scholarly journals Composition and Activity of an Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture

2009 ◽  
Vol 75 (21) ◽  
pp. 6937-6940 ◽  
Author(s):  
Marco Blöthe ◽  
Eric E. Roden
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Enrichment Culture ◽  
Rrna Gene ◽  
Appl Environ ◽  
Nitrate Reducers ◽  
Primary Responsibility ◽  
Gene Homology ◽  
Gene Libraries

ABSTRACT 16S rRNA gene libraries from the lithoautotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458-1460, 1996) were dominated by a phylotype related (95% 16S rRNA gene homology) to the autotrophic Fe(II) oxidizer Sideroxydans lithotrophicus. The libraries also contained phylotypes related to known heterotrophic nitrate reducers Comamonas badia, Parvibaculum lavamentivorans, and Rhodanobacter thiooxidans. The three heterotrophs were isolated and found to be capable of only partial (12 to 24%) Fe(II) oxidation, suggesting that the Sideroxydans species has primary responsibility for Fe(II) oxidation in the enrichment culture.

scholarly journals Characterization of the Community Structure of a Dechlorinating Mixed Culture and Comparisons of Gene Expression in Planktonic and Biofloc-Associated “Dehalococcoides” and Methanospirillum Species

2008 ◽  
Vol 74 (21) ◽  
pp. 6709-6719 ◽  
Author(s):  
Annette R. Rowe ◽  
Brendan J. Lazar ◽  
Robert M. Morris ◽  
Ruth E. Richardson
Keyword(s):  
Gene Expression ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Population Distribution ◽  
Enrichment Culture ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Rrna Gene ◽  
Hydrogenase Gene

ABSTRACT This study sought to characterize bacterial and archaeal populations in a perchloroethene- and butyrate-fed enrichment culture containing hydrogen-consuming “Dehalococcoides ethenogenes” strain 195 and a Methanospirillum hungatei strain. Phylogenetic characterization of this microbial community was done via 16S rRNA gene clone library and gradient gel electrophoresis analyses. Fluorescence in situ hybridization was used to quantify populations of “Dehalococcoides” and Archaea and to examine the colocalization of these two groups within culture bioflocs. A technique for enrichment of planktonic and biofloc-associated biomass was developed and used to assess differences in population distribution and gene expression patterns following provision of substrate. On a per-milliliter-of-culture basis, most D. ethenogenes genes (the hydrogenase gene hupL; the highly expressed gene for an oxidoreductase of unknown function, fdhA; the RNA polymerase subunit gene rpoB; and the 16S rRNA gene) showed no statistical difference in expression between planktonic and biofloc enrichments at either time point studied (1 to 2 and 6 h postfeeding). Normalization of transcripts to ribosome (16S rRNA) levels supported that planktonic and biofloc-associated D. ethenogenes had similar gene expression profiles, with one notable exception; planktonic D. ethenogenes showed higher expression of tceA relative to biofloc-associated cells at 6 h postfeeding. These trends were compared to those for the hydrogen-consuming methanogen in the culture, M. hungatei. The vast majority of M. hungatei cells, ribosomes (16S rRNA), and transcripts of the hydrogenase gene mvrD and the housekeeping gene rpoE were observed in the biofloc enrichments. This suggests that, unlike the comparable activity of D. ethenogenes from both enrichments, planktonic M. hungatei is responsible for only a small fraction of the hydrogenotrophic methanogenesis in this culture.

Chilling and cultivar type affect the diversity of bacterial endophytes colonizing sweet pepper (Capsicum anuumL.)

2006 ◽  
Vol 52 (11) ◽  
pp. 1036-1045 ◽  
Author(s):  
Frank Rasche ◽  
Robert Trondl ◽  
Christina Naglreiter ◽  
Thomas G Reichenauer ◽  
Angela Sessitsch
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sweet Pepper ◽  
Gene Analysis ◽  
Rrna Gene ◽  
Temperature Sensitive ◽  
Bacterial Endophytes ◽  
Community Members ◽  
16S Rrna Gene Analysis ◽  
Gene Libraries

A climate chamber experiment was conducted to assay the effect of low temperatures (chilling) on the diversity of bacteria colonizing the endospheres of two thermophilic sweet pepper (Capsicum anuum L.) cultivars, Milder Spiral and Ziegenhorn Bello. Structural diversity was analyzed by 16S rRNA-based terminal restriction fragment length polymorphism (T-RFLP) analysis and by the generation of 16S rRNA gene libraries to determine dominant community members in T-RFLP profiles. Cultivable community members colonizing lines Milder Spiral and Ziegenhorn Bello were identified by 16S rRNA gene analysis. T-RFLP profiles and 16S rRNA gene libraries revealed a high heterogeneity of community composition due to chilling and suggested further the existence of cultivar-specific communities. The majority of isolates obtained from the cultivar Milder Spiral were assigned as high-G+C Gram-positive bacteria (Microbacterium sp., Micrococcus sp., Rhodococcus sp.) and Firmicutes (Staphylococcus sp.). Of the isolated endophytes obtained from cultivar Zeigenhorn Bello, 93% were affiliated with Staphylococcus aureus and Bacillus sp. (Firmicutes). The experimental set-up was suited to demonstrate that chilling and cultivar type can influence the diversity of bacterial endophytes colonizing sweet pepper. We propose additional chilling experiments to investigate the effect of chilling on functional, plant-beneficial abilities of bacterial endophytes associated with low-temperature-sensitive crops, such as sweet pepper.Key words: chilling, thermophilic sweet pepper, bacterial endophyte diversity, 16S rRNA gene analysis.

scholarly journals Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Claudia Tominski ◽  
Helene Heyer ◽  
Tina Lösekann-Behrens ◽  
Sebastian Behrens ◽  
Andreas Kappler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Enrichment Culture ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Content Type ◽  
Heterotrophic Denitrification

ABSTRACTMost isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer,Gallionellaceaesp., and less abundant heterotrophic strains (e.g.,Bradyrhizobiumsp.,Nocardioidessp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the familyGallionellaceaedominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated withBradyrhizobiumsp.Gallionellaceaesp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II).Bradyrhizobiumspp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O2.IMPORTANCENitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizerGallionellaceaesp. and several heterotrophic strains (e.g.,Bradyrhizobiumsp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed andBradyrhizobiumbecame the dominant community member, Fe(II) was still oxidized byGallionellaceaesp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate.

scholarly journals Bacterial diversity in the saliva of patients with different oral hygiene indexes

2012 ◽  
Vol 23 (4) ◽  
pp. 409-416 ◽  
Author(s):  
Juliana Vianna Pereira ◽  
Luciana Leomil ◽  
Fabíola Rodrigues-Albuquerque ◽  
José Odair Pereira ◽  
Spartaco Astolfi-Filho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Oral Hygiene ◽  
Dental Plaque ◽  
High Index ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Gene Libraries ◽  
The 16S Rrna Gene

The objective of the present study was to evaluate the bacterial diversity in the saliva of patients with different oral hygiene indexes using of two 16S rRNA gene libraries. Each library was composed of samples from patients with different averages of the differentiated Silness-Löe biofilm index: the first library (A) with an index between 1.0 and 3.0 (considered a high index) and the second library (B) between 0 and 0.5 (considered a low index). Saliva DNA was extracted and the 16S rRNA gene was amplified and cloned. The obtained sequences were compared with those stored at NCBI and RDP GenBank. The saliva of patients with high index presented five known genera - Streptococcus, Granulicatella, Gemella, Veillonella and Peptostreptococcus - and 33.3% of nonculturable bacteria grouped into 23 operational taxonomic units (OTUs). The saliva of patients with low index differed significantly from the first library (p=0.000) and was composed of 42 OTUs distributed into 11 known genera - Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces - including 24.87% of nonculturable bacteria. It was possible to conclude that there is greater bacterial diversity in the saliva of patients with low dental plaque in relation to patients with high dental plaque.

scholarly journals Microbial Communities Involved in Anaerobic Degradation of Unsaturated or Saturated Long-Chain Fatty Acids

2006 ◽  
Vol 73 (4) ◽  
pp. 1054-1064 ◽  
Author(s):  
Diana Z. Sousa ◽  
M. Alcina Pereira ◽  
Alfons J. M. Stams ◽  
M. Madalena Alves ◽  
Hauke Smidt
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Enrichment Culture ◽  
Methane Yield ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Dgge Profile ◽  
Enrichment Cultures ◽  
Long Chain

ABSTRACTAnaerobic long-chain fatty acid (LCFA)-degrading bacteria were identified by combining selective enrichment studies with molecular approaches. Two distinct enrichment cultures growing on unsaturated and saturated LCFAs were obtained by successive transfers in medium containing oleate and palmitate, respectively, as the sole carbon and energy sources. Changes in the microbial composition during enrichment were analyzed by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Prominent DGGE bands of the enrichment cultures were identified by 16S rRNA gene sequencing. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. Bacteria corresponding to predominant DGGE bands in oleate and palmitate enrichment cultures clustered with fatty acid-oxidizing bacteria withinSyntrophomonadaceaeandSyntrophobacteraceaefamilies. A low methane yield, corresponding to 9 to 18% of the theoretical value, was observed in the oleate enrichment, and acetate, produced according to the expected stoichiometry, was not further converted to methane. In the palmitate enrichment culture, the acetate produced was completely mineralized and a methane yield of 48 to 70% was achieved from palmitate degradation. Furthermore, the oleate enrichment culture was able to use palmitate without detectable changes in the DGGE profile. However, the palmitate-specialized consortia degraded oleate only after a lag phase of 3 months, after which the DGGE profile had changed. Two predominant bands appeared, and sequence analysis showed affiliation with theSyntrophomonasgenus. These bands were also present in the oleate enrichment culture, suggesting that these bacteria are directly involved in oleate degradation, emphasizing possible differences between the degradation of unsaturated and saturated LCFAs.

A PCR Assay for Detection of Acetic Acid–Tolerant Lactic Acid Bacteria in Acidic Food Products

2004 ◽  
Vol 67 (3) ◽  
pp. 610-615 ◽  
Author(s):  
SHIGERU NAKANO ◽  
ATSUSHI MATSUMURA ◽  
TOSHIHIRO YAMADA
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Enrichment Culture ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Pcr Assay ◽  
Acid Tolerant

A PCR assay for the detection of acetic acid–tolerant lactic acid bacteria in the genera of Lactobacillus and Pediococcus was developed in this study. Primers targeting the bacterial 16S rRNA gene were newly designed and used in this PCR assay. To determine the specificity of the assay, 56 different bacterial strains (of 33 genera), 2 fungi, 3 animals, and 4 plants were tested. Results were positive for most tested bacterial members of 16S rRNA gene–based phylogenetic groups (classi ed in the Lactobacillus casei and Pediococcus group), including Lactobacillus fructivorans, Lactobacillus brevis, Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus paracasei. For all other bacterial strains and eukaryote tested, results were negative. Bacterial DNA for PCR was prepared with a simple procedure with the use of Chelex 100 resin from culture after growth in deMan Rogosa Sharpe broth (pH 6.0). To test this PCR assay for the monitoring of the acetic acid–tolerant lactic acid bacteria, L. fructivorans was inoculated into several acidic food as an indicator. Before the PCR, the inoculation of 10 to 50 CFU of bacteria per g of food was followed by a 28-h enrichment culture step, and the PCR assay allowed the detection of bacterial cells. Including the enrichment culture step, the entire PCR detection process can be completed within 30 h.

scholarly journals Molecular Diversity of Rumen Methanogens from Sheep in Western Australia

2004 ◽  
Vol 70 (3) ◽  
pp. 1263-1270 ◽  
Author(s):  
Andr�-Denis G. Wright ◽  
Andrew J. Williams ◽  
Barbara Winder ◽  
Claus T. Christophersen ◽  
Sharon L. Rodgers ◽  
...  
Keyword(s):  
New Species ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Western Australia ◽  
Molecular Diversity ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sheep Grazing ◽  
Merino Sheep ◽  
Gene Libraries

ABSTRACT The molecular diversity of rumen methanogens in sheep in Australia was investigated by using individual 16S rRNA gene libraries prepared from the rumen contents obtained from six merino sheep grazing pasture (326 clones), six sheep fed an oaten hay-based diet (275 clones), and five sheep fed a lucerne hay-based diet (132 clones). A total of 733 clones were examined, and the analysis revealed 65 phylotypes whose sequences (1,260 bp) were similar to those of cultivated methanogens belonging to the order Methanobacteriales. Pasture-grazed sheep had more methanogen diversity than sheep fed either the oaten hay or lucerne hay diet. Methanobrevibacter strains SM9, M6, and NT7 accounted for over 90% of the total number of clones identified. M6 was more prevalent in grazing sheep, and SM9, despite being found in 16 of the 17 sheep, was more prevalent in sheep fed the lucerne-based diet. Five new species were identified. Two of these species exhibited very little sequence similarity to any cultivated methanogens and were found eight times in two of the six sheep that were grazing pasture. These unique sequences appear to represent a novel group of rumen archaea that are atypical for the rumen environment.

scholarly journals Methanogenic Population and CH4Production in Swedish Dairy Cows Fed Different Levels of Forage

2012 ◽  
Vol 78 (17) ◽  
pp. 6172-6179 ◽  
Author(s):  
R. Danielsson ◽  
A. Schnürer ◽  
V. Arthurson ◽  
J. Bertilsson
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dairy Cows ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Methanobrevibacter Ruminantium ◽  
Gene Libraries ◽  
Swedish Dairy ◽  
The 16S Rrna Gene

ABSTRACTMethanogenic community structure, methane production (CH4), and volatile fatty acid (VFA) profiles were investigated in Swedish dairy cows fed a diet with a forage/concentrate ratio of 500/500 or 900/100 g/kg of dry matter (DM) of total DM intake (DMI). The rumen methanogenic population was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR (qRT-PCR). Mean CH4yields did not differ (P> 0.05) between diets, being 16.9 and 20.2 g/kg DMI for the 500/500 and 900/100 diets, respectively. The T-RFLP analysis revealed that populations differed between individual cows and that each individual population responded differently to the diets. The 16S rRNA gene libraries revealed thatMethanobrevibacterspp. dominated for both diets. CH4production was positively correlated with a dominance of sequences representing T-RFs related toMethanobrevibacter thaueri,Methanobrevibacter millerae, andMethanobrevibacter smithiirelative toMethanobrevibacter ruminantiumandMethanobrevibacter olleyae. Total numbers of methanogens and total numbers ofMethanobacterialeswere significantly higher with the 500/500 diet (P< 0.0004 andP< 0.002, respectively). However, no relationship was found between CH4production and total number of methanogens. No differences were seen in total VFA, propionic acid, or acetic acid contents, but the molar proportion of butyric acid in the rumen was higher for the 500/500 diet than for the 900/100 diet (P< 0.05). Interestingly, the results also revealed that a division of the identified methanogenic species into two groups, suggested in the work of King et al. (E. E. King, R. P. Smith, B. St-Pierre, and A. D. G. Wright, Appl. Environ. Microbiol.77:5682–5687, 2011), increased the understanding of the variation in CH4production between different cows.

scholarly journals Rumen Microbial Population Dynamics during Adaptation to a High-Grain Diet

2010 ◽  
Vol 76 (22) ◽  
pp. 7482-7490 ◽  
Author(s):  
S. C. Fernando ◽  
H. T. Purvis ◽  
F. Z. Najar ◽  
L. O. Sukharnikov ◽  
C. R. Krehbiel ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Population ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Libraries ◽  
The 16S Rrna Gene ◽  
Number Of Bacteria

ABSTRACT High-grain adaptation programs are widely used with feedlot cattle to balance enhanced growth performance against the risk of acidosis. This adaptation to a high-grain diet from a high-forage diet is known to change the rumen microbial population structure and help establish a stable microbial population within the rumen. Therefore, to evaluate bacterial population dynamics during adaptation to a high-grain diet, 4 ruminally cannulated beef steers were adapted to a high-grain diet using a step-up diet regimen containing grain and hay at ratios of 20:80, 40:60, 60:40, and 80:20. The rumen bacterial populations were evaluated at each stage of the step-up diet after 1 week of adaptation, before the steers were transitioned to the next stage of the diet, using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR. The T-RFLP analysis displayed a shift in the rumen microbial population structure during the final two stages of the step-up diet. The 16S rRNA gene libraries demonstrated two distinct rumen microbial populations in hay-fed and high-grain-fed animals and detected only 24 common operational taxonomic units out of 398 and 315, respectively. The 16S rRNA gene libraries of hay-fed animals contained a significantly higher number of bacteria belonging to the phylum Fibrobacteres, whereas the 16S rRNA gene libraries of grain-fed animals contained a significantly higher number of bacteria belonging to the phylum Bacteroidetes. Real-time PCR analysis detected significant fold increases in the Megasphaera elsdenii, Streptococcus bovis, Selenomonas ruminantium, and Prevotella bryantii populations during adaptation to the high-concentrate (high-grain) diet, whereas the Butyrivibrio fibrisolvens and Fibrobacter succinogenes populations gradually decreased as the animals were adapted to the high-concentrate diet. This study evaluates the rumen microbial population using several molecular approaches and presents a broader picture of the rumen microbial population structure during adaptation to a high-grain diet from a forage diet.

scholarly journals The Microbial Community Structure in Petroleum-Contaminated Sediments Corresponds to Geophysical Signatures

2007 ◽  
Vol 73 (9) ◽  
pp. 2860-2870 ◽  
Author(s):  
Jonathan P. Allen ◽  
Estella A. Atekwana ◽  
Eliot A. Atekwana ◽  
Joseph W. Duris ◽  
D. Dale Werkema ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Sediments ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Community Structures ◽  
Microbial Community Structures ◽  
Gene Libraries ◽  
Cost Efficient

ABSTRACT The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueous-phase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes.

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