PCR-amplified 16S rRNA Gene Research Articles

Soluble corn fiber modulates calcium absorption by altering colonic microbiota

Soluble corn fiber (SCF) has been shown to increase calcium (Ca) absorption. Animal models suggest colonic bacteria can influence Ca absorption; the mechanism is not understood in humans. This study assessed the effect of SCF on fecal microbiota in relation to Ca absorption in a racially diverse group of teens. Twenty‐four boys and girls (12–15 y; 45.8% Asian, 25% Hispanic, 29.2% Multiracial) participated in two 3‐week metabolic Ca balance studies testing 0 and 12 g/d SCF on a low Ca diet (600 mg/d), characteristic of usual intakes. Microbial community composition, evaluated in fecal samples collected during each treatment, was assessed with 454 pyrosequencing of PCR amplified 16S rRNA genes. Ca absorption increased by 12% with SCF consumption compared to no SCF. This increase correlated with a decrease in other Erysipelotrichaceae (P<0.04) and increases in Bacteroides (P<0.03), Alistipes (P<0.05), Butyricicoccus (P<0.04), Oscillibacter (P<0.008) and Dialister (P<0.003) but not changes in Lactobacillus (P=0.07) and Parabacteroides (P=0.07). These bacterial genera have been identified as short chain fatty acid producers while Bacteroides is capable of fermenting fibers like SCF. The bacterial changes suggest SCF may increase Ca absorption through fermentation. This is the first study to show that increases in specific bacteria were significantly correlated with the observed increase in calcium absorption.Grant Funding Source: Tate & Lyle Health & Nutrition Sciences

Green sulphur bacteria as a component of the photosynthetic plankton community in small dimictic humic lakes with an anoxic hypolimnion

High bacteriochlorophyll (BChl) concentrations in the anoxic water layers of some humic lakes have indicated that green sulphur bacteria (GSB) may be ecologically significant. The abundance and spatial distribution of GSB were therefore addressed in 13 small humic lakes using fragment analysis and sequencing of PCR-amplified 16S rRNA genes. GSB were detected from lakes where the photosynthetically active radiation was at least 1.1 µE m �2 s �1 at the oxic� anoxic boundary layer. In these lakes, 13 to 42% of the 16S rRNA gene sequences of the anoxic water column were assigned to GSB. The spatial distribution of GSB was tightly correlated with the spectrophotometrically measured BChl concentration during the summer season. Maximum BChl concentrations were observed in the uppermost part of the anoxic water layer, covering most of the chlorophyll pigment in these lakes. The GSB of the humic lakes typically belonged to a phylogenetically homogenous group closely related to Chlorobium clathratiforme.

Reactor performance and microbial community dynamics during solid-state anaerobic digestion of corn stover at mesophilic and thermophilic conditions

Reactor performance and microbial community dynamics were investigated during solid state anaerobic digestion (SS-AD) of corn stover at mesophilic and thermophilic conditions. Thermophilic SS-AD led to faster and greater reductions of cellulose and hemicelluloses during the first 12days compared to mesophilic SS-AD. However, accumulation of volatile fatty acids (VFAs) was 5-fold higher at thermophilic than mesophilic temperatures, resulting in a large pH drop during days 6–12 in the thermophilic reactors. Culture-based enumeration revealed 10–50 times greater populations of cellulolytic and xylanolytic microbes during thermophilic SS-AD than mesophilic SS-AD. DGGE analysis of PCR amplified 16S rRNA genes showed dynamic shifts, especially during the thermophilic SS-AD, of bacterial and archaeal communities over the 38days of SS-AD as a result of acclimation of the initial seed microbial consortia to the lignocellulosic feedstock. The findings of this study can guide future studies to improve efficiency and stability of SS-AD.

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.

Effects of wet and dry seasons on the aquatic bacterial community structure of the Three Gorges Reservoir

This study investigated effects of wet and dry seasons on the bacterial community structure of the Three Gorges Reservoir by using denaturing gradient gel electrophoresis analysis of the PCR-amplified bacterial 16S rRNA gene. Bacterial diversity, as determined by the Shannon index, the Simpson's index, and the Richness, dramatically changed in between the dry and wet seasons. The changes in the diversity and relative abundance of microbial populations among the five sites during the wet season have become more marked than those observed during the dry season. Furthermore, cluster analysis also showed these changes. The phylogenetic analysis indicated that Betaproteobacteria is the dominant population, followed by Actinobacterium, in both the wet season and dry season. The water quality parameters were quite stable at all five sites during the same season but noticeably varied from season to season. Canonical correspondence analysis also indicated that the changes in the bacterial community composition were primarily correlated with the variations in temperature, transparency, and the concentrations of NH4 (+)-N. Slight changes in bacterial community composition among the five sites during the dry season were correlated with different environments. However, during the wet season, major changes were correlated not only with environments, but also it may be associated with the bacterial populations from the surrounding areas and tributaries of the Three Gorges Reservoir.

Comparative Study of PCR-Based Approaches for the Genetic Characterization of Three Strains of Acidithiobacillus caldus Isolated from Different Sites in China

Comparative study of the genetic characteristics among three Acidithiobacillus caldus strains isolated from different typical environments in China was performed using a combination of molecular methods, namely sequencing analysis of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers (ITS), repetitive element PCR (rep-PCR), arbitrarily primed PCR (AP-PCR) fingerprinting and random amplified polymorphic DNA (RAPD). Both of the 16S rRNA gene and 16S-23S rRNA gene intergenic spacers sequences of the three strains exhibited small variations, with 99.9-100%, 99.7-100% identity respectively. In contrast, according to the analysis of bacterial diversity based on rep-PCR and AP-PCR fingerprinting, they produced highly discriminatory banding patterns, and the similarity values between them varied from 61.97% to 71.64%. RAPD analysis showed that banding profiles of their genomic DNA exhibited obvious differences from each other with 53.44-75% similarity. These results suggested that in contrast to 16S rRNA genes and 16S-23S rRNA gene intergenic spacers sequencing analysis, rep-PCR, AP-PCR fingerprinting and RAPD analysis possessed higher discriminatory power in identifying these closely related strains. And they could be used as rapid and highly discriminatory typing techniques in studying bacterial diversity, especially in differentiating bacteria within Acidithiobacillus caldus.

Enrichment and characterization of a bacterial culture that can degrade 4-aminopyridine

BackgroundThe agrichemical 4-aminopyridine is used as a bird repellent in crop fields and has an epileptogenic action in a variety of animals, including man and mouse. 4-Aminopyridine is biodegraded in the environment through an unknown mechanism.ResultsA 4-aminopyridine-degrading enrichment culture utilized 4-aminopyridine as a carbon, nitrogen, and energy source, generating 4-amino-3-hydroxypyridine, 3,4-dihydroxypyridine, and formate as intermediates. 4-Amino-3-hydroxypyridine could not be further metabolized and probably accumulated as a dead-end product in the culture. Biodegradability tests and partial sequence analysis of the enrichment culture indicated that 4-aminopyridine was mainly degraded via 3,4-dihydroxypyridine and that the metabolite is probably cleaved by 3-hydroxy-4-pyridone dioxygenase. Seven culturable predominant bacterial strains (strains 4AP-A to 4AP-G) were isolated on nutrient agar plates. Changes in the bacterial populations of 4-aminopyridine, 3,4-dihydroxypyridine, or formate/ammonium chloride enrichment cultures were monitored by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Sequence analysis of the 16S rRNA gene fragments derived from predominant DGGE bands indicated that Pseudomonas nitroreducens 4AP-A and Enterobacter sp. 4AP-G were predominant in the three tested enrichment cultures and that the unculturable strains Hyphomicrobium sp. 4AP-Y and Elizabethkingia sp. 4AP-Z were predominant in 4-aminopyridine and formate/ammonium chloride enrichment cultures and in the 3,4-dihydroxypyridine enrichment culture, respectively. Among the culturable strains, strain 4AP-A could utilize 3,4-dihydroxypyridine as a growth substrate. Although we could not isolate strain 4AP-Y on several media, PCR-DGGE analysis and microscopy indicated that the unique bi-polar filamentous bacterial cells gradually became more dominant with increasing 4-aminopyridine concentration in the medium.ConclusionsHyphomicrobium sp. 4AP-Y, P. nitroreducens 4AP-A, and Elizabethkingia sp. 4AP-Z probably play important roles in 4-aminopyridine degradation in crop fields. In the enrichment culture, 3,4-dihydroxypyridine and its metabolites including formate might be shared as growth substrates and maintain the enrichment culture, including these indispensable strains.

Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal “filamentous streamer” communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5–7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.

The versatile in situ gene expression of an Epsilonproteobacteria‐dominated biofilm from a hydrothermal chimney

The Epsilonproteobacteria, including members of the genus Sulfurovum, are regarded as important primary producers in hydrothermal systems. However, their in situ gene expression in this habitat has so far not been investigated. We report a metatranscriptomic analysis of a Sulfurovum-dominated biofilm from one of the chimneys at the Loki's Castle hydrothermal system, located at the Arctic Mid Ocean Ridge. Transcripts involved in hydrogen oxidation, oxidation of sulfur species, aerobic respiration and denitrification were abundant and mostly assigned to Sulfurovum, indicating that members of this genus utilize multiple chemical energy sources simultaneously for primary production. Sulfurovum also seemed to have a diverse expression of transposases, potentially involved in horizontal gene transfer. Other transcripts were involved in CO₂ fixation by the reverse TCA cycle, the CRISPR-Cas system, heavy metal resistance, and sensing and responding to changing environmental conditions. Through pyrosequencing of PCR amplified 16S rRNA genes, the Sulfurovum-dominated biofilm was compared with another biofilm from the same chimney, revealing a large shift in the community structure of Epsilonproteobacteria-dominated biofilms over a few metres.

Effect of galactooligosaccharides andBifidobacterium animalisBb-12 on growth ofLactobacillus amylovorusDSM 16698, microbial community structure, and metabolite production in anin vitrocolonic model set up with human or pig microbiota

A validated in vitro model of the large intestine (TIM-2), set up with human or pig faeces, was used to evaluate the impact of potentially probiotic Lactobacillus amylovorus DSM 16698, administered alone (i), in the presence of prebiotic galactooligosaccharides (GOS) (ii), and co-administered with probiotic Bifidobacterium animalis ssp. lactis Bb-12 (Bb-12) (iii) on GOS degradation, microbial growth (L. amylovorus, lactobacilli, bifidobacteria and total bacteria) and metabolite production. High performance anion exchange chromatography revealed that GOS degradation was more pronounced in TIM-2 inoculated with pig faeces than with human faeces. Denaturing gradient gel electrophoresis profiling of PCR-amplified 16S rRNA genes detected a more complex Lactobacillus spp. community in pig faecal material than in human faecal inoculum. According to 16S rRNA gene-targeted qPCR, GOS stimulated the growth of lactobacilli and bifidobacteria in faecal material from both materials. The cumulative production of short chain fatty acids and ammonia was higher (P < 0.05) for pig than for human faeces. However, lactate accumulation was higher (P < 0.05) in the human model and increased after co-administration with GOS and Bb-12. This study reinforced the notion that differences in microbiota composition between target host organisms need to be considered when animal data are extrapolated to human, as is often done with pre- and probiotic intervention studies.

Bt 벼의 토양미생물상 영향 비교평가

경제적 및 농업적 장점은 유전자 변형 작물 재배면적의 증가를 가져왔다. 그러나 유전자 변형 작물의 상업적 재배전에 유전자 변형 작물의 인간건강 및 환경에 미칠 잠재적 위해성에 대한 면밀한 검토가 필수적이다. 본 연구에서는 Bt벼의 토양미생물 군집에 미치는 영향을 조사하였다. 토양화학성분을 분석한 결과, Bt벼와 낙동벼 근권토양 간 화학성분의 유의성 있는 차이는 없는 것으로 조사되었다. 재배전, 재배초기, 최고분얼기의 토양미생물 군집밀도를 조사했을 때 Bt벼 근권토양의 세균, 방선균, 진균 군집밀도는 낙동벼와 유사한 수준으로 나타났다. 시기별 DGGE 분석결과 Bt 벼 근권토양 전체미생물상은 낙동벼와 차이가 없는 것으로 조사되었다. Pyrosequencing을 통한 Bt벼와 낙동벼의 미생물 군집조성을 조사한 결과 주요 미생물상 분포에 있어서도 매우 유사한 양상을 나타내었다. 위의 결과들을 종합해볼때 Bt 재배에 따른 토양미생물상에 미치는 영향은 미미한 것으로 사료된다. 수확 후 벼 잔존물이 토양환경에 미치는 영향에 대해서는 좀 더 연구가 진행되어야 할 것이다. The cultivation of genetically modified (GM) crops has increased due to their economic and agronomic advantages. Before commercialization of GM crops, however, we must assess the potential risks of GM crops on human health and environment. The aim of this study was to investigate the possible impact of Bt rice on the soil microbial community. Microbial communities were isolated from the rhizosphere soil cultivated with Bt rice and Nakdong, parental cultivar and were subjected to be analyzed using both culture-dependent and molecular methods. The total counts of bacteria, fungi, and actinomycetes in the rhizosphere of transgenic and conventional rice were not significantly different. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes revealed that the bacterial community structures during cultural periods were very similar each other. Analysis of dominant isolates in the rhizosphere cultivated with Bt and Nakdong rice showed that the dominant isolates from the soil of Bt rice and Nakdong belonged to the Proteobacteria, Cloroflexi, Actinobacteria, Firmicutes, and Acidobacteria. These results indicate that the Bt rice has no significant impact on the soil microbial communities during cultivation period. Further study remains to be investigated whether the residue of Bt rice effect on the soil environment.

Community and Proteomic Analysis of Methanogenic Consortia Degrading Terephthalate

Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122-130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that Pelotomaculum, Methanosaeta, and Methanolinea were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed in situ. The results confirmed that TA was degraded by Pelotomaculum spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H(2)/CO(2), and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.

Use of cassette-electrode microbial fuel cell for wastewater treatment

Cassette-electrode microbial fuel cells (CE-MFCs) have been developed for the conversion of biomass wastes into electric energy. The present study modified CE-MFC for its application to wastewater treatment and examined its utility in a long-term (240 days) experiment to treat a synthetic wastewater, containing starch, yeast extract, peptone, plant oil, and a detergent (approximately 500mg of total chemical oxygen demand [COD] per liter). A test MFC reactor (1l in capacity) was equipped with 10 cassette electrodes with total anode and cathode projection areas of 1440cm(2), and the operation was initiated by inoculating with rice paddy-field soil. It was demonstrated that CE-MFC achieved COD removal rates of 80% at hydraulic-retention times of 6h or greater, and electricity was generated at a maximum power density of 150mWm(-2) and Coulombic efficiency of 20%. Microbial communities established on anodes of CEs were analyzed by pyrosequencing of PCR-amplified 16S rRNA gene fragments, showing that Geobacter, Clostridium, and Geothrix were abundantly detected in anode biofilms. These results demonstrate the utility of CE-MFC for wastewater treatment, in which Geobacter and Geothrix would be involved in the electricity generation.

Diversity analysis of bacterial community compositions in sediments of urban lakes by terminal restriction fragment length polymorphism (T-RFLP)

Bacteria are crucial components in lake sediments and play important role in various environmental processes. Urban lakes in the densely populated cities are often small, shallow, highly artificial and hypereutrophic compared to rural and natural lakes and have been overlooked for a long time. In the present study, bacterial community compositions in surface sediments of three urban lakes (Lake Mochou, Lake Qianhu and Lake Zixia) in Nanjing City, China, were investigated using the terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries. Remarkable differences in the T-RFLP patterns were observed in different lakes or different sampling stations of the same lake. Canonical correspondence analysis indicated that total nitrogen (TN) had significant effects on bacterial community structure in the lake sediments. Chloroflexi were the most dominant bacterial group in the clone library from Lake Mochou (21.7% of the total clones) which was partly associated with its higher TN and organic matters concentrations. However, Bacteroidetes appeared to be dominated colonizers in the sediments of Lake Zixia (20.4% of the total clones). Our study gives a comprehensive insight into the structure of bacterial community of urban lake sediments, indicating that the environmental factors played a key role in influencing the bacterial community composition in the freshwater ecosystems.

The Dynamic Cultivation System: A new method for the detection of temporal shifts in microbial community structure in clay

A major problem in the analysis of natural bacterial populations is that probably less than 1% of species were so far cultured and described. In order to overcome this disadvantage, culture independent DNA based methods, such as comparison of PCR-amplified 16S rRNA genes, are used for the description of the bacterial diversity and the identification of various species. Unfortunately, each molecule of DNA, including those of dead organisms and allochthonous genomes, can be detected by PCR-based molecular fingerprint techniques within a sample besides the DNA of native organisms. Hence, an adequate image of the actually active population composition cannot be projected with these methods. An additional challenge is the extraction of DNA from charged particles and the presence of inhibitors for downstream molecular analyses. This study reports the results of a new cultivation approach that allows to overcome these problems and to obtain almost total environmental DNA of microorganisms for subsequent genetic DNA fingerprint techniques.This new approach, the Dynamic Cultivation System (DCS) is characterized by special nutrient availability to simulate the bacterial natural habitat and the cell–cell interaction for various processes, such as collective degradation of compounds.The DCS was applied in combination with the genetic fingerprint technique Denaturing Gradient Gel Electrophoresis (DGGE) to study changes in the population composition during an alteration process of clay. The results indicate a changing bacterial diversity over time which seems to correlate to the changing pH in the clay samples in situ. This effect was most evident after cultivation on the DCS.

Influence of filling ratio and carrier type on organic matter removal in a moving bed biofilm reactor with pretreatment of electrocoagulation in wastewater treatment

At present, there is great concern about limited water resources and water quality, which require a more advanced technology. The Moving Bed Biofilm Reactor (MBBR) has been shown to be an efficient technology for removal of organic matter and nutrients in industrial and urban wastewater treatment. However, there are some pollutants which are more difficult to remove by biological processes, so this process can be improved with additional physical and chemical treatments such as electrocoagulation, which appears to be a promising technology in electrochemical treatments. In this research, urban wastewater was treated in an MBBR plant with an electrocoagulation pre-treatment. K1 from AnoxKaldnes® and AQWISE ABC5 from Aqwise were the carriers studied under three different filling ratios (20, 35, and 50%). The experimental pilot plant had four bioreactors with 20 L of operation volume and a common feed tank with 100 L of operation volume. The movement of the carriers was generated by aeration and stirrer systems. Organic matter removal was studied by analysis of soluble chemical oxygen demand (sCOD). The maximum organic matter removal in this MBBR system was 65.8% ± 1.4% and 78.4% ± 0.1% for K1 and Aqwise ABC5 carriers, respectively. Moreover, the bacterial diversity of the biofilm was studied by temperature-gradient gel electrophoresis (TGGE) of PCR-amplified partial 16S rRNA genes. 20 prominent TGGE bands were successfully reamplified and sequenced, being the predominant population: β-Proteobacteria, α-Proteobacteria, and Actinobacteria.

High Level of Bacterial Diversity and Novel Taxa in Continental Shelf Sediment

The bacterial diversity of the continental shelf sediment in the Yellow Sea was investigated by the cloning and sequencing of PCR-amplified 16S rRNA genes. The majority of the cloned sequences were distinct phylotypes that were novel at the species level. The richness estimator indicated that the sediment sample might harbor up to 32 phylum-level taxa. A large number of low-abundance, phylum-level taxa accounted for most of the observed phylogenetic diversity at our study site, suggesting that these low-abundance taxa might play crucial roles in the shelf sediment ecosystem.

Epibiotic bacterial community of Sphaeroma serratum (Crustacea, Isopoda): relationship with molt status

Sphaeroma serratum is a marine isopod species that inhabits seashores from Europe to West Africa. The individuals live under stones in direct contact with reduced sediments and harbour a diverse bacterial community on the cuticle of their pleopods. We investigated the diversity of these epibiotic bacteria on male (pubescent and senescent) and female specimens with electron microscopic obser vations and molecular tools. The microbial community of S. serratum was shown to be composed of at least 5 bacterial morphotypes observed on the pleopodal cuticle in all male specimens. Using fluorescence in situ hybridization, we identified 5 major phylogenetic groups (α-, β-, γ- and δ-Proteobacteria and Archaea) whereas denaturing gradient gel electro - phoresis (DGGE) of PCR-amplified 16S rRNA gene fragments of epibiotic bacteria revealed 50 bands. The bacterial community associated with S. serratum seems more diverse than in other marine crustaceans, such as Rimicaris. The relative diversity of this bacterial community was also studied in relation to the molt cycle. The comparison of DGGE band patterns of several individuals from female, pubescent male and senescent male groups revealed that the bacterial community diversity was dependent on the sex and the age of the individuals and more generally on the molt status.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations.

Molecular characterization of the microbial communities in the subcaudal gland secretion of the European badger (Meles meles)

Many mammals possess specialized scent glands, which convey information about the marking individual. As the chemical profile of scent marks is likely to be affected by bacteria metabolizing the primary gland products, the variation in bacterial communities between different individuals has been proposed to underpin olfactory communication. However, few studies have investigated the dependency of microbiota residing in the scent organs on the host's individual-specific parameters. Here, we used terminal restriction fragment length polymorphism analysis of the PCR-amplified 16S rRNA gene and clone library construction to investigate the microbial communities in the subcaudal gland secretion of the European badger (Meles meles). As the secretion has been shown to encode individual-specific information, we investigated the correlation of the microbiota with different individual-specific parameters (age, sex, body condition, reproductive status, and season). We discovered a high number of bacterial species (56 operational taxonomic units from four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes), dominated by Actinobacteria (76.0%). The bacterial communities of cubs and adults differed significantly. Cubs possessed considerably more diverse communities dominated by Firmicutes, while in adults the communities were less diverse and dominated by Actinobacteria, suggesting that the acquisition of a 'mature bacterial community' is an ontogenetic process related to physiological changes during maturation.