scholarly journals Comparative Analysis of 16S rRNA andamoAGenes from Archaea Selected with Organic and Inorganic Amendments in Enrichment Culture

2012 ◽  
Vol 78 (7) ◽  
pp. 2137-2146 ◽  
Author(s):  
Mouzhong Xu ◽  
Jon Schnorr ◽  
Brandon Keibler ◽  
Holly M. Simon
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
Ammonia Oxidation ◽  
Organic Amendment ◽  
Enrichment Culture ◽  
Plant Root ◽  
Rrna Gene ◽  
Potential Growth ◽  
Inorganic Amendments ◽  
Coupled Growth

ABSTRACTWe took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA andamoAgenes indicated that specific archaeal clades were selected under different conditions. ThreeamoAsequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the “root” clade, we detected no correspondingamoAgene. TheamoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis ofamoAgene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, althoughamoA-containing group 1.1a archaea were present in enrichments, we detected neither expression ofamoAgenes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

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.

scholarly journals Comparative Analysis of Bacterial Diversity in Freshwater Sediment of a Shallow Eutrophic Lake by Molecular and Improved Cultivation-Based Techniques

2005 ◽  
Vol 71 (4) ◽  
pp. 2162-2169 ◽  
Author(s):  
Hideyuki Tamaki ◽  
Yuji Sekiguchi ◽  
Satoshi Hanada ◽  
Kazunori Nakamura ◽  
Nakao Nomura ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Clone Library ◽  
Eutrophic Lake ◽  
Freshwater Sediment ◽  
Gene Clone ◽  
Rrna Gene ◽  
Shallow Eutrophic Lake

ABSTRACT Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.

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 Investigating the anti-acne potential of endophytic bacterial extracts isolated from Mangifera casturi in indigenous South Borneo, Indonesia

2020 ◽  
Vol 1 (2) ◽  
pp. 54-63
Author(s):  
Julius Riyanto ◽  
Sogandi
Keyword(s):  
16S Rrna ◽  
Endophytic Bacteria ◽  
Propionibacterium Acnes ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Disc Diffusion ◽  
Potential Growth ◽  
Antibacterial Compounds ◽  
Potential Activity ◽  
Sequence Similarities

Endophytic bacteria are beneficial microorganisms living in the tis-sues system of various parts of a plant, including fruits, leaves, twigs, and roots. The bacteria are stated as forming colonies without caus-ing any damage to the plant. Thus, this study aimed at isolating endo-phytic bacterial from the leaves, barks, and fruits of Kasturi plant (Mangifera casturi), screening its endophytic bacteria, determining the potential of those endophytic bacteria, identifying 16S rRNA and analyzing potential growth of the bacteria. The isolated endophytic bacteria appeared to show potential activity against pathogenic bac-teria Propionibacterium acnes with disc-diffusion methods. Besides, the observations on bacterial activities showed isolate L2, S2 and F4 isolated from leaves, bark and fruits, respectively, as the most potent producers of antibacterial compounds. Technically, those activities were indicated by the formation of clear zones. Molecular identifica-tion was investigated by applying PCR amplification on 16S rRNA gene. Furthermore, the isolate L2 was identified as Enterobacter clo-acae with 99% sequence similarities; however, isolates S2 and F4 were identified as Escherichia coli. Therefore, these findings sug-gested that the identified strains would contribute to any further searches for new sources of anti-acne substances.

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

2021 ◽  
Author(s):  
Sinchan Banerjee ◽  
András Táncsics ◽  
Erika Tóth ◽  
Fruzsina Révész ◽  
Károly Bóka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Enrichment Culture ◽  
Draft Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Para Xylene

A benzene, para- and meta-xylene-degrading Gram-stain-negative, aerobic, yellow-pigmented bacterium, designated as D2P1T, was isolated from a para-xylene-degrading enrichment culture. Phylogenetic analyses based on 16S rRNA genes showed that D2P1T shares a distinct phyletic lineage within the genus Hydrogenophaga and shows highest 16S rRNA gene sequence similarity to Hydrogenophaga taeniospiralis NBRC 102512T (99.2 %) and Hydrogenophaga palleronii NBRC 102513T (98.3 %). The draft genome sequence of D2P1T is 5.63 Mb long and the genomic DNA G+C content is 65.5 %. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed low genomic relatedness to its closest relatives (OrthoANI <86 %; dDDH <30 %). D2P1T contains ubiquinone 8 (Q-8) as the only respiratory quinone and phospholipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol as major polar lipids. The main whole-cell fatty acids of D2P1T are summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). The polyphasic taxonomic results indicated that strain D2P1T represents a novel species of the genus Hydrogenophaga , for which the name Hydrogenophaga aromaticivorans sp. nov. is proposed. The type strain is D2P1T (=LMG 31780T=NCAIM B 02655T).

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 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.

Sign in / Sign up

Export Citation Format

Share Document