scholarly journals Diversity of Beta-Propeller Phytase Genes in the Intestinal Contents of Grass Carp Provides Insight into the Release of Major Phosphorus from Phytate in Nature

2009 ◽  
Vol 75 (6) ◽  
pp. 1508-1516 ◽  
Author(s):  
Huoqing Huang ◽  
Pengjun Shi ◽  
Yaru Wang ◽  
Huiying Luo ◽  
Na Shao ◽  
...  
Keyword(s):  
Grass Carp ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Organic Phosphorus ◽  
Aquatic Communities ◽  
Intestinal Contents ◽  
Gradient Gel Electrophoresis ◽  
Unculturable Bacteria ◽  
Phosphorus Recycling ◽  
Dominant Bacteria

ABSTRACT Phytate is the most abundant organic phosphorus compound in nature, and microbial mineralization of phytate by phytase is a key process for phosphorus recycling in the biosphere. In the present study, beta-propeller phytase (BPP) gene fragments were readily amplified from the intestinal contents of grass carp (Ctenopharyngodon idellus) directly or from phytate-degrading isolates from the same source, confirming the widespread occurrence of BPP in aquatic communities. The amounts of sequences collected using these two methods differed (88 distinct genes versus 10 isolates), but the sequences showed the same general topology based on phylogenetic analysis. All of the sequences fell in five clusters and were distinct from those of Anabaena, Gloeobacter, Streptomyces, Flavobacterium, Prosthecochloris, and Desulfuromonas, which have never been found in the grass carp intestine. Analysis of the microbial diversity by denaturing gradient gel electrophoresis demonstrated that unculturable bacteria were dominant bacteria in the grass carp intestine and thus the predominant phytate-degrading organisms. The predominant cultured species corresponding to the phytate-degrading isolates, Pseudomonas, Bacillus and Shewanella species, might be the main source of known BPPs. A phytase from Brevundimonas was first obtained from cultured species. Combining our results with Lim et al.'s inference that phytate-mineralizing bacteria are widely distributed and highly diverse in nature (B. L. Lim, P. Yeung, C. Cheng, and J. E. Hill, ISME J. 1:321-330, 2007), we concluded that BPP is the major phytate-degrading enzyme in nature, that most of this enzyme might originate from unculturable bacteria, and that the distribution of BPP may be related to the type of niche. To our knowledge, this is the first study to experimentally estimate BPP diversity in situ.

Profiles ofMycobacteriumcommunities under polycyclic aromatic hydrocarbon contamination stress in the Shenfu Irrigation Area, northeast China

2013 ◽  
Vol 59 (10) ◽  
pp. 694-700 ◽  
Author(s):  
Xinyu Li ◽  
Xu Li ◽  
Jian Wang ◽  
Xiujuan Wang ◽  
Jian Sun ◽  
...  
Keyword(s):  
Rice Field ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Diversity ◽  
Hydrocarbon Contamination ◽  
Contaminated Sites ◽  
Field Soils ◽  
Polycyclic Aromatic Hydrocarbon Contamination ◽  
Polycyclic Aromatic ◽  
Gradient Gel Electrophoresis

Indigenous Mycobacterium communities play an important role in the degradation of polycyclic aromatic hydrocarbons (PAHs), but little is known about Mycobacterium distribution in situ at PAH-contaminated sites. In this study, the diversity and distribution of Mycobacterium communities were investigated in sediments and soils at sites upstream, midstream, and downstream of an oil-sewage irrigation channel, using denaturing gradient gel electrophoresis (DGGE). The results show that heavy PAH contamination in upstream sites negatively affected Mycobacterium community diversity compared with midstream and downstream sites in all 3 sample types (sediments, corn field soils, and rice field soils). There was a correlation between the distribution of Mycobacterium communities and PAH contamination, as indicated by canonical correspondence analysis. Mycobacterium diversity and distribution was found to vary between the 3 sample types.

scholarly journals Biodiversity of Thermophilic Prokaryotes with Hydrolytic Activities in Hot Springs of Uzon Caldera, Kamchatka (Russia)

2008 ◽  
Vol 75 (1) ◽  
pp. 286-291 ◽  
Author(s):  
Ilya V. Kublanov ◽  
Anna A. Perevalova ◽  
Galina B. Slobodkina ◽  
Aleksander V. Lebedinsky ◽  
Salima K. Bidzhieva ◽  
...  
Keyword(s):  
Hot Springs ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Specific Primers ◽  
Uzon Caldera ◽  
Dgge Analysis ◽  
Hydrolytic Activities ◽  
Gradient Gel Electrophoresis ◽  
Polymeric Substrates

ABSTRACT Samples of water from the hot springs of Uzon Caldera with temperatures from 68 to 87�C and pHs of 4.1 to 7.0, supplemented with proteinaceous (albumin, casein, or α- or β-keratin) or carbohydrate (cellulose, carboxymethyl cellulose, chitin, or agarose) biological polymers, were filled with thermal water and incubated at the same sites, with the contents of the tubes freely accessible to the hydrothermal fluid. As a result, several enrichment cultures growing in situ on different polymeric substrates were obtained. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments obtained after PCR with Bacteria-specific primers showed that the bacterial communities developing on carbohydrates included the genera Caldicellulosiruptor and Dictyoglomus and that those developing on proteins contained members of the Thermotogales order. DGGE analysis performed after PCR with Archaea- and Crenarchaeota-specific primers showed that archaea related to uncultured environmental clones, particularly those of the Crenarchaeota phylum, were present in both carbohydrate- and protein-degrading communities. Five isolates obtained from in situ enrichments or corresponding natural samples of water and sediments represented the bacterial genera Dictyoglomus and Caldanaerobacter as well as new archaea of the Crenarchaeota phylum. Thus, in situ enrichment and consequent isolation showed the diversity of thermophilic prokaryotes competing for biopolymers in microbial communities of terrestrial hot springs.

Degradation of Nonylphenol Polyethoxylates and its Microflora Structure in an Anoxic-Oxic Activated Sludge Process

2012 ◽  
Vol 610-613 ◽  
pp. 331-336
Author(s):  
Yuan Hua Xie ◽  
Tong Zhu ◽  
Xiao Jiang Liu ◽  
Hui Liu ◽  
Jin Han
Keyword(s):  
In Situ Hybridization ◽  
Activated Sludge ◽  
Removal Efficiency ◽  
Gel Electrophoresis ◽  
Loading Rate ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Oxygen Demand ◽  
Activated Sludge Process ◽  
Gradient Gel Electrophoresis

An anoxic-oxic activated sludge process (AOASP) was carried out to degrade nonylphenol polyethoxylates (NPEOs). The carbon source in influent was replaced stepwise by a mixture of nonylphenol decaethoxylate (M-NP10EO). The 2nd-derivative UV-spectrometry was applied to determine the total amount of M-NP10EO in water samples. Chemical oxygen demand (COD) removal efficiency achieves about 85% under the highest M-NP10EO loading rate, and M-NP10EO removal efficiency is about 80%. Denaturing gradient gel electrophoresis (DGGE) results of activated sludges show that the microbe species decrease but gradually stabilize with the increase of M-NP10EO concentration in influent. Fluorescence in situ hybridization (FISH) results of activated sludges showe that the dominant microflora under the highest M-NP10EO loading rate is β-Proteobacteria (35%), followed by α-Proteobacteria (15%), γ-Proteobacteria (5%) and Actinobateria (4%).

scholarly journals Characterization of a Culturable Alphaproteobacterial Symbiont Common to Many Marine Sponges and Evidence for Vertical Transmission via Sponge Larvae

2006 ◽  
Vol 72 (5) ◽  
pp. 3724-3732 ◽  
Author(s):  
Julie J. Enticknap ◽  
Michelle Kelly ◽  
Olivier Peraud ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Marine Sponges ◽  
Rrna Gene ◽  
Surrounding Water ◽  
Axinella Corrugata ◽  
Gradient Gel Electrophoresis ◽  
Related Group

ABSTRACT A closely related group of alphaproteobacteria were found to be present in seven genera of marine sponges from several locations and were shown to be transferred between sponge generations through the larvae in one of these sponges. Isolates of the alphaproteobacterium were cultured from the sponges Axinella corrugata, Mycale laxissima, Monanchora unguifera, and Niphates digitalis from Key Largo, Florida; Didiscus oxeata and Monanchora unguifera from Discovery Bay, Jamaica; an Acanthostronglyophora sp. from Manado, Indonesia; and Microciona prolifera from the Cheasapeake Bay in Maryland. Isolates were very similar to each other on the basis of 16S rRNA gene sequence (>99% identity) and are closely related to Pseudovibrio denitrificans. The bacterium was never isolated from surrounding water samples and was cultured from larvae of M. laxissima, indicating that it is a vertically transmitted symbiont in this sponge. Denaturing gradient gel electrophoresis, 16S rRNA gene clone library analysis, and fluorescent in situ hybridization with probes specific to the alphaproteobacterium confirmed the presence of this bacterium in the M. laxissima larvae. The alphaproteobacterium was densely associated with the larvae rather than being evenly distributed throughout the mesohyl. This is the first report of the successful culture of a bacterial symbiont of a sponge that is transferred through the gametes.

Are some putative glycogen accumulating organisms (GAO) in anaerobic : aerobic activated sludge systems members of the α-Proteobacteria?

Microbiology ◽  
2004 ◽  
Vol 150 (7) ◽  
pp. 2267-2275 ◽  
Author(s):  
Michael Beer ◽  
Yun H. Kong ◽  
Robert J. Seviour
Keyword(s):  
Activated Sludge ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Batch Reactors ◽  
Sequencing Batch Reactors ◽  
Bacterial Populations ◽  
Removal Capacity ◽  
Large Numbers ◽  
Gradient Gel Electrophoresis ◽  
Polyphosphate Accumulating Organisms

Activated sludge plants designed to remove phosphorus microbiologically often perform unreliably. One suggestion is that the polyphosphate-accumulating organisms (PAO) are out-competed for substrates by another group of bacteria, the glycogen-accumulating organisms (GAO) in the anaerobic zones of these processes. This study used fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) to analyse the communities from laboratory-scale anaerobic : aerobic sequencing batch reactors. Members of the genus Sphingomonas in the α-Proteobacteria were present in large numbers in communities with poor phosphorus removal capacity where the biomass had a high glycogen content. Their ability to store poly-β-hydroxyalkanoates anaerobically, but not aerobically, and not accumulate polyphosphate aerobically is consistent with these organisms behaving as GAO there. No evidence was found to support an important role for the γ-Proteobacteria as possible GAO in these communities, although these bacterial populations have been considered in other studies to act as possible competitors for the PAO.

Analysis of Bacterial Communities in A2O Membrane Bioreactor Treating Oily Wastewater

2013 ◽  
Vol 641-642 ◽  
pp. 87-91 ◽  
Author(s):  
Zheng Hua Duan ◽  
Liu Ming Pan ◽  
Hua Wang ◽  
Ning Tao Li
Keyword(s):  
Activated Sludge ◽  
Bacterial Communities ◽  
Membrane Bioreactor ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Membrane Separation ◽  
Diversity Index ◽  
Oily Wastewater ◽  
Wastewater Purification ◽  
Gradient Gel Electrophoresis ◽  
Dominant Bacteria

To improve the efficiency of oily wastewater purification, a laboratory-scale anaerobic/anoxic/aerobic (A2O) membrane bioreactor was designed to treat the oily wastewater based on the conventional A2O activated sludge process and membrane separation technology, and the variation of bacterial community structure in the activated sludge of key reactors were investigated by PCR-DGGE (denaturing gradient gel electrophoresis). The result of Shannon diversity index comparing indicated that MBR seemed to be more constant than the A/0 system. Four sensitive dominant bacteria were verified in the treatment of oily wastewater. They were Uncultured Comamonadaceae bacterium, Hydrogenophaga sp., uncultured beta proteobacterium, and uncultured Thiobacillus sp. It suggested that PCR-DGGE can be used as an effective supplementary method for verifying cultural dominant microorganisms in activated sludge of oily wastewater.

Composition of the bacterial biota in slime developed in two machines at a Canadian paper mill

2011 ◽  
Vol 57 (2) ◽  
pp. 91-104 ◽  
Author(s):  
Julie Disnard ◽  
Carole Beaulieu ◽  
Richard Villemur
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Paper Mill ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Paper Machines ◽  
Gradient Gel Electrophoresis ◽  
Candidate Division ◽  
Catalyzed Reporter Deposition

During the process of papermaking by pulp and paper plants, a thick and viscous deposits, termed slime, is quickly formed around the paper machines, which can affect the papermaking process. In this study, we explored the composition of the bacterial biota in slime that developed on shower pipes from 2 machines at a Canadian paper mill. Firstly, the composition was assessed for 12 months by DNA profiling with polymerase chain reaction coupled with denaturing gradient gel electrophoresis. Except for short periods (2–3 months), clustered analyses showed that the bacterial composition of the slime varied substantially over the year, with less than 50% similarity between the denaturing gradient gel electrophoresis profiles. Secondly, the screening of 16S rRNA gene libraries derived from 2 slime samples showed that the most abundant bacteria were related to 6 lineages, including Chloroflexi, candidate division OP10, Clostridiales, Bacillales, Burkholderiales, and the genus Deinococcus . Finally, the proportion of 8 bacterial lineages, such as Deinococcus sp., Meiothermus sp., and Chloroflexi, was determined by the Catalyzed Reporter Deposition – Fluorescence In Situ Hybridization in 2 slime samples. The results showed a high proportion of Chloroflexi, Tepidimonas spp., and Schlegelella spp. in the slime samples.

scholarly journals Changes in Activity and Community Structure of Methane-Oxidizing Bacteria over the Growth Period of Rice

2001 ◽  
Vol 67 (6) ◽  
pp. 2395-2403 ◽  
Author(s):  
Gundula Eller ◽  
Peter Frenzel
Keyword(s):  
Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Growth Period ◽  
Fish Analysis ◽  
Rice Plants ◽  
Cell Counts ◽  
Methane Oxidizing Bacteria ◽  
The Family ◽  
Gradient Gel Electrophoresis

ABSTRACT The activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. In situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. The in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was greatest in the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH) with family-specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected only for members of the Methylococcaceae and could be associated only with changes in the genusMethylobacter and not with changes in the dominance of different genera in the family Methylococcaceae. For the family Methylocystaceae stable communities in all compartments for the whole season were observed. FISH analysis revealed evidence of in situ dominance of the Methylocystaceae in all compartments. The numbers of Methylococcaceae cells were relatively high only in the rhizoplane, demonstrating the importance of rice roots for growth and maintenance of methanotrophic diversity in the soil.

scholarly journals Composition of Bacterial Communities Associated with Natural and Laboratory Populations of Asobara tabida Infected with Wolbachia

2009 ◽  
Vol 75 (11) ◽  
pp. 3755-3764 ◽  
Author(s):  
Karima Zouache ◽  
Denis Voronin ◽  
Van Tran-Van ◽  
Patrick Mavingui
Keyword(s):  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Culture Methods ◽  
Asobara Tabida ◽  
The Family ◽  
Laboratory Populations ◽  
Gradient Gel Electrophoresis ◽  
Laboratory Colonies ◽  
And Control

ABSTRACT Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.

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