rRNA Gene Clone Library Analysis Research Articles

Bacterial community structure associated with the rhizosphere soils and roots of Stellera chamaejasme L. along a Tibetan elevation gradient

The effect of altitude on the composition and diversity of microbial communities have attracted highly attention recently but is still poorly understood. We used 16S rRNA gene clone library analyses to characterize the bacterial communities from the rhizosphere and roots of Stellera chamaejasme in the Tibetan Plateau. Our results revealed that Actinobacteria and Proteobacteria were dominant bacteria in this medicinal plant in the rhizosphere and root communities. The Shannon diversity index showed that the bacterial diversity of rhizosphere follows a small saddle pattern, while the roots possesses of a hump-backed trend. Significant differences in the composition of bacterial communities between rhizosphere and roots were detected based on multiple comparisons analysis. The community of Actinobacteria was found to be significantly negative correlated with soil available P (p < 0.01), while the phylum of Proteobacteria showed a positive relationship with available P (p < 0.05). Moreover, redundancy analysis indicated that soil phosphorus, pH, latitude, elevation and potassium positively correlated with bacterial communities associated with rhizosphere soils. Taken together, we provide evidence that bacterial communities associated with S. chamaejasme exhibited some certain elevational pattern, and bacterial communities of rhizosphere soil were regulated by environmental characteristics along elevational gradients in this alpine ecosystem.

Stromatolites on the rise in peat-bound karstic wetlands

Stromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living examples. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.

Diagnostic Approach to Ocular Infections Using Various Techniques From Conventional Culture to Next-Generation Sequencing Analysis.

Ocular infection is caused by both endogenous (resident) and exogenous (environmental) microbes. As the ocular surface interacts with both outer environment and its own resident microbiota, clinical ocular samples are predicted to contain a diverse set of microorganisms. Microscopy of sample smears is an important step in the diagnostic process of infectious diseases to interpret the culture results. Traditional culture techniques have several limitations in the detection and/or identification of uncharacterized bacteria of environmental origin. Molecular biological techniques, such as polymerase chain reaction of pathogen-specific virulence genes, 16S rRNA gene clone library analysis, and next-generation sequencing of 16S rDNA amplicons, compensate for diagnostic culture techniques in diagnosing infectious diseases. These techniques are expected to provide novel insights into the ocular microbiota and pathology of ocular infections. In this article, we describe various ocular infections, including contact lens-related keratitis, silicone buckle infection, and dacryocystitis, which were analyzed using molecular biological techniques. The advantages and disadvantages of these highly sensitive and inclusive microbiological detection systems for ocular infections are discussed.

Analysis of stable 1,2-dichlorobenzene-degrading enrichments and two newly isolated degrading strains, Acidovorax sp. sk40 and Ralstonia sp. sk41.

Stable degrading 1,2-dichlorobenzene (1,2-DCB) enrichments were generated from original contaminated soil and groundwater via enrichment procedures using a mineral salt medium containing 1,2-DCB as the sole carbon and energy source. Four transferred enrichments showed stable 1,2-DCB-degrading ability and completely degraded 1,2-DCB within 32h. PCR-denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analyses indicated that two bacterial strains, belonging to Acidovorax spp. and Ralstonia spp., respectively, were the predominant organisms in each enrichment. Moreover, these strains maintained a stable coexistence in the four transferred enrichments. These two bacteria were subsequently identified as Acidovorax sp. strain sk40 and Ralstonia sp. strain sk41. Strain sk40 was more tolerant to higher concentrations of 1,2-DCB than strain sk41, while strain sk41 maintained a shorter degradation time under lower concentrations of 1,2-DCB. Notably, however, both strains exhibited similar growth rates and degradation rates in media containing 40mg/l 1,2-DCB, as well as complete degradation of the 1,2-DCB (40mg/l) within 32h. It is expected that these two strains will be used in future applications of bioremediation of 1,2-DCB contamination.

Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil

ABSTRACTThe bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H′) and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil.

Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments

ABSTRACTNitrification represents one of the key steps in the global nitrogen cycle. While originally considered an exclusive metabolic capability of bacteria, the identification of the Thaumarchaeota revealed that ammonia-oxidizing archaea (AOA) are also important contributors to this process, particularly in acidic environments. Nonetheless, the relative contribution of AOA to global nitrification remains difficult to ascertain, particularly in underexplored neutrophilic and alkalinophilic terrestrial systems. In this study we examined the contribution of AOA to nitrification within alkaline (pH 8.3–8.7) cave environments using quantitative PCR, crenarchaeol lipid identification and measurement of potential nitrification rates. Our results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments. The dominance of Thaumarchaeota in the archaeal communities was confirmed by both archaeal 16S rRNA gene clone library and membrane lipid analyses, while potential nitrification rates suggest that Thaumarchaeota may contribute up to 100% of ammonia oxidation in these sediments. Phylogenetic analysis of Thaumarchaeota amoA gene sequences demonstrated similarity to amoA clones across a range of terrestrial habitats, including acidic ecosystems. These data suggest that despite the alkaline conditions within the cave, the low NH3 concentrations measured continue to favor growth of AOA over AOB populations. In addition to providing important information regarding niche differentiation within Thaumarchaeota, these data may provide important clues as to the factors that have historically led to nitrate accumulation within cave sediments.

Biodegradation of Enteromorpha polysaccharides by intestinal micro-community from Siganus oramin

Micro-communities are supposed to have more potential functions of biodegradation of polysaccharides than single strain; however, the intestinal micro-communities involved in the biodegradation of Enteromorpha polysaccharides (EP) were seldom reported. In order to obtain the EP-degrading micro-community, the intestines of Siganus oramin was obtained to isolate the micro-communities, which were enriched by 0.3% of EP as the sole carbon source. A stable micro-community with EP degradative capability was achieved after seven generations of subculture, named H1. Results showed that H1 was able to degrade 75% of EP within 24 hours, and the activity of EP lyases reached 500 U mL−1 in 32 hours. With denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analysis, ten bacteria closely related to Marinomonas pontica, Microbacterium sp., Leucobacter chironomi, Cyclobacterium sp., Algoriphagus winogradskyi, Pseudoalteromonas sp. and Vibrio sp. were determined. Furthermore, compared with the DGGE bands sequence and the clone library analysis, the dominant bacteria of the EP-biodegrading micro- community were Pseudoalteromonas sp. and Vibrio sp., with the respective proportion of 38% and 46%, and they should play an important role in EP degradation together with other degrading bacteria in the micro-community H1.

Bacterial Diversity in Linglong Gold Mine, China

ABSTRACTBacteria have been actively regulating cycles of various elements in the environment. To explore the potential bacterial role in gold biogeochemical cycling, this study analyzed the bacterial diversity of mine rock (MR) and surface soil (SS) samples from Linglong gold mine using 16S rRNA gene clone library analysis and cultivation method. From MR, 24 operational taxonomic units (OTUs) were identified from MR, covering 3 phyla and 18 genera. Meanwhile, 24 OTUs were identified from SS, including 4 phyla and 18 genera. Compared with 16S rRNA gene clone library analysis, 28 aerobic and 34 anaerobic isolates were obtained, whereas 26 aerobic and 71 anaerobic strains were isolated from SS. The cultivable bacteria were affiliated with Firmicutes, Proteobacteria and Actinobacteria phyla, and dominated by Firmicutes. These results underscore the high level of bacterial diversity in the gold mine. Our study provides information on the microbial diversity in Linglong gold mine and sheds light on the existence and potential function of bacteria in the gold biogeochemical cycling.

Distribution and activity of anaerobic ammonium-oxidising bacteria in natural freshwater wetland soils.

Anaerobic ammonium oxidation (anammox) process plays a significant role in the marine nitrogen cycle. However, the quantitative importance of this process in nitrogen removal in wetland systems, particularly in natural freshwater wetlands, is still not determined. In the present study, we provided the evidence of the distribution and activity of anammox bacteria in a natural freshwater wetland, located in southeastern China, by using (15)N stable isotope measurements, quantitative PCR assays and 16S rRNA gene clone library analysis. The potential anammox rates measured in this wetland system ranged between 2.5 and 25.5 nmol N2 g(-1) soil day(-1), and up to 20% soil dinitrogen gas production could be attributed to the anammox process. Phylogenetic analysis of 16S rRNA genes showed that anammox bacteria related to Candidatus Brocadia, Candidatus Kuenenia, Candidatus Anammoxoglobus and two novel anammox clusters coexisted in the collected soil cores, with Candidatus Brocadia and Candidatus Kuenenia being the dominant anammox genera. Quantitative PCR of hydrazine synthase genes showed that the abundance of anammox bacteria varied from 2.3 × 10(5) to 2.2 × 10(6) copies g(-1) soil in the examined soil cores. Correlation analyses suggested that the soil ammonium concentration had significant influence on the activity of anammox bacteria. On the basis of (15)N tracing technology, it is estimated that a total loss of 31.1 g N m(-2) per year could be linked the anammox process in the examined wetland.

The physical form of corn influences the rumen bacterial biodiversity – preliminary results

The aim of this study was to investigate the rumen bacteria in terms of genetic biodiversity and variation due to different physical form of corn in cow diet. A total of twenty dry cows were fed for 3 months with the same diet, only differed for corn physical form, ten received corn grains, while the other ones received corn flour. To investigate the biodiversity of the bacterial 16S rRNA gene clone library analysis has been conducted and then the sequencing has been carried out using Ion Torrent PGM? System. Bacterial population was tested using R statistical software. The Kruskal-Wallis one-way analysis of variance (Kruskal-Wallis, 1952) confirmed that the bacterial populations were different when the animals were fed grain compared with flour corn. Both the OUT's abundance (Operational Taxonomic Unit) and the biodiversity indexes presented a significant difference among the two sample groups, underlining the large changes that take place even with small diet modifications in ruminal environment. There is still the need to deepen how exactly the diet changes the rumen phylogenetic structure and the consequences on bacteria's activity.

Use of stable isotope probing to identify bacterial species involved in CO&lt;sub&gt;2&lt;/sub&gt; fixation in the water just below the oxycline of the meromictic Lake Suigetsu, Japan

In this study, stable isotope probing was used to identify a bacterial community involved with bicarbonate fixation in the water just below the oxycline of the meromictic Lake Suigetsu, Japan. Water samples were incubated with 13C-labeled bicarbonate under either light or dark conditions. The identity of active bicarbonate-fixing bacteria was revealed by 16S rRNA gene clone library analysis of 13C-labeled DNA fractions. Bacterial clones closely related to the green sulfur bacterial genus Chlorobium were detected under light conditions. Clone sequences phylogenetically affiliated with the genera Arcobacter and Desulfocapsa were also detected under light conditions. In the dark incubation, clones belonging to the class Epsilonproteobacteria were detected. Clone sequences belonging to a clade containing the genus Thiomicrospira were also retrieved from dark incubation samples. These results indicated that phylogenetically diverse bacteria might fix CO2 in the water below the oxycline of Lake Suigetsu.

Purification of high ammonia wastewater in a biofilm airlift loop bioreactor with microbial communities analysis.

A 70m(3) gas-liquid-solid three-phase flow airlift loop bioreactor, in which biofilm attached on granular active carbon carriers, was used for purification of the high ammonia wastewater from bioethanol production. Under the optimum operating conditions, COD and NH4 (+)-N average removal rate of 89.0 and 98.6% were obtained at hydraulic retention time of 10h. Scanning electron microscopy was applied for observation of the biofilm formation. High contaminants removal efficiency was achieved by holding high biomass concentration in the reactor due to the attached biofilm over the carriers. The 16S rRNA gene clone library analysis indicated that 68.6% of the clones were affiliated with the two phyla Bacteroidetes and Proteobacteria, and residual clones clustered with various sequences from uncultured bacteria. The presence of various anoxic/anaerobic bacteria indicated that the oxygen gradient inside the biofilm could provide appropriate micro-environment for nitrogen removal through simultaneous nitrification and denitrification.

Microbial Diversity in Uranium Deposits from Jaduguda and Bagjata Uranium Mines, India as Revealed by Clone Library and Denaturing Gradient Gel Electrophoresis Analyses

Microbial communities within subsurface uranium (U) deposits were explored to understand the nature of community composition and their potential role in biogeochemical cycle and bioremediation. Geochemical analysis revealed that the U ores were mainly hosted on metamorphosed chlorite-biotite schists, containing varied organic carbon and elevated level of several heavy metals (U, Cu, Cr, Zn, etc.). Microbial diversity as explored by 16S rRNA gene clone library and DGGE analyses revealed predominance of Proteobacteria, Acidobacteria, Bacteroidetes along with Firmicutes and candidate division OP9 within the domain Bacteria and Euryarchaeota within the domain Archaea. Among the physiochemical parameters, level of organic carbon showed considerable impact on influencing community diversity and composition. Samples from Jaduguda with high organic carbon showed abundance of bacteria known for metabolizing different carbon compounds and affiliated to unclassified uncultured members of Chitnophagaceae (Bacteroidetes), Gp4 of Acidobacteria and unclassified β-Proteobacteria and halophilic, nitrate-reducing γ-Proteobacteria. A relatively diverse assemblage of species capable of autotrophic/heterotrophic N2 fixation, CH4 utilization, H2(0)/Fe(II)/Mn(II)/S(0) oxidation, NO3/Fe(III) reduction, U and other metal precipitation/mineralization and affiliated to families Rhizobiaceae, Bradyrhizobiaceae, Caulobacteraceae, Comamonadaceae and genera Acinetobacter, Marinobacter and Alcanivorax constituted the Bagjata samples. Distribution and interrelations among abundance of various bacterial groups detected in other U mines/radioactive waste sites were compared with our data. Overall, the study reported distinct compositions of indigenous microbial communities among the samples from two mines and provided a better insight in geomicrobiology of U deposits.

Microbial diversity and biogenic methane potential of a thermogenic-gas coal mine

The microbial communities and biogenic methane potential of a gas coal mine were investigated by cultivation-independent and cultivation-dependent approaches. Stable carbon isotopic analysis indicated that in situ methane in the coal mine was dominantly of a thermogenic origin. However, a high level of diversity of bacteria and methanogens that were present in the coal mine was revealed by 454 pyrosequencing, and included various fermentative bacteria in the phyla of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, and acetotrophic, hydrogenotrophic, and methylotrophic methanogens. Methane was produced in enrichments of mine water samples supplemented with acetate under laboratory conditions. The microbial flora obtained from the enrichments could stimulate methane formation from coal samples. 16S rRNA gene clone library analysis indicated that the microbial community from coal cultivation samples supplemented with the enriched microbial consortium was dominated by the anaerobic fermentative Clostridiales and facultative acetoclastic Methanosarcina. This study suggests that the biogenic methane potential in the thermogenic-gas coal mine could be stimulated by the indigenous microorganisms.

Methanogen prevalence throughout the gastrointestinal tract of pre-weaned dairy calves

The methanogenic community throughout the gastrointestinal tract (GIT) of pre-weaned calves has not been well studied. The current study firstly investigated the distribution and composition of the methanogenic community in the rumen, ileum, and colon of 3–4 week-old milk-fed dairy calves (n = 4) using 16S rRNA gene clone library analysis. The occurrence of methanogens in the GIT of pre-weaned calves was further validated by using PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and quantitative real-time PCR (qPCR) was applied to quantify the methanogenic community in the rumen, jejunum, ileum, cecum, colon and rectum of 8 3–4 week old animals. Both cloning libraries and PCR-DGGE revealed that phylotypes close to Methanobrevibacter were the main taxon along the GIT in pre-weaned sucking calves. The composition and abundance of methanogens varied significantly among individual animals, suggesting that host conditions may influence the composition of the symbiotic microbiota. Segregation of methanogenic communities throughout the GIT was also observed within individual animals, suggesting possible functional differences among methanogens residing in different GIT regions. This is the first study to analyze methanogenic communities throughout the GIT of milk-fed newborn dairy calves and reveal both their diversity and abundance. The identification of methanogens in the lower GIT of pre-weaned dairy calves warrants further investigation to better define methanogen roles in GIT function and their impact on host metabolism and health.

Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L.).

Plant health and soil fertility are affected by plant–microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including Acidobacteriales, Burkholderiales, Bdellovibrionales, and so on, also were affected by plant age.

Influence of Calcium Nitrate on Microbial Community Structure of Acidophilic Microorganisms

The influence of different concentrations of calcium nitrate on the growth and activity of acidophilic microorganisms were studied and the microbial community structures were compared by 16S rRNA gene clone library analysis. The addition of Ca (NO3)2 has a certain effect on the solution potential, and that the time needed to reach the steady potential were prolonged with the increase of Ca (NO3)2 concentration but not obvious when it was above 1.64 g.L-1. It also can be observed that the cell numbers decreased with the increase of Ca (NO3)2 concentration which can alter the cell osmolarity, and that the time entering the stationary phase of cell concentration was delayed with the addtion of Ca (NO3)2. With the addition of 0.41g.L-1 Ca (NO3)2, the percentage of Leptospirillum ferriphilum and Acidiphilium cryptum didn’t have great changes, while the uncultured Sulfobacillus sp., Acidithiobacillus ferrooxidans and Alicyclobacillus tolerans were also detected. With the addition of 2.05 g.L-1 Ca (NO3)2 or more, the Acidithiobacillus ferrooxidans become the dominant bacterium (which accounted for more than 90%).

Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation.

The purpose of present study was the simulation of an oil spill accompanied by burial of significant amount of petroleum hydrocarbons (PHs) in coastal sediments. Approximately 1000 kg of sediments collected in Messina harbor were spiked with Bunker C furnace fuel oil (6500 ppm). The rapid consumption of oxygen by aerobic heterotrophs created highly reduced conditions in the sediments with subsequent recession of biodegradation rates. As follows, after 3 months of ageing, the anaerobic sediments did not exhibit any significant levels of biodegradation and more than 80% of added Bunker C fuel oil remained buried. Anaerobic microbial community exhibited a strong enrichment in sulfate-reducing PHs-degrading and PHs-associated Deltaproteobacteria. As an effective bioremediation strategy to clean up these contaminated sediments, we applied a Modular Slurry System (MSS) allowing the containment of sediments and their physical–chemical treatment, e.g., aeration. Aeration for 3 months has increased the removal of main PHs contaminants up to 98%. As revealed by CARD-FISH, qPCR, and 16S rRNA gene clone library analyses, addition of Bunker C fuel oil initially affected the activity of autochthonous aerobic obligate marine hydrocarbonoclastic bacteria (OMHCB), and after 1 month more than the third of microbial population was represented by Alcanivorax-, Cycloclasticus-, and Marinobacter-related organisms. In the end of the experiment, the microbial community composition has returned to a status typically observed in pristine marine ecosystems with no detectable OMHCB present. Eco-toxicological bioassay revealed that the toxicity of sediments after treatment was substantially decreased. Thus, our studies demonstrated that petroleum-contaminated anaerobic marine sediments could efficiently be cleaned through an in situ oxygenation which stimulates their self-cleaning potential due to reawakening of allochtonous aerobic OMHCB.

Bacterial Communities of Traditional Salted and Fermented Seafoods from Jeju Island of Korea Using 16S rRNA Gene Clone Library Analysis

Jeotgal, which is widely consumed as a nutritional supplement in Korea, is traditional type of preserved seafood that is prepared by salting and fermenting. Here, we report on the bacterial community structure and diversity of jeotgal obtained from the Korean island of Jeju, which has a subtropical climate. Two samples of Jeotgal were collected from Jeju, made from either damselfish (Chromis notata; jari-dom-jeot, J1 and J2) or silver-stripe round herring (Spratelloides gracilis; ggot-myulchi-jeot, K1 and K2). The physical characteristics (pH and salinity) were assessed and the bacterial communities characterized using 16S rRNA gene-clone library analysis and cultural isolation. No difference was found in the community composition between the J and K fermented seafoods. Both fermented seafoods had relatively high salinity (26% to 33%) and high pH values (pH 6.08 to 6.72). Based on the 16S rRNA gene sequences, the halophilic lactic-acid bacteria Tetragenococcus halophilus and T. muriaticus were observed to be dominant in the J and K fermented seafoods, accompanied by halophilic bacteria including Halanaerobium spp., Halomonas spp., and Chromohalobacter spp. When compared with 7 other types of fermented seafood from a previous study, the communities of the J and K fermented seafoods were separated by the most influential group, the genus Tetragenococcus. The results suggest that these 2 types of traditional salted fermented seafood from Jeju have distinct communities dominated by Tetragenococcus spp., which are derived from the raw ingredients and are dependent on the physical conditions. This may explain how the seafoods that are made in Jeju may differ from other jeotgals.

Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands

The process of nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and shown to be mediated by "Candidatus Methylomirabilis oxyfera" (M. oxyfera). Here, evidence for n-damo in three different freshwater wetlands located in southeastern China was obtained using stable isotope measurements, quantitative PCR assays, and 16S rRNA and particulate methane monooxygenase gene clone library analyses. Stable isotope experiments confirmed the occurrence of n-damo in the examined wetlands, and the potential n-damo rates ranged from 0.31 to 5.43 nmol CO2 per gram of dry soil per day at different depths of soil cores. A combined analysis of 16S rRNA and particulate methane monooxygenase genes demonstrated that M. oxyfera-like bacteria were mainly present in the deep soil with a maximum abundance of 3.2 × 10(7) gene copies per gram of dry soil. It is estimated that ∼0.51 g of CH4 m(-2) per year could be linked to the n-damo process in the examined wetlands based on the measured potential n-damo rates. This study presents previously unidentified confirmation that the n-damo process is a previously overlooked microbial methane sink in wetlands, and n-damo has the potential to be a globally important methane sink due to increasing nitrogen pollution.