Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment.

Abstract:

:In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.

journal_name

Curr Microbiol

journal_title

Current microbiology

authors

Wagner AO,Praeg N,Illmer P

doi

10.1007/s00284-019-01772-y

subject

Has Abstract

pub_date

2019-12-01 00:00:00

pages

1425-1434

issue

12

eissn

0343-8651

issn

1432-0991

pii

10.1007/s00284-019-01772-y

journal_volume

76

pub_type

杂志文章
  • Species Diversity and Functional Prediction of Soil Bacterial Communities in Constructed Wetlands with Different Plant Conditions.

    abstract::The diversities of soil bacterial communities in the Phragmites australis, Phalaris arundinacea, and non-plantation constructed wetlands were compared and analyzed by through high-throughput Illumina sequencing. At the phylum level, the ten dominant bacterial phyla in the three types of constructed wetlands were the s...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-019-01634-7

    authors: Fu W,Wang Y,Wei W,Li P

    更新日期:2019-03-01 00:00:00

  • Identification and Characterization of Pediococcus Species from Piper betle (Betel) Leaves.

    abstract::Betel vine is an edible creeper used in folk medicine to aid digestion since time immemorial. It is an ideal candidate deemed for the bioprospection of endophytic microorganisms with valuable attributes. This study aimed at the characterization of potential bacteria from fermented betel leaves. We report the presence ...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-020-02270-2

    authors: Keerthana C,Narayanan RB

    更新日期:2021-01-01 00:00:00

  • Characterization of the DNA adenine 5'-GATC-3' methylase HpyIIIM from Helicobacter pylori.

    abstract::The effect of inactivation of the 5'-GATC-3' methylase HpyIIIM in Helicobacter pylori (H. pylori) on mismatch repair, adherence, and in vitro fitness was examined. Chromosomal DNA from 90 H. pylori strains was isolated, and restriction enzyme digestion indicated all strains examined possess HpyIIIM. Wild-type H. pylor...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-004-4244-4

    authors: Simala-Grant JL,Lam E,Keelan M,Taylor DE

    更新日期:2004-07-01 00:00:00

  • Genetic Characterization of Influenza A (H1N1) Pandemic 2009 Virus Isolates from Mumbai.

    abstract::Pandemic influenza A (H1N1) 2009 virus was first detected in India in May 2009 which subsequently became endemic in many parts of the country. Influenza A viruses have the ability to evade the immune response through its ability of antigenic variations. The study aims to characterize influenza A (H1N1) pdm 09 viruses ...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-017-1262-6

    authors: Gohil D,Kothari S,Shinde P,Meharunkar R,Warke R,Chowdhary A,Deshmukh R

    更新日期:2017-08-01 00:00:00

  • Identification and initial characterization of a putative Mycoplasma gallinarum leucine aminopeptidase gene.

    abstract::Aminopeptidases (APN) may play a role in host colonization of M. gallinarum. Characterization of endogenous APN activity suggests that the leucine APN (LAP) of M. gallinarum is a metallo-aminopeptidase activated by Mn2+ and is present in the cytosol and possibly associated with the inner leaflet of the membrane. A 1.3...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-003-4098-1

    authors: Wan X,Branton SL,Hanson LA,Pharr GT

    更新日期:2004-01-01 00:00:00

  • Degradation of mono-chlorinated dibenzo-p-dioxins by Janibacter sp. strain YA isolated from river sediment.

    abstract::Strain YA was newly isolated from an enrichment culture of river sediment and was identified as Janibacter sp. It was able to utilize dibenzofuran as the sole source of carbon and energy. Strain YA degraded > 90% of 1-chloro-dibenzo-p-dioxin (1-CDD) and > 80% of 2-chloro-dibenzo-p-dioxin in 18 hours with each initial ...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-005-0099-6

    authors: Iwai S,Yamazoe A,Takahashi R,Kurisu F,Yagi O

    更新日期:2005-11-01 00:00:00

  • Display of Bombyx mori nucleopolyhedrovirus GP64 on the Bacillus subtilis spore coat.

    abstract::To investigate whether Bombyx mori immunized with Bacillus subtilis spore displaying GP64 escape from the B. mori nucleopolyhedrovirus (BmNPV) attack, a recombinant integrative plasmid named pJS700-GP64 was constructed, which carries a recombinant cotC-Gp64 gene under the control of the cotC promoter. In this study, p...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-011-9867-7

    authors: Li G,Tang Q,Chen H,Yao Q,Ning D,Chen K

    更新日期:2011-05-01 00:00:00

  • Achromobacter xylosoxidans: an emerging pathogen carrying different elements involved in horizontal genetic transfer.

    abstract::In the last few years, numerous cases of multidrug-resistant Achromobacter xylosoxidans infections have been documented in immunocompromised and cystic fibrosis patients. To gain insights into the molecular mechanisms and mobile elements related to multidrug resistance in this bacterium, we studied 24 non-epidemiologi...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-012-0213-5

    authors: Traglia GM,Almuzara M,Merkier AK,Adams C,Galanternik L,Vay C,Centrón D,Ramírez MS

    更新日期:2012-12-01 00:00:00

  • Spontaneous white sectored-mutants in Streptomyces hygroscopicus 111-81: characterization and antibiotic productivity.

    abstract::Spontaneous white mutants from sectors of Streptomyces hygroscopicus 111-81 were isolated. The comparison of morphological, cultural, and biochemical properties of the mutants and ancestor showed the differences in colors of aerial, substrate mycelia, and sporulation. Changes in resistance to antibiotics and sensitivi...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-008-9165-1

    authors: Gesheva V

    更新日期:2008-08-01 00:00:00

  • Strategies for Biofilm Inhibition and Virulence Attenuation of Foodborne Pathogen-Escherichia coli O157:H7.

    abstract::Enterohemorrhagic Escherichia coli (E. coli) O157:H7, a gram-negative bacteria identified as a foodborne pathogen causing severe disease is of great concern worldwide. The pathogenicity of E. coli O157:H7 is due to the presence of some virulence factors and its ability to form biofilm which resist antimicrobial compou...

    journal_title:Current microbiology

    pub_type: 杂志文章,评审

    doi:10.1007/s00284-017-1314-y

    authors: Oloketuyi SF,Khan F

    更新日期:2017-12-01 00:00:00

  • Characterization of a novel Cr6+ reducing Pseudomonas sp. with plant growth-promoting potential.

    abstract::The isolate RNP4 obtained from a long-term tannery waste contaminated soil was characterized and presumptively identified as Pseudomonas sp. The strain RNP4 tolerated concentrations up to 450 mg Cr(6+)/L on a Luria-Bartani (LB) agar medium and reduced a substantial amount of Cr(6+) to Cr(3+) in the LB liquid medium. T...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-005-4470-4

    authors: Rajkumar M,Nagendran R,Lee KJ,Lee WH

    更新日期:2005-05-01 00:00:00

  • Use of 16S rDNA sequences as signature characters to identify Xylella fastidiosa.

    abstract::The nucleotide sequences of 16S rDNAs (coding for the small subunit ribosomal RNAs) were used to identify Xylella fastidiosa, a nutritionally fastidious plant pathogenic bacterium. The near-complete 16S rDNAs from nine strains of Xyl. fastidiosa, including seven pathotypes and one strain of Xanthomonas campestris pv. ...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s002849910006

    authors: Chen J,Banks D,Jarret RL,Chang CJ,Smith BJ

    更新日期:2000-01-01 00:00:00

  • PCR methods for identification and specific detection of probiotic lactic acid bacteria.

    abstract::Probiotics are defined as "microbes improving animal feed." Three lactic acid bacteria, previously selected as probiotic for pig feeding, were identified by sequencing the variable V1 region of the 16S rDNA after PCR amplification primed in the flanking constant region. A VR region showing strong nucleotide difference...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s002849900082

    authors: Castellanos MI,Chauvet A,Deschamps A,Barreau C

    更新日期:1996-08-01 00:00:00

  • Cloning of lipoxygenase genes from a cyanobacterium, Nostoc punctiforme, and its expression in Eschelichia coli.

    abstract::Oxylipin metabolism represents one of the important hormonal and defensive mechanisms employed by plants, algae, or animals. It begins mostly with the reaction of lipoxygenases (LOXs), which catalyze the oxygenation of polyunsaturated fatty acids to form the corresponding hydroperoxides. At present, little information...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-006-0512-9

    authors: Koeduka T,Kajiwara T,Matsui K

    更新日期:2007-04-01 00:00:00

  • Aniline-induced tryptophan production and identification of indole derivatives from three purple bacteria.

    abstract::Growth on aniline by three purple non-sulfur bacteria (Rhodospirillum rubrum ATCC 11170, Rhodobacter sphaeroides DSM 158, and Rubrivivax benzoatiliticus JA2) as nitrogen, or carbon source could not be demonstrated. However in its presence, production of indole derivatives was observed with all the strains tested. At l...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-010-9609-2

    authors: Mujahid M,Sasikala Ch,Ramana ChV

    更新日期:2010-10-01 00:00:00

  • Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.

    abstract::A Gram-negative, short-rod-shaped bacterial strain with gliding motility, designated as DG5A(T), was isolated from a rice field soil in South Korea. Phylogenic analysis using 16S rRNA gene sequence of the new isolate showed that strain DG5A(T) belong to the genus Spirosoma in the family Spirosomaceae, and the highest ...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-014-0584-x

    authors: Lee JJ,Srinivasan S,Lim S,Joe M,Im S,Bae SI,Park KR,Han JH,Park SH,Joo BM,Park SJ,Kim MK

    更新日期:2014-09-01 00:00:00

  • Pseudomonas pratensis sp. nov., Isolated from Grassland Soil from Inner Mongolia, China.

    abstract::A novel bacterial strain, designated MHJ-10JT, was isolated from a soil sample obtained from a grassland in Inner Mongolia, China. MHJ-10JT strain could grow at 4-37 °C (optimum: 30 °C) and pH 4-9 (optimum: pH 6), as well as in the presence of 0-6% NaCl (optimum: 1%). Cells of strain MHJ-10JT are Gram-negative, rod-sh...

    journal_title:Current microbiology

    pub_type: 杂志文章,评审

    doi:10.1007/s00284-020-02296-6

    authors: Zhang M,Shen L,Shi J,Chen L,Luo Y,Sun J,Fan D,Hara S,Bao Z

    更新日期:2021-01-02 00:00:00

  • The Saccharomyces cerevisiae MLF6/YPL244C gene, which encodes a possible yeast homologue of mammalian UDP-galactose transporter, confers resistance to the immunosuppressive drug, leflunomide.

    abstract::The immunosuppressant leflunomide (LFM) inhibits the growth of cytokine-stimulated proliferation of lymphoid cells in vitro and also inhibits the growth of eukaryotic microorganism, Saccharomyces cerevisiae. As a first step to elucidate the molecular mechanism of LFM action in human, yeast gene which suppresses the an...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s002840010267

    authors: Fujimura H

    更新日期:2001-08-01 00:00:00

  • Transcriptional regulation of the Prevotella ruminicola recA gene.

    abstract::The regulation of the recA gene expression in the obligately anaerobic rumen bacterium Prevotella ruminicola was investigated by monitoring the recA-specific transcript level. P. ruminicola recA forms a monocistronic unit, but no SOS-box sequences resembling those of Escherichia coli or Bacillus subtilis can be identi...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s002849900306

    authors: Aminov RI,Tajima K,Ogata K,Nagamine T,Sugiura M,Benno Y

    更新日期:1998-05-01 00:00:00

  • Larkinella harenae sp. nov., Isolated from Korean Beach Soil.

    abstract::A Gram-negative, short rod-shaped, gliding motile, and pale pink-pigmented bacterial strain, designated 15J9-9T, was isolated from the soil of Iho Tewoo Beach, Jeju Island, Korea, and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 15J9-9T belonge...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-017-1246-6

    authors: Park SJ,Lee JJ,Lee SY,Lee DS,Kim MK,Ten LN,Jung HY

    更新日期:2017-07-01 00:00:00

  • Tellurite Resistance in Shiga Toxin-Producing Escherichia coli.

    abstract::Potassium tellurite (K2TeO3) is an effective selective agent for O157:H7 Shiga toxin-producing Escherichia coli (STEC), whereas tellurite resistance in non-O157 STEC is variable with information on O45 minimal. High-level K2TeO3 resistance in STEC is attributable to the ter gene cluster with terD an indicator of the c...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-018-1444-x

    authors: Lewis GL,Jorgensen QR,Loy JD,Moxley RA

    更新日期:2018-06-01 00:00:00

  • Characterization of Extracellular Biosurfactants Expressed by a Pseudomonas putida Strain Isolated from the Interior of Healthy Roots from Sida hermaphrodita Grown in a Heavy Metal Contaminated Soil.

    abstract::Pseudomonas putida E41 isolated from root interior of Sida hermaphrodita (grown on a field contaminated with heavy metals) showed high biosurfactant activity. In this paper, we describe data from mass spectrometry and genome analysis, to improve our understanding on the phenotypic properties of the strain. Supernatant...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-019-01757-x

    authors: Bernat P,Nesme J,Paraszkiewicz K,Schloter M,Płaza G

    更新日期:2019-11-01 00:00:00

  • Cloning and expression of the pediocin operon in Streptococcus thermophilus and other lactic fermentation bacteria.

    abstract::Production of pediocin in Pediococcus acidilactici is associated with pMBR1.0, which encodes prepediocin, a pediocin immunity protein, and two proteins involved in secretion and precursor processing. These four genes are organized as an operon under control of a single promoter. We have constructed shuttle vectors tha...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s002849900462

    authors: Coderre PE,Somkuti GA

    更新日期:1999-11-01 00:00:00

  • Bacteria associated with butterfly stain of Chilean tepa.

    abstract::Butterfly stain, common in Chilean tepa (Laureliopsis philippiana [Looser] Schodde) trees, appears in cross-section of the stem as a series of partially overlapping orange-brown arcs that in early stages resembles a butterfly. Bacterial isolates from stained tepa wood samples cultured under aerobic and anaerobic condi...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s002849910016

    authors: McLemore JB,Tainter FH,McElreath SD

    更新日期:2000-02-01 00:00:00

  • Extended serotyping scheme for Vibrio anguillarum with the definition and characterization of seven provisional O-serogroups.

    abstract::The present paper summarizes the serotyping scheme of the fish pathogenic bacterium Vibrio anguillarum and defines seven additional O-serogroups. Strains, collected in our laboratories that were nontypable with antisera against the previously defined 16 O-serotypes, were used for generating new antisera and were chara...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/pl00006784

    authors: Pedersen K,Grisez L,van Houdt R,Tiainen T,Ollevier F,Larsen JL

    更新日期:1999-03-01 00:00:00

  • Complete Genome Sequence of Actinosynnema pretiosum X47, An Industrial Strain that Produces the Antibiotic Ansamitocin AP-3.

    abstract::Ansamitocins are extraordinarily potent antitumor agents. Ansamitocin P-3 (AP-3), which is produced by Actinosynnema pretiosum, has been developed as a cytotoxic drug for breast cancer. Despite its importance, AP-3 is of limited applicability because of the low production yield. A. pretiosum strain X47 was developed f...

    journal_title:Current microbiology

    pub_type: 信件

    doi:10.1007/s00284-018-1521-1

    authors: Zhong C,Zong G,Qian S,Liu M,Fu J,Zhang P,Li J,Cao G

    更新日期:2019-08-01 00:00:00

  • Label-Free Quantitative Proteomic Reveals Differentially Expressed Proteins in Aeromonas-Immunostimulated Leukocytes of Lampetra japonica.

    abstract::Lamprey was considered to be one of the most basal jawless vertebrate representatives for studying vertebrate evolution, embryo development, and the origin of adaptive immunity. Here we investigated the effect of the gut-derived Aeromonas on the lamprey leukocytes proteome using the label-free liquid chromatography-ta...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-018-1468-2

    authors: Li Y,Zhang W,Zuo Y,Zhu T,Pang Y,Li T,Li Q

    更新日期:2018-07-01 00:00:00

  • Identification and partial sequence of the BchA gene of Rhodospirillum rubrum.

    abstract::The DNA sequence was determined for a region upstream of the puf operon of Rhodospirillum rubrum. A partial ORF was identified. The DNA sequence and the inferred amino acid sequences were aligned with those of bchA of Rhodobacter capsulatus and other phototrophic bacteria. Based on this alignment and genetic evidence,...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/BF01570863

    authors: Lee IY,Collins ML

    更新日期:1993-08-01 00:00:00

  • In Vitro Activity of Fosfomycin in Double and Triple Combinations with Imipenem, Ciprofloxacin and Tobramycin Against Multidrug-Resistant Escherichia coli.

    abstract::The rates of urinary tract infection with multidrug-resistant (MDR) Escherichia coli have dramatically increased and the treatment of these infections with single and double antibiotic combinations became limited or ineffective. The present study aimed at finding effective antibiotic combinations against MDR uropathog...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-019-01871-w

    authors: El-Wafa WMA,Ibrahim YM

    更新日期:2020-05-01 00:00:00

  • Phylogenetic analyses and diterpenoid production by marine bacteria of the genus Saprospira.

    abstract::The relationship between 16S rRNA gene sequence-derived phylogeny and the bacterial production of diterpenoids from 18 isolates of marine bacteria belonging to the genus Saprospira was determined. Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified 16S rRNA genes of these isolates indicated f...

    journal_title:Current microbiology

    pub_type: 杂志文章

    doi:10.1007/s00284-004-4358-8

    authors: Mincer TJ,Spyere A,Jensen PR,Fenical W

    更新日期:2004-10-01 00:00:00