was 57.20% of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

Comparative analysis of midgut bacterial communities of Aedes aegypti mosquito strains varying in vector competence to dengue virus

Differences in midgut bacterial communities of Aedes aegypti, the primary mosquito vector of dengue viruses (DENV), might influence the susceptibility of these mosquitoes to infection by DENV. As a first step toward addressing this hypothesis, comparative analysis of bacterial communities from midguts of mosquito strains with differential genetic susceptibility to DENV was performed. 16S rRNA gene libraries and real-time PCR approaches were used to characterize midgut bacterial community composition and abundance in three Aedes aegypti strains: MOYO, MOYO-R, and MOYO-S. Although Pseudomonas spp.-related clones were predominant across all libraries, some interesting and potentially significant differences were found in midgut bacterial communities among the three strains. Pedobacter sp.- and Janthinobacterium sp.-related phylotypes were identified only in the MOYO-R strain libraries, while Bacillus sp. was detected only in the MOYO-S strain. Rahnella sp. was found in MOYO-R and MOYO strains libraries but was absent in MOYO-S libraries. Both 16S rRNA gene library and real-time PCR approaches confirmed the presence of Pedobacter sp. only in the MOYO-R strain. Further, real-time PCR-based quantification of 16S rRNA gene copies showed bacterial abundance in midguts of the MOYO-R strain mosquitoes to be at least 10-100-folds higher than in the MOYO-S and MOYO strain mosquitoes. Our study identified some putative bacteria with characteristic physiological properties that could affect the infectivity of dengue virus. This analysis represents the first report of comparisons of midgut bacterial communities with respect to refractoriness and susceptibility of Aedes aegypti mosquitoes to DENV and will guide future efforts to address the potential interactive role of midgut bacteria of Aedes aegypti mosquitoes in determining vectorial capacity for DENV.

Effects of inorganic fertilizer and manure on soil archaeal abundance at two experimental farms during three consecutive rotation-cropping seasons

Soil archaeal population dynamics at two experimental sites of the same clay-loam type in Ottawa and Woodslee, Ontario, were investigated to determine fertilizer and manure effects following their different long-term crop rotation and fertilization schemes. Phylogenetic analysis of cloned soil archaeal 16S rRNA gene libraries of both sites identified them with group 1.1b of Thaumarchaeota. The gene population dynamics subtly varied in the order of 107copiesg−1 soil when monitored by quantitative real-time PCR during three growing seasons (2007–2009). In Ottawa, where plots were amended with dairy-farm manure, soil thaumarchaeal gene abundance was double of the unamended plots. At the Woodslee N-P-K-fertilized plots, it remained at least 30% fewer than that of the unfertilized ones. These cultivated plots showed soil carbon limitation while the fertilized ones were low in soil pH (ca. 5.5). Surface soils from an unfertilized sod plot and an adjacent deciduous forest had higher total carbon content (C:N ratio of 9 and 11, respectively). Their thaumarchaeal gene abundance varied up to 4.8×107 and 7.0×107copiesg−1 soil, respectively. The former value was also attained at the manure-amended plots in Ottawa, where the C:N ratio was just below 10. Where soil pH was above 6.0, there was a weak and positive correlation between soil total C and the estimated gene abundance. Such gene population dynamics consistently demonstrated the stimulating and suppressive effects of dairy-farm manure (Ottawa site) and inorganic fertilizers (Woodslee site), respectively, on soil thaumarchaea. At both sites archaeal amoA and 16S rRNA gene abundance were similarly affected. Archaeal amoA gene abundance also outnumbered bacterial amoA abundance, suggesting that ammonia-oxidizing archaea might be dominant in these soils. Only minor crop effects on gene population dynamics were detected.

The 16S rRNA and mcrA gene based comparative diversity of methanogens in cattle fed on high fibre based diet

In the present study, the diversity of rumen methanogens in crossbred Karan Fries cattle was determined by constructing 16S rRNA and mcrA (methyl coenzyme-M reductase α subunit) gene libraries using specific primers. All thirteen OTUs or phylotypes from 16S rRNA library clustered with order Methanobacteriales, twelve of which aligned with Methanobrevibacter spp., whereas one OTU resemble with Methanosphaera stadtmanae. Out of eighteen OTUs identified from mcrA gene library, fifteen clustered with order Methanobacteriales, two resemble with Methanomicrobiales and remaining one grouped with Methanosarcinales. These results revealed that Methanobrevibacter phylotype was predominantly present in Karan Fries crossbred cattle fed on high fibrous diet containing wheat straw. Compared to 16S rRNA gene, mcrA gene OTUs clustered in three orders providing better insights of rumen methanogens diversity in cattle.

English

Guiyu, a town in south China, seriously polluted by heavy metals and toxic organic compounds, takes an important part in the cycle of the Waste Electrical and Electronic Equipment. Here, culture-independent approaches were used to analyze the bacterial community structure of 7 soil and sediment samples. The objective of this paper was to examine the distribution of microbial communities in the e-waste contaminated areas of Guiyu. High concentrations of metals (Cu, Pb, Zn and Al) were detected in the soil and sediment samples collected from the e-waste contaminated areas at Guiyu. Denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene library technology were used to investigate the microbial communities. The 16S rRNA gene library could detect more bacteria than&nbsp;polymerase chain reaction (PCR)-DGGE. The main bacteria in the soil and sediment samples were&nbsp;Deltaproteobacteria&nbsp;(36%),&nbsp;Firmicutes&nbsp;(16%),Alphaproteobacteria&nbsp;(9%),&nbsp;Bacteroidetes&nbsp;(7%),&nbsp;Verrucomicrobia&nbsp;(7%)&nbsp;and&nbsp;Acidobacteria(5%); and 20% of the sequences in the 16S rRNA gene library had sequence identities less than 92% with known sequences. &nbsp; Key words:&nbsp;Guiyu,&nbsp;microbial&nbsp;diversity,&nbsp;DGGE,&nbsp;16S rRNA&nbsp;gene&nbsp;library.

Phylogenetically Diverse Denitrifying and Ammonia-Oxidizing Bacteria in Corals Alcyonium gracillimum and Tubastraea coccinea

To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis.

Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil

Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2% (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3%) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1(T), was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.

Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air

To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their bacterial population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P<0·05) in the bacterial populations at each time point. The alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in bacterial diversity. In-depth 16S rRNA gene sequence analysis revealed significant bacterial population structure changes during ensiling and again during exposure to air. This in-depth description of the bacterial population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes.

Higher seasonal variation of actinobacterial communities than spatial heterogeneity in the surface sediments of Taihu Lake, China

Much more attention has been paid to the actinobacterial community in soils or water columns of aquatic habitats. However, there are few studies on their composition and diversity in lake sediments. Here, we used denaturing gradient gel electrophoresis and clone libraries of partial 16S rRNA gene to study the spatial variations of actinobacterial communities across 4 seasons in the surface sediments of the shallow, subtropical Taihu Lake. Cluster analysis based on fingerprints showed clear spatiotemporal variations of actinobacterial communities and higher seasonal variation than spatial heterogeneity. Based on clone libraries, this pattern was supported by the principal coordinates analysis in the phylogenetic context and by detrended correspondence analysis on the operational taxonomic unit table. Additionally, phylogenetic analysis showed that the putative freshwater-specific actinobacterial lineages (e.g., acI) were also detected in the lake sediments, which suggests that these subclusters may also adapt to the sediment environments. Summarily, our results suggested that actinobacterial communities of the surface sediments were more affected by seasonal variation than spatial heterogeneity in the intrahabitat of Taihu Lake.

Study of anaerobic ammonium oxidation bacterial community in the aged refuse bioreactor with 16S rRNA gene library technique

In order to investigate the anaerobic ammonium-oxidation (Anammox) nitrogen removal pathway of the aged refuse bioreactor treating landfill leachate, a lab-scale bioreactor was established and run for 35 weeks, the performance of the bioreactor and its bacterial community structure of Planctomycetes were analyzed. The results showed that the average TN removal rate of landfill leachate could be reached to 89%. 16S rRNA gene library of Planctomycetes revealed that Anammox sequences accounted for 28.3% of the total Planctomycetes sequences in the bioreactor, and previously recognized Anammox bacterium Candidatus Kuenenia stuttgartiensis was the only detected Anammox species in the reactor. It was also found that Anammox bacteria distributed at different sites of the bioreactor while mostly concentrated in the middle and low-middle part. Results above confirmed that Anammox process could happen in aged refuse bioreactor treating landfill leachate and provided an alternative nitrogen removal pathway in practical landfills.

Submerged macrophytes modify bacterial community composition in sediments in a large, shallow, freshwater lake

Submerged aquatic macrophytes are an important part of the lacustrine ecosystem. In this study, the bacterial community compositions in the rhizosphere sediments from three kinds of submerged macrophytes (Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans) were investigated to determine whether submerged macrophytes could drive the variation of bacterial community in the eutrophic Taihu Lake, China. Molecular techniques, including terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries, were employed to analyze the bacterial community compositions. Remarkable differences of the T-RFLP patterns were observed among the different samples, and the results of LIBSHUFF analysis also confirmed that the bacterial community compositions in the rhizosphere sediments of three kinds of submerged macrophytes were statistically different from that of the unvegetated sediment. Acidobacteria, Deltaproteobacteria, and Betaproteobacteria were the dominant bacterial groups in the rhizosphere sediments of Ceratophyllum demersum, Potamogeton crispus, and Vallisneria natans, respectively, accounting for 15.38%, 29.03%, and 18.00% of the total bacterial abundances. Our study demonstrated that submerged macrophytes could influence the bacterial community compositions in their rhizosphere sediments, suggesting that macrophytes have an effect on the cycling and transportation of nutrients in the freshwater lake ecosystem.

Long-Term Anaerobic Mineralization of Pentachlorophenol in a Continuous-Flow System Using Only Lactate as an External Nutrient

A simple anaerobic upflow column system (15 cm long, 5 cm inner diameter) for complete pentachlorophenol (PCP) mineralization has been established using a microbial consortium requiring only lactate as the external nutrient. With lactate as an electron donor, PCP was dechlorinated to 3-chlorophenol (3-CP) and phenol. The degradation of 3-CP and phenol proceeded without an external electron acceptor, indicating fermentative or syntrophic characteristics. A tracer experiment using (14)C-U-ring-labeled PCP confirmed the conversion of PCP into CO(2) (54.1%), CH(4) (48.1%), and biomass (0.6%). The nitrogen required for degradation was supplied by N(2)-fixation, evidenced from the nitrogen balance and an acetylene reduction assay. A 16S rRNA gene library analysis showed that bottom of the upflow column harbored the potential dechlorinators, Dehalobacter and Desulfitobacterium, and the phenol/3-CP fermentative or syntrophic degraders, Cryptanaerobacter and Syntrophus. The nitrogen-fixing facultative anaerobes, Rhizobiales, were detected in the top of the upflow column, with other possible nitrogen-fixers at both bottom and top of the upflow column. The mineralization rate reached 1.96 μmoles L(-1) d(-1) for 50 μM of the initial PCP concentration: one of the highest efficiencies reported. This compact anaerobic mineralization system requiring no external supply of an electron acceptor would be useful for the remediation of chlorinated aromatic compounds under anaerobic conditions.