Proteobacteria Research Articles

Structural difference of gut microbiota in obese patients with or without acanthosis nigricans

Objective To investigate the distribution of gut microbiota in obese patients with or without acanthosis nigricans. Methods Totally 131 obese patients and 25 healthy participants were divided into three groups: the obesity with acanthosis nigricans (AN) group (n=59), the simple obesity (OB) group (n=79), and the control (CON) group (n=25). The fresh stool samples were collected, and the clinical and biochemistry markers were measured. Pyrosequencing technology was performed based on the 16s rRNA of fecal samples to identify and analyze the distribution pattern of gut microbiota in each group. Results The AN group had significantly higher body mass index[(37.45±5.12)kg/m2vs. (33.34±2.54)kg/m2vs.(20.35±1.68)kg/m2, P=0.045, P<0.001], insulin[32.77(25.18)mU/L vs. 20.73(9.30)mU/L vs. 8.70(6.18)mU/L, P<0.001, P<0.001], insulin resistance[7.78(6.87) vs. 4.71(2.88)vs.1.81(1.40), P<0.001, P<0.001], and interleukin (IL)-6[(3.64±2.23)ng/L vs.(2.71±0.78)ng/L vs.(2.17±0.86)ng/L, P=0.040, P=0.009] levels than OB and CON groups compared with OB and CON groups, AN group had significantly decreased diversity of bacterial flora (P=0.015, P=0.001), while no significant difference was observed in the abundance of bacterial flora. At the phylum level, the composition of flora among these three groups was similar, mainly including bacteroidetes, firmicutes, proteobacteria, and actinomycetes. Although the proportions of main bacteria flora were different, the difference was not statistically significant. At the genus level, the bacteria flora in AN and OB groups were primarily composed of Bacteroides, Megamonas, Faecalibacterium and Escherichia-Shigella. In addition, compared to OB and CON groups, AN group had significantly lower proportion of Ruminococcus (P=0.023, P=0.043, respectively) and higher proportion of Veillonella (P=0.048, P=0.043, respectively). Furthermore, the proportion of Weissella was higher in AN and OB groups than in CON group (P=0.045, P=0.025). Conclusion Obese patients with AN have more severe insulin resistance and inflammation status than those with simple obesity, and the distribution feature of gut microbiota also differ between these two patient populations. Key words: Obesity; Acanthosis nigricans; Enterobacteriaceae; Interleukin-6; 16s rRNA

High-throughput sequencing analysis of gut microbiome in patients with severe acne vulgaris and healthy individuals

Objective To compare differences of gut microbiome between patients with severe acne vulgaris and healthy individuals by using high-throughput sequencing technology. Methods Stool samples were collected from 10 outpatients with severe acne vulgaris and 10 age- and sex-matched healthy controls. Then, the bacterial DNA was extracted and subjected to 16S rRNA sequencing for the identification of microbial species, and the differences of gut microbiome were compared between the patients and controls. Results There were no significant differences in the diversity of intestinal microflora, but only the relative abundance of a few bacteria differed significantly between the two groups. Gut microbiome in the two groups mainly consisted of Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria. There were no significant differences in the relative abundance of bacteria at the phylum and genus levels between the two groups. However, the relative abundance of Blautia producta and Coprococcus eutactus at the species level differed remarkably between the two groups. Conclusion No significant differences in the bacterial diversity indices are found, but some bacterial species significantly differ between the patients with severe acne vulgaris and healthy controls. Key words: Acne vulgaris; Gut microbiome; High-throughput sequencing

A preliminary analysis of changes in composition of intestinal microbiota during infancy using polymerase chain reaction-denaturing gradient gel electrophoresis

To investigate the composition of bacteria in the stools of infants and the colonization of intestinal microbiota during infancy. Fresh stools were collected from 15 healthy infants at 0, 2, 4, 7, 10, 14, and 28 days and 3, 6, and 12 months after birth. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the composition of intestinal microbiota, perform sequencing of dominant bacteria, and to analyze the changes in the composition of intestinal microbiota during infancy. DGGE fingerprint showed that the composition of intestinal microbiota during infancy changed significantly over time after birth. The cloning and sequencing results indicated that Proteobacteria colonized the earliest, mainly the obligate aerobes Enterobacter and Pseudomonas, followed by the obligate anaerobes (Clostridium hathewayi and Veillonella parvula) and the facultative anaerobe Clostridium ramosum in Firmicutes, and Verrucomicrobia. Actinobacteria colonized the latest, mainly Bifidobacterium, and gradually became dominant bacteria. During infancy, obligate aerobes colonize the intestinal tract the earliest, followed by obligate anaerobes and facultative anaerobes. Proteobacteria colonizes the earliest, followed by Firmicutes and Verrucomicrobia, and Actinobacteria, mainly Bifidobacterium, colonizes the latest.

Insights into the fecal microbiota of captive Iberian lynx (Lynx pardinus).

The Iberian lynx (Lynx pardinus) is an endangered species restricted to several areas of Spain and Portugal. Its low genetic diversity likely provokes immune depression and high susceptibility to infectious diseases. The intestinal microbiota is closely related to host health and nutrition. In order to contribute to the knowledge of the Iberian lynx intestinal microbiota, fecal microbiota of captive specimens from two breeding centers ("La Olivilla" and "El Acebuche"), located in Southern Spain, were studied by Denaturing Gradient Gel Electrophoresis (DGGE). Results grouped microbiota in two main clusters (I and III) which included DGGE patterns of 19 out of 36 specimens, cluster I being the most frequent in "La Olivilla" (50%) and cluster III in "El Acebuche" (55.55 %) specimens. Bacteroidetes, Firmicutes and Proteobacteria phyla were identified. Segregation of clusters I and III was attributed to different microorganism presence (Pseudomonas koreensis, Pseudomonas migulae, Carnobacterium sp., Arthrobacter, Robinsoniella peorensis and Ornithinibacillus sp.) and ability to use different carbon sources. Biolog EcoPlates® results indicate high functional diversity of fecal microbiota, it being higher in cluster III. The great impact of intestinal microbiota on host health supports the importance of its microbial composition understanding. This study is the first report of captive Iberian lynx fecal microbiota composition. [Int Microbiol 20(1): 31-41 (2017)].

Bioreactor performance and microbial community dynamics in a production-scale biogas plant in northeastern China

In cold regions, heating is necessary to maintain the continuous and steady year-round operation of biogas fermentation. In this study, changes in the liquid composition, biogas production, and microbial diversity in heated- and unheated-phase samples were evaluated in a production-scale biogas plant that was fed continuously with cattle manure as a mono-substrate in Heilongjiang province in northeastern China. The volatile solid (VS) and volatile fatty acid (VFA) contents both gradually decreased in the heated and unheated fermentation processes. The chemical oxygen demand (COD) removal efficiency in the unheated phase sampled on June 15 (s-6-15) and October 15 (a-10-15) and in the heated phase sampled on January 15 (w-1-15) was 63.35%, 44.2% and 44.0%, respectively. The biogas production yields were in agreement with the results obtained for the VS and VFA contents and COD removal efficiency. The performance of the reactor in the heated phase was less efficient than that in the unheated phase, and the biogas production efficiency in June-August was higher than that in the other months. However, the CH4 content in the biogas remained similar all year. Moreover, ARDRA (Amplified Ribosomal DNA Restriction Analysis) was used to study the microbial community composition in the fermentation process. The results showed that the methanogenic archaeal consortium consisted mainly of members of the genera Methanomicrobiales and Methanosarcinales. In the heated phase, hydrogenotrophic methanogens represented the dominant methanogen in w-1-15 feedstock. After fermentation, the strict aceticlastic methanogen Methanosaeta became the dominant methanogen. In the unheated phase, the hydrogenotrophic methanogens and aceticlastic methanogens were equivalent in s-6-15 feedstock and effluent, and aceticlastic methanogens were dominant in both a-10-15 feedstock and effluent. Assessments of the bacteria diversity of the microbial communities revealed that the common strains in the feed and effluent of the three samples included the rumen bacteria, Bacteroides, Clostridium, Ruminococcaceae and Proteobacteria. Keywords: biogas production, production-scale plant, dairy manure, microbial community, northeast of China DOI: 10.3965/j.ijabe.20171001.2025 Citation: Gao Y M, Yang A Y, Bao J, Ma R X, Yan L, Wang Y J, et al. Bioreactor performance and microbial community dynamics in a production-scale biogas plant in northeastern China. Int J Agric & Biol Eng, 2017; 10(1): 191－201.

The first record of nine bacterial species belonging to the phylum Proteobacteria in Korea

As part of a larger study with the aim to discover indigenous prokaryotic species in Korea, nine bacterial strains were isolated and assigned to the phylum Proteobacteria in 2016. High 16S rRNA gene sequence similarity (>98.5%) and formation of a robust phylogenetic clades with known species indi...

Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient.

Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.

Antibiotics Susceptibility Pattern and Plasmid Profile of Bacteria Isolated from Public Motorcycle Helmets

The shared use of motorcycle helmets amongst commuters could serve as a source of spread of antibiotic resistant bacteria. In this study, the antibiotic susceptibility pattern and plasmid profile of bacteria isolated from motorcycle helmets in Lagos, Nigeria were investigated. Bacteria were isolated from forty randomly sampled motorcycle helmets and characterized using morphological and biochemical tests. A total of 83 isolates belonging to the phyla Firmicutes (74.7%) and Proteobacteria (25.3%) were obtained, and included species such as Bacillus subtilis, Bacillus anthracis, Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, Salmonella spp., Shigellla spp., Staphylococcus aureus, and Staphylococcus spp. We identified species with multiple resistance patterns to commonly used antibiotics such as the β-lactams: augumentin, amoxicillin and cloxacilin, as well as the broad spectrum antibiotics gentamicin. The calculated multiple antibiotic resistance index ranged from 0.3 to 1.0. A number of the isolated species had plasmid DNA which on curing, influenced the overall sensitivity of bacteria to antibiotics. These results suggests (without outright proof) presence of antibiotic resistant plasmids in commercial motorcycle helmets and points to the possible role of plasmids in the response of bacteria to antibiotics tested. Findings of this study further highlights the epidemiological significance of motorcycle helmets sharing amongst commuters.

Characterization of the microbiota associated to Pecten maximus gonads using 454-pyrosequencing.

A next-generation sequencing (NGS) approach was used to study the microbiota associated to Pecten maximus broodstock, applying pyrosequencing of PCR-amplified V1-V4 16S rRNA gene regions. We analysed the resident bacterial communities in female and male scallop gonads before and after spawning. DNA samples were amplified and quality-filtered reads were assigned to family and genus taxonomic levels using the Ribosomal Database Project classifier. A total of 18,520 sequences were detected, belonging to 13 phyla, including Proteobacteria (55%), Bacteroidetes (11,7%), Firmicutes (3%), Actinobacteria (2%) and Spirochaetes (1,2%), and 110 genera. The major fraction of the sequences detected corresponded to Proteobacteria, Beta- and Gammaprotebacteria being the most abundant classes. The microbiota of P. maximus gonad harbour a wide diversity, however differences on male and female samples were observed, where female gonad samples show a larger number of genera and families. The dominant bacterial genera appeared to be Delftia, Acinetobacter, Hydrotalea, Aquabacterium, Bacillus, Sediminibacterium, Sphingomonas, and Pseudomonas that were present among the four analysed samples. This next generation sequencing technique, applied for the first time in P. maximus (great scallop) gonads was useful for the study of the bacterial communities in this mollusc, unravelling the great bacterial diversity in its microbiota. [Int Microbiol 19(2): 93-99(2016)].

Intestinal microbiota composition with probiotic potential of three species of the genus Chirostoma

The aim of this research was to identify the microbiota that was found in C, jordani, C. humboldtianum and C. estor to obtain those strains with probiotic capacity and can be used in Chirostoma sp. culture. Pre-adult stages were obtained for dissection and gain an intestinal tissue portion and get pure strains throughout consecutive reseeding in NHI and TSA agar plates. Then proceeded to the molecular identification with RNAr 16S sequencing gen and establish their probiotic capacity growing them in acid pH, bile salts, pathogen inhibition to Aeromonas hydrophila and Vibrio fluvialisin vitro and with antibiotics according to FAO (2006) and Balcazar et al . (2006) techniques. Results shown that analyzed Chirostoma sp. from intestinal tract were dominated by Proteobacteria, Actinobacteria and Firmicutes identifying 60 strains, 40% of them were from C. jordani ; 30% from C. humboldtianum and 20% of strains were from C. estor . The three analyzed species share some bacterial groups even if they were grown in different environmental conditions. The common species strains were Lactobacillus sp., L.crispatus , Bacillus subtilis , B. sp., Aeromonashydrophila, A. hydrophila caviae, Vibrio fluvialis and Pseudomonaluteola . The only bacterial species that resisted stress experiments, correspond to Bacillus sp. genus represented by Bacillus subtilis , Bacillus sp. and Bacillus laterodporus , so they are good probiotics candidates for culture of Chirostoma sp. genus.

Intestinal microbiota of ornamental fish Carassius auratus

Intestinal microbiota is an essential component for any organism life, because it directly affects nutrient assimilation, growth and health processes. However, in many animals and in case of fish is unknown how Intestinal microbiota is formed, which species are dominant and which one has capacity probiotic for use in aquaculture. The goal of this study was to establish the bacterial load that dominates the back intestine of Carassius auratus. A batch of 200 healthyjuvenilefishes were obtained from an ornamental fish farm in Mexico City. The fish were maintained in two culture beakers of 100 L during 15 day to acclimatization to ensure any sign of injury disease. To extract the back of gastrointestinal tract, which was rinse several times with distilled water for food and feces residues elimination. The sample was inoculated in 9 mL of sterile saline solution and from this, three dilutions in a 1:10 relation were made, inoculating 0.1 mL from each dilution in agar plates MRS, BHI and TCBS, and were incubated at 27oC for 24 hours. Subsequently a colony forming units (CFU mL-1) count was made, with the help of a Quebec counter type. Colonies were purified through successive inoculations. The molecular identification was made out by sequencing the gene RNAr 16S using Wizard Genomic. Molecular identification showed that the back region of the intestinal tract of C. auratus was dominated by phylum Proteobacteria and Firmicutes represented by the genus Bacillus , Vibrio , Vagococcus , Brevibacillus , Aeromonas , Pseudomonas , Shewanella , Enterococcus , Paenibacillus and Morganella. In relation to bacterial abundance by specie it was established that Bacillus sp. and Pseudomonas stutzeri were the most abundant reaching CFU mL -1 counts of 210 and 167 respectively, followed by Paenibacillus lactis with 103 CFU mL -1 and Bacillus cereus with 100 CFU mL -1 while Enterococcus eurekensis was the least abundant with an average value of 6 CFU mL -1 .

Functional symbiosis and communication in microbial ecosystems. The case of wood-eating termites and cockroaches.

Animal hosts typically have strong specificity for microbial symbionts and their functions. The symbiotic relationships have enhanced the limited metabolic networks of most eukaryotes by contributing several prokaryotic metabolic capabilities, such as methanogenesis, chemolithoautotrophy, nitrogen assimilation, etc. This review will examine the characteristics that determine bacterial "fidelity" to certain groups of animals (e.g., xylophagous insects, such as termites and cockroaches) over generations and throughout evolution. The hindgut bacteria of wood-feeding termites and cockroaches belong to several phyla, including Proteobacteria, especially Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinomycetes, Spirochetes, Verrucomicrobia, and Actinobacteria, as detected by 16S rRNA. Termites effectively feed on many types of lignocelluloses assisted by their gut microbial symbionts. Although the community structures differ between the hosts (termites and cockroaches), with changes in the relative abundances of particular bacterial taxa, the composition of the bacterial community could reflect at least in part the host evolution in that the microbiota may derive from the microbiota of a common ancestor. Therefore, factors other than host phylogeny, such as diet could have had strong influence in shaping the bacterial community structure.

16S rRNA Amplicons Survey Revealed Unprecedented Bacterial Community in Solid Biomedical Wastes

Despite known risks of inappropriate disposal of biomedical solid waste; most cities in developing countries are still disposing unsorted and untreated solid biomedical waste in common dumpsites. While many studies reported the presence of pathogens in fresh biomedical waste from hospitals, none has reported on the abundance and diversity of bacterial community in aged solid biomedical waste from a common dumpsite. A qualitative survey was done to identify types of solid biomedical waste on the dumpsite. Soils, sludge or washings of biomedical wastes were sampled. Total DNA was extracted and v4 region of 16S rRNA amplicons were sequenced using an Illumina MiSeq platform. A total of 1,706,442 sequences from 15 samples passed quality control. The number of sequences per sample ranged from 70664 to 174456 (mean 121765, SD 35853). Diversity was high with an InvSimpson index of 63 (Range 5 – 496, SD 121). Thirty five phyla were identified, but only 9 accounted for 96% of all sequences. The dominant phyla were Proteobacteria 37.4%, Firmicutes 34.4%, Bacteroidetes 14.1 %, Actinobacteria 5.6% and Chloroflex 1.7%. Catchall analysis predicted a mean of 9399 species per sample. Overall, 31402 operational taxonomic units (OTUs) were detected, however, only 19.8% (6,202) OTUs were found more than ten times. The most predominant OTUs were Proteinclasticum (10.4%), Acinetobacter (6.9), Halomonas (3.9), Pseudomonas (1.7%), Escherichia/Shigella 1.5% and Planococcus (1.3%). Proteiniclasticum spp and Acinetobacter spp were found in 67% (10/15) of all samples at relative abundance of 1%. Taxonomic-to-phenotype mapping revealed the presence of 36.2% related to bacteria involved in dehalogenation, 11.6% degraders of aromatic hydrocarbons, 14.8% chitin degraders, 8.5% chlorophenol degradation and Atrazine metabolism 8.3%. Taxonomy-to human pathogen mapping found 34% related to human pathogens and 39.4% were unknown. Conclusions There’s rich and diverse bacterial community in aged solid biomedical waste. Some of the predominant OTUs are related to bacteria of industrial use. We found a good number of OTUs mapping to human pathogens. Most of OTUs mapped to unknown metabolism and also to group unknown whether they human pathogens or not. To our knowledge, this is the first reports on bacteria related to industrial use from solid biomedical waste. This finding will facilitate to design further research using functional metagenomics to better understand the potential of bacteria from aged solid biomedical waste.

Microbial profile of asymptomatic and symptomatic teeth with primary endodontic infections by pyrosequencing

Objectives: The purpose of this in vivo study was to investigate the microbial diversity in symptomatic and asymptomatic canals with primary endodontic infections by using GS FLX Titanium pyrosequencing. Materials and Methods: Sequencing was performed on 6 teeth (symptomatic, n = 3; asymptomatic, n = 3) with primary endodontic infections. Amplicons from hypervariable region of the small-subunit ribosomal RNA gene were generated by polymerized chain reaction (PCR), and sequenced by means of the GS FLX Titanium pyrosequencing. Results: On average, 10,639 and 45,455 16S rRNA sequences for asymptomatic and symptomatic teeth were obtained, respectively. Based on Ribosomal Database Project Classifier analysis, pyrosequencing iden- tified the 141 bacterial genera in 13 phyla. The vast majority of sequences belonged to one of the seven phyla: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteo bacteria, Spirochetes, and Synergistetes . In genus level, Pyramidobacter, Streptococcus, and Leptotrichia constituted about 50% of microbial profile in asymptomatic teeth, whereas Neisseria, Propionibacterium, and Tessaracoccus were frequently found in symptomatic teeth (69%). Grouping the sequences in operational taxonomic units (3%) yielded 450 and 1,997 species level phylotypes in asymptomatic and symptomatic teeth, respectively. The total bacteria counts were significantly higher in symptomatic teeth than that of asymptomatic teeth ( p < 0.05). Conclusions: GS FLX Titanium pyrosequencing could reveal a previously unidentified high bacterial diver- sity in primary endodontic infections. (J Kor Acad Cons Dent 2011;36(6):498-505.) ABSTRACT

Prokaryotic community structure in photosynthetic biofilms from extreme acidic streams, Río Tinto (SW, Spain)

Four algal photosynthetic biofilms were collected from the Rio Tinto (SW Spain) at four localities: AG, Euglena and Pinnularia biofilms; ANG, Chlorella and Pinnularia biofilms; RI, Cyanidium and Dunaliella biofilms; and CEM, Cyanidium , Euglena and Pinnularia biofilms. Community composition and structure were studied by a polyphasic approach consisting of 16S rRNA analysis, scanning electron microscopy by back-scattered electron detection mode (SEM-BSE), and fluorescence in-situ hybridization (FISH). Acidophilic prokaryotes associated with algal photosynthetic biofilms included sequences related to the Alpha-, Beta-, and Gammaproteobacteria (phylum Proteobacteria) and to the phyla Nitrospira, Actinobacteria, Acidobacteria and Firmicutes. Sequences from the Archaea domain were also identified. No more than seven distinct lineages were detected in any biofilm, except for those from RI, which contained fewer groups of Bacteria . Prokaryotic communities of the thinnest algal photosynthetic biofilms ( 200 μm) generate microniches that could facilitate the development of less-adapted microorganisms (coming from the surrounding environment) to extreme conditions, thus resulting in a more diverse prokaryotic biofilm. [ Int Microbiol 2008; 11(4):251-260]

The taxophysiological paradox: changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host.

The phylogenetic relationships of symbiotic bacteria from the xylophagous cockroach Cryptocercus (Cryptocercidae, Blattaria) were compared to those described in previous reports in lower termites. The 16S rDNA bacterial genes were PCR-amplified from DNA isolated from the entire hindgut using Bacteria-selective primers, and the 16S rDNA amplicons were cloned into Escherichia coli. The changes in the gut microbiota of Cryptocercus under three physiological conditions, "active," "fasting," and "dead," were studied. Analysis of the active-clone library revealed 45 new phylotypes (clones sharing >97% sequence identity were grouped into the same phylotype) from 54 analyzed clones. The clones were affiliated with the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, Synergistetes, Verrucomicrobia, and candidate phylum Termite Group 1 (TG1). Clones belonging to Spirochaetes, Bacteroidetes, and TG1 phyla clustered with previously reported sequences obtained from the guts of several termites, suggesting that these clones are common constituents of the intestinal microbiota of lower termites and Cryptocercus. In the fasting-clone library, 19 new phylotypes, from 49 clones studied, were distinguished. The new phylotypes were affiliated with the phyla Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Spirochaetes, Synergistetes, and the candidate phylum TM7. Finally, in the dead-clone library, 24 new phylotypes from 50 studied clones were found. The new phylotypes were affiliated with the phyla Firmicutes, Actinobacteria, and Proteobacteria. Thus, from active, to fasting, to dead physiological states, a decrease in the number of phyla present in the whole microbial gut was evident. However, in the dead physiological state, each phylum conserved contained more new phylotypes. This poses a taxophysiological paradox, because a stable, active physiological state of Cryptocercus-due to a continuous input of wood-supports a higher diversity of bacterial phyla, probably necessary to maintain a sharp O(2)-H(2) gradient in the gut. By contrast, in the dead state, nutrient input is limited to the residual gut microbiota that is killed by the newly oxic environment, thus providing a food source for other, aerobic or facultative anaerobic bacteria. This results in an increase in the internal diversity of the few remaining phyla.

A Preliminary Study on the Diversity of Bacteria in the Xisha Trough Sediment, the South China Sea

The bulk DNA was isolated from bacterial habits in sediments of the Xisha trough,the south China sea.Using a pair of primers special for most common bacteria,the researchers amplified partial sequences of bacterial 16S rDNA gene and thus constructed a 16S rDNA clone library.A total of 22 clones were used to reconstruct the bacterial 16S rDNA phylogenetic tree.Guided by the phylogenetic tree,bacteria fell into four main lineages: Proteobacteria,Planctomycene,Actinabacteria and Low G+C Gram-positive bacterium.Among them,49% belonged to Proteobacteria,22% to Planctomycene,the same to Low G+C Gram-positive bacterium,and the remaining 7% to Planctomycene.The group of Proteobacteria clustered in three subgroups: α-,γ-and δ-Proteobacteria,and the subgroup of δ-Proteobacteria predominated in them.Furthermore,the abundance of two groups of Planctomycene and Low G+C Gram-positive bacterium,living commonly in shallow marine deposits,was higher in sediments of the Xisha Trough than in other deep-sea sediments.Most members of these two groups were probably brought from the shelf into the trough sediment by the turbid.

Bacterial diversity within the planktonic community of an artesian water supply

Culture and molecular methods were used to describe the planktonic bacterial diversity of an artesian water supply in rural Latah County, Idaho, within the drainage of a small perennial stream, Thorn Creek. The surrounding depth to groundwater at this location is thought to be significant (>100 m), and this transitional zone (basalt-granite) of the Palouse aquifer system is little studied. The water produced by this artesian source is consistent even in years of drought and is of high quality, both mineralogically and microbiologically. A culture-based analysis using 30 media types and four incubation temperatures demonstrated that several metabolic types were present in the water. 16S rRNA gene fragments amplified from the DNA of pooled cultured cells and from the DNA extracted from 1 L of the source water were compared using denaturing gradient gel electrophoresis. The results indicated that the two DNA samples did not have similar 16S rRNA gene compositions and that several uncultured phyla were present in the community DNA sample. These results indicated that large-scale culturing did not accurately represent the structure planktonic community. 16S rRNA gene sequences from 17 different genera were obtained from the community DNA sample; the most abundant were similar to Rhodoferax, Rhodobacter, and Polaromonas species. Sequences related to the Proteo bacteria, Bacteroidetes/Chlorobi, Firmicutes, and Acidobacterium/Fibrobacter divisions were also detected.

Preliminary investigations on suppression of Meloidogyne incognita (Kofoid & White) Chitwood (Nematoda: Heteroderidae) by antagonistic rhizobacteria

Summary Fluorescent Pseudomonad strains have been obtained from diseased second juveniles from Meloidogyne incognita (Kofoid & White, 1919) Chitwood, 1949 (Nematoda: Heteroderidae) infected tomato roots. After the screening in vivo made by 5 different isolated strains, Strain Pat1 has been selected to test the antagonistic effects on the root-knot nematodes. Strain Pat1 has been identified as non plant pathogenic Pseudomonas fluorescens Migula, 1895 (Proteobacteria: Pseudomonadaceae) according to the test result. Cucumber (Cucumis sativus) cv Sardes has been used as test plant. Bacterial suspension (10 9 cfu/ml) was applied by three different ways: 1) Seed bacterization; 2) Seed bacterization plus seedling drenching; and 3) Seedling drenching. The eggs of rootknot nematodes have been obtained from diseased tomato roots by blender-sieve method for infection cucumber seedlings with root-knot nematodes. 20 000 eggs/plant have been given to cucumber seedlings during transplanting. The plants have been observed for symptom development for 10-11 weeks in climatized room under controlled conditions. Symptom development has been evaluated by using 0-4 scale for upper parts of plants, and 0-10 Zeck’s root-knot scale for the roots. When seed bacterization and seed bacterization plus seedling drenching applicat ions compared with positive control; plants infected with root-knot nematodes alone, it was determined that disease symptoms on upper parts of the plants were reduced 35 % and 21 %; gal formation on the roots were reduced 44 % and 39 %, * This study was presented at the VIII th European Congress of Entomology held on 17-22 September 2006 in Izmir (TURKEY) and published as an abstract.

Depth-related distribution of bacterial community in sediments of eutrophic Guanting reservoir

In this study, DNAs were extracted from sediment samples at depths of 5, 35, and 69 cm from eutrophic Guanting reservoir, China. 16S rDNAs were amplified by PCR and clone libraries were constructed. The depth-related distribution of bacterial community in the sediment was characterized by using amplified 16S rDNA restriction analysis (ARDRA) and sequencing of the dominant clones. The results indicated that species diversity in the sediment of Guanting reservoir was rather high with the Shannon-Wiener index about 5.8. Bacterial richness varied in different depths: the highest in the sample of 35 cm in depth; followed by the sample of 5 cm in depth; and the lowest bacterial richness in the sample of 69 cm. Dominant species from the three samples were different although there were some common clones. Phylogenetic analysis showed that all of the dominant clones in the three layers were uncultured bacteria and distantly related to the previously reported species in beta or gamma subclass of proteobacteria, including bacterial groups that have the ability to degrade aromatic hydrocarbons, n-alkanes, chlorinated organic compounds, or to accumulate polyphosphate, etc. Changes of depth-related bacterial community in the Guanting reservoir sediment might reflect the pollution history and the water quality of the reservoir. In addition, the cloned sequences from the Guanting reservoir sediment were all different from the presently reported ones, indicating that there were some particular bacteria in that environment.