scholarly journals Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9326
Author(s):  
Yukino Mizutani ◽  
Tetsushi Mori ◽  
Taeko Miyazaki ◽  
Satoshi Fukuzaki ◽  
Reiji Tanaka
Keyword(s):  
Nested Pcr ◽  
Gill Tissue ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Specific Primers ◽  
Abalone Species ◽  
Chemosynthetic Bacteria

Gills are important organs for aquatic invertebrates because they harbor chemosynthetic bacteria, which fix inorganic carbon and/or nitrogen and provide their hosts with organic compounds. Nevertheless, in contrast to the intensive researches related to the gut microbiota, much is still needed to further understand the microbiota within the gills of invertebrates. Using abalones as a model, we investigated the community structure of microbes associated with the gills of these invertebrates using next-generation sequencing. Molecular identification of representative bacterial sequences was performed using cloning, nested PCR and fluorescence in situ hybridization (FISH) analysis with specific primers or probes. We examined three abalone species, namely Haliotis gigantea, H. discus and H. diversicolor using seawater and stones as controls. Microbiome analysis suggested that the gills of all three abalones had the unclassified Spirochaetaceae (one OTU, 15.7 ± 0.04%) and Mycoplasma sp. (one OTU, 9.1 ± 0.03%) as the core microbes. In most libraries from the gills of H. gigantea, however, a previously unknown epsilonproteobacterium species (one OTU) was considered as the dominant bacterium, which accounted for 62.2% of the relative abundance. The epsilonproteobacterium was only detected in the gills of H. diversicolor at 0.2% and not in H. discus suggesting that it may be unique to H. gigantea. Phylogenetic analysis performed using a near full-length 16S rRNA gene placed the uncultured epsilonproteobacterium species at the root of the family Helicobacteraceae. Interestingly, the uncultured epsilonproteobacterium was commonly detected from gill tissue rather than from the gut and foot tissues using a nested PCR assay with uncultured epsilonproteobacterium-specific primers. FISH analysis with the uncultured epsilonproteobacterium-specific probe revealed that probe-reactive cells in H. gigantea had a coccus-like morphology and formed microcolonies on gill tissue. This is the first report to show that epsilonproteobacterium has the potential to be a dominant species in the gills of the coastal gastropod, H. gigantea.

Microbial community analysis during continuous fermentation of thermally hydrolysed waste activated sludge

2012 ◽  
Vol 65 (1) ◽  
pp. 7-14 ◽  
Author(s):  
D. G. Cirne ◽  
P. Bond ◽  
S. Pratt ◽  
P. Lant ◽  
D. J. Batstone
Keyword(s):  
Activated Sludge ◽  
Continuous Fermentation ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Waste Activated Sludge ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Taxonomic Groups ◽  
Bacterial Groups

Acidogenic fermentation of thermally hydrolysed waste activated sludge was carried out at laboratory scale in two reactors operated under different hydraulic retention times (HRT). Process performance was assessed in terms of volatile fatty acid (VFA) composition and yield. The diversity of the microbial population was investigated by constructing a 16S rRNA gene library and subsequent phylogenetic analysis of clones. Fluorescence in situ hybridization (FISH) was used to assess the relative abundance of different bacterial groups. Bacteroidetes and Firmicutes were the dominant taxonomic groups representing 93% of the total sequences obtained in the reactor with 4 d HRT. A similar VFA yield (0.4–0.5 g VFACOD g SCOD−1) was obtained for the HRTs tested (1–4 d), indicating that extended retention times were not useful. Within Firmicutes, Clostridia was the major group detected in the clone sequences. These had close affiliation to Sporanaerobacter acetigenes, suggesting organisms of this group were important for hydrolysis of the protein fraction of the substrate. However, FISH analysis failed to detect the major portion of the bacteria, and this is most likely due to the lack of appropriate probes. This work emphasizes the diversity of fermentative communities, and indicates that more work is needed to identify and detect the important members.

Microbial community analysis involved in the aerobic/extended-idle process performing biological phosphorus removal

2013 ◽  
Vol 67 (3) ◽  
pp. 485-493 ◽  
Author(s):  
Tian-jing Zeng ◽  
Guo-jing Yang ◽  
Dong-bo Wang ◽  
Xiao-ming Li ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Phosphorus Removal ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Fish Analysis ◽  
Biological Phosphorus Removal ◽  
Acclimation Period ◽  
Polyphosphate Accumulating Organisms ◽  
Biological Phosphorus ◽  
Total Bacteria

Recently, it has been found that biological phosphorus removal can be achieved in an aerobic/extended-idle (AEI) process using both glucose and acetate as the sole substrate. However, the microbial consortiums involved in glucose-fed and acetate-fed systems have not yet been characterized. Thus the aims of this paper were to investigate the diversities and dynamics of bacterial communities during the acclimation period, and to quantify polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in the systems. The phylogenetic analysis showed that the microbial communities were mainly composed of phylum Proteobacteria, Bacteroidetes, Chlorobi and another six kinds of unclassified bacteria. Fluorescence in-situ hybridization (FISH) analysis revealed that PAOs and GAOs accounted for 43 ± 7 and 16 ± 3% of all bacteria in the glucose-fed system, and 19 ± 4 and 35 ± 5% of total bacteria in the acetate-fed system, respectively. The results showed that the conventional PAOs could thrive in the AEI process, and a defined anaerobic zone was not necessarily required for putative PAOs growth.

Performance and microbial community analysis of anaerobic sludge digestion enhanced by in-situ microaeration

2021 ◽  
Vol 42 ◽  
pp. 102171
Author(s):  
Zhen Zhou ◽  
Qiang Ming ◽  
Ying An ◽  
Danian Ruan ◽  
Guang Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Anaerobic Sludge ◽  
Sludge Digestion ◽  
Anaerobic Sludge Digestion

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

Microbial Community Analysis inside a Biooxidation Heap for Gold Recovery in Equador

2017 ◽  
Vol 262 ◽  
pp. 135-138 ◽  
Author(s):  
Carlos L. Aspiazu ◽  
Paulina Aguirre ◽  
Sabrina Hedrich ◽  
Axel Schippers
Keyword(s):  
Microbial Community ◽  
Fine Fraction ◽  
Community Analysis ◽  
Gold Recovery ◽  
Microbial Community Analysis ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Cell Numbers ◽  
Cell Counts

In a mine owned by the company Orenas S.A. (Equador), a biooxidation process for gold recovery has been developed. Refractory gold ore was crushed, milled and 500 ton of flotation concentrate was agglomerated by coating a support rock. This was piled up on a liner and the biooxidation process in the heap of 35x25x6 m3 was run for approximately 150 days. The oxidized material was subsequently removed for further processing. An outcrop allowed for depth dependent sampling of altogether 36 samples at three sites over the complete depth of 6 m. The fine fraction was removed from the host rock and sent to the laboratory for analysis of the microbial community. The pH ranged between 2.2 and 2.9. Total cell counts determined via counting under a fluorescence microscope after SYBR Green staining indicated a high microbial colonialization of the heap in all depths between 106 to 109 cells per g concentrate, however the highest cell numbers were mainly found in the upper 50 cm. Most-probable-number determination of living, acidophilic iron (II)-oxidizers for one site also revealed a decrease of cell numbers with depth (between 104 to 108 cells per g concentrate). Further molecular analyses of the community composition based on extracted DNA and 16S rRNA gene analyses by TRFLP and qPCR revealed a complex archaeal and bacterial community within the heap. It can be stated that an active community of acidophiles runs the biooxidation process in all sampled parts of the heap.

scholarly journals Diversity and Morphology of Members of the Phylum “Synergistetes” in Periodontal Health and Disease

2009 ◽  
Vol 75 (11) ◽  
pp. 3777-3786 ◽  
Author(s):  
S. R. Vartoukian ◽  
R. M. Palmer ◽  
W. G. Wade
Keyword(s):  
Oral Health ◽  
Oral Cavity ◽  
Positive Sample ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Subgingival Plaque ◽  
Pcr Cloning ◽  
Human Oral Cavity ◽  
Health And Disease

ABSTRACT Members of the phylum “Synergistetes” have frequently been detected in the human oral cavity at sites of dental disease, but they have rarely been detected in studies of oral health. Only two oral “Synergistetes” taxa are cultivable. The aims of this study were to investigate the diversity of “Synergistetes” in the oral cavity, to establish whether “Synergistetes” taxa are more strongly associated with periodontitis than with oral health, and to visualize unculturable “Synergistetes” in situ. Sixty samples (saliva, dental plaque, and mucosal swabs) were collected from five subjects with periodontitis and five periodontally healthy controls. Using phylum-specific 16S rRNA gene primers, “Synergistetes” were identified by PCR, cloning, and sequencing of 48 clones per PCR-positive sample. Subgingival plaque samples were labeled with probes targeting rRNA of unculturable oral “Synergistetes” using fluorescent in situ hybridization (FISH). Analysis of 1,664 clones revealed 12 “Synergistetes” operational taxonomic units (OTUs) at the 99% sequence identity level, 5 of which were novel. “Synergistetes” OTU 4.2 was found in significantly more subjects with periodontitis than controls (P = 0.048) and was more abundant in subgingival plaque at diseased sites than at healthy sites in subjects with periodontitis (P = 0.019) or controls (P = 0.019). FISH analysis revealed that unculturable oral “Synergistetes” cells were large curved bacilli. The human oral cavity harbors a diverse population of “Synergistetes.” “Synergistetes” OTU 4.2 is associated with periodontitis and may have a pathogenic role.

Overestimation of Streptococcus mutans prevalence by nested PCR detection of the 16S rRNA gene

2006 ◽  
Vol 55 (1) ◽  
pp. 109-113 ◽  
Author(s):  
Ali Al-Ahmad ◽  
Thorsten Mathias Auschill ◽  
Gabriele Braun ◽  
Elmar Hellwig ◽  
Nicole Birgit Arweiler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Streptococcus Mutans ◽  
Nested Pcr ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Direct Pcr ◽  
Specific Primers ◽  
The 16S Rrna Gene

This study was carried out in order to compare two PCR-based methods in the detection of Streptococcus mutans. The first PCR method was based on primers for the 16S rRNA gene and the second method was based on specific primers that targeted the glucosyltransferase gene (gtfB). Each PCR was performed with eight different streptococci from the viridans group, five other streptococci and 17 different non-streptococcal bacterial strains. Direct use of the S. mutans 16S rRNA gene-specific primers revealed that Streptococcus gordonii and Streptococcus infantis were also detected. After amplifying the 16S rRNA gene with universal primers and subsequently performing nested PCR, the S. mutans-specific nested primers based on the 16S rRNA gene detected all tested streptococci. There was no cross-reaction of the gtfB primers after direct PCR. Our results indicate that direct PCR and nested PCR based on 16S rRNA genes can reveal false-positive results for oral streptococci and lead to an overestimation of the prevalence of S. mutans with regards to its role as the most prevalent causative agent of dental caries.

Performance and microbial community analysis of the anaerobic reactor with coke oven gas biomethanation and in situ biogas upgrading

2013 ◽  
Vol 146 ◽  
pp. 234-239 ◽  
Author(s):  
Wen Wang ◽  
Li Xie ◽  
Gang Luo ◽  
Qi Zhou ◽  
Irini Angelidaki
Keyword(s):  
Microbial Community ◽  
Community Analysis ◽  
Coke Oven ◽  
Microbial Community Analysis ◽  
Coke Oven Gas ◽  
Biogas Upgrading ◽  
Anaerobic Reactor

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.

scholarly journals Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy

2010 ◽  
Vol 76 (17) ◽  
pp. 5902-5910 ◽  
Author(s):  
D. S. Jones ◽  
D. J. Tobler ◽  
I. Schaperdoth ◽  
M. Mainiero ◽  
J. L. Macalady
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
Specific Conductivity ◽  
Ground Surface ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Ecological Success ◽  
Cave Waters

ABSTRACT We performed a microbial community analysis of biofilms inhabiting thermal (35 to 50°C) waters more than 60 m below the ground surface near Acquasanta Terme, Italy. The groundwater hosting the biofilms has 400 to 830 μM sulfide, <10 μM O2, pH of 6.3 to 6.7, and specific conductivity of 8,500 to 10,500 μS/cm. Based on the results of 16S rRNA gene cloning and fluorescent in situ hybridization (FISH), the biofilms have low species richness, and lithoautotrophic (or possibly mixotrophic) Gamma- and Epsilonproteobacteria are the principle biofilm architects. Deltaproteobacteria sequences retrieved from the biofilms have <90% 16S rRNA similarity to their closest relatives in public databases and may represent novel sulfate-reducing bacteria. The Acquasanta biofilms share few species in common with Frasassi cave biofilms (13°C, 80 km distant) but have a similar community structure, with representatives in the same major clades. The ecological success of Sulfurovumales-group Epsilonproteobacteria in the Acquasanta biofilms is consistent with previous observations of their dominance in sulfidic cave waters with turbulent water flow and high dissolved sulfide/oxygen ratios.

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