메뉴 건너뛰기




Volumn 2, Issue , 2016, Pages

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Author keywords

[No Author keywords available]

Indexed keywords


EID: 85006826367     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/nmicrobiol.2016.242     Document Type: Article
Times cited : (625)

References (50)
  • 2
    • 59449100317 scopus 로고    scopus 로고
    • Extracellular DNA in soil and sediment: Fate and ecological relevance
    • Pietramellara, G. et al. Extracellular DNA in soil and sediment: fate and ecological relevance. Biol. Fertil. Soils 45, 219-235 (2009).
    • (2009) Biol. Fertil. Soils , vol.45 , pp. 219-235
    • Pietramellara, G.1
  • 3
    • 34548546604 scopus 로고    scopus 로고
    • Cycling of extracellular DNA in the soil environment
    • Levy-Booth, D. J. et al. Cycling of extracellular DNA in the soil environment. Soil Biol. Biochem. 39, 2977-2991 (2007).
    • (2007) Soil Biol. Biochem. , vol.39 , pp. 2977-2991
    • Levy-Booth, D.J.1
  • 4
  • 5
    • 34547800097 scopus 로고    scopus 로고
    • Pyrosequencing enumerates and contrasts soil microbial diversity
    • Roesch, L. F. W. et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1, 283-290 (2007).
    • (2007) ISME J. , vol.1 , pp. 283-290
    • Roesch, L.F.W.1
  • 6
    • 23944525404 scopus 로고    scopus 로고
    • Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    • Gans, J., Wolinsky, M. & Dunbar, J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387-1390 (2005).
    • (2005) Science , vol.309 , pp. 1387-1390
    • Gans, J.1    Wolinsky, M.2    Dunbar, J.3
  • 7
    • 35948953592 scopus 로고    scopus 로고
    • Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
    • Fierer, N. et al. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Environ. Microbiol. 73, 7059-7066 (2007).
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 7059-7066
    • Fierer, N.1
  • 8
    • 84936942726 scopus 로고    scopus 로고
    • Unusual biology across a group comprising more than 15% of domain bacteria
    • Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain bacteria. Nature 523, 208-211 (2015).
    • (2015) Nature , vol.523 , pp. 208-211
    • Brown, C.T.1
  • 9
    • 79958294748 scopus 로고    scopus 로고
    • Discovery of novel intermediate forms redefines the fungal tree of life
    • Jones, M. D. M. et al. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474, 200-203 (2011).
    • (2011) Nature , vol.474 , pp. 200-203
    • Jones, M.D.M.1
  • 10
    • 83555174830 scopus 로고    scopus 로고
    • Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
    • Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368-371 (2011).
    • (2011) Nature , vol.480 , pp. 368-371
    • Mackelprang, R.1
  • 14
    • 1842812502 scopus 로고    scopus 로고
    • Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA
    • Agnelli, A. et al. Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol. Biochem. 36, 859-868 (2004).
    • (2004) Soil Biol. Biochem. , vol.36 , pp. 859-868
    • Agnelli, A.1
  • 15
    • 84935864978 scopus 로고    scopus 로고
    • Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils
    • Dlott, G., Maul, J. E., Buyer, J. & Yarwood, S. Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils. J. Microbiol. Methods 115, 112-120 (2015).
    • (2015) J. Microbiol. Methods , vol.115 , pp. 112-120
    • Dlott, G.1    Maul, J.E.2    Buyer, J.3    Yarwood, S.4
  • 16
    • 33748746842 scopus 로고    scopus 로고
    • Comparison of propidiummonoazide with ethidium monoazide for differentiation of live vs. Dead bacteria by selective removal of DNA from dead cells
    • Nocker, A., Cheung, C.-Y. & Camper, A. K. Comparison of propidiummonoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods 67, 310-320 (2006).
    • (2006) J. Microbiol. Methods , vol.67 , pp. 310-320
    • Nocker, A.1    Cheung, C.-Y.2    Camper, A.K.3
  • 17
    • 84907033647 scopus 로고    scopus 로고
    • Dead or alive: Molecular assessment of microbial viability
    • Cangelosi, G. A. & Meschke, J. S. Dead or alive: molecular assessment of microbial viability. Appl. Environ. Microbiol. 80, 5884-5891 (2014).
    • (2014) Appl. Environ. Microbiol. , vol.80 , pp. 5884-5891
    • Cangelosi, G.A.1    Meschke, J.S.2
  • 18
    • 84867754639 scopus 로고    scopus 로고
    • Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification
    • Fittipaldi, M., Nocker, A. & Codony, F. Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. J. Microbiol. Methods 91, 276-289 (2012).
    • (2012) J. Microbiol. Methods , vol.91 , pp. 276-289
    • Fittipaldi, M.1    Nocker, A.2    Codony, F.3
  • 19
    • 79251586529 scopus 로고    scopus 로고
    • Discrimination between live and dead cellsin bacterial communities from environmental water samples analyzed by 454 pyrosequencing
    • Nocker, A., Richter-Heitmann, T., Montijn, R., Schuren, F. & Kort, R. Discrimination between live and dead cellsin bacterial communities from environmental water samples analyzed by 454 pyrosequencing. Int. Microbiol. 13, 59-65 (2010).
    • (2010) Int. Microbiol. , vol.13 , pp. 59-65
    • Nocker, A.1    Richter-Heitmann, T.2    Montijn, R.3    Schuren, F.4    Kort, R.5
  • 20
    • 84927627455 scopus 로고    scopus 로고
    • Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil
    • Wagner, A. O., Praeg, N., Reitschuler, C., Illmer, P. & Illmer, P. Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil. Appl. Soil Ecol. 93, 56-64 (2015).
    • (2015) Appl. Soil Ecol. , vol.93 , pp. 56-64
    • Wagner, A.O.1    Praeg, N.2    Reitschuler, C.3    Illmer, P.4    Illmer, P.5
  • 21
    • 84937735251 scopus 로고    scopus 로고
    • Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed
    • Rocca, J. D. et al. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed. ISME J. 9, 1693-1699 (2015).
    • (2015) ISME J. , vol.9 , pp. 1693-1699
    • Rocca, J.D.1
  • 22
    • 83455177145 scopus 로고    scopus 로고
    • Effects of long-term fertilization of forest soils on potential nitrification and on the abundance and community structure of ammonia oxidizers and nitrite oxidizers
    • Wertz, S., Leigh, A. K. K. & Grayston, S. J. Effects of long-term fertilization of forest soils on potential nitrification and on the abundance and community structure of ammonia oxidizers and nitrite oxidizers. FEMS Microbiol. Ecol. 79, 142-154 (2012).
    • (2012) FEMS Microbiol. Ecol. , vol.79 , pp. 142-154
    • Wertz, S.1    Leigh, A.K.K.2    Grayston, S.J.3
  • 23
    • 0026305412 scopus 로고
    • A critical review on the role of mycorrhizal fungi in the uptake of phosphorus by plants
    • Bolan, N. S. A critical review on the role of mycorrhizal fungi in the uptake of phosphorus by plants. Plant Soil 134, 189-207 (1991).
    • (1991) Plant Soil , vol.134 , pp. 189-207
    • Bolan, N.S.1
  • 24
    • 84914142313 scopus 로고    scopus 로고
    • Global diversity and geography of soil fungi
    • Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
    • (2014) Science , vol.346 , pp. 1256688
    • Tedersoo, L.1
  • 25
    • 67651247607 scopus 로고    scopus 로고
    • Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
    • Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111-5120 (2009).
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 5111-5120
    • Lauber, C.L.1    Hamady, M.2    Knight, R.3    Fierer, N.4
  • 26
    • 79958013695 scopus 로고    scopus 로고
    • The bacterial biogeography of British soils
    • Griffiths, R. I. et al. The bacterial biogeography of British soils. Environ. Microbiol. 13, 1642-1654 (2011).
    • (2011) Environ. Microbiol. , vol.13 , pp. 1642-1654
    • Griffiths, R.I.1
  • 27
    • 84920079021 scopus 로고    scopus 로고
    • Water content differences have stronger effects than plant functional groups on soil bacteria in a steppe ecosystem
    • Zhang, X., Barberán, A., Zhu, X., Zhang, G. & Han, X.Water content differences have stronger effects than plant functional groups on soil bacteria in a steppe ecosystem. PLoS ONE 9, e115798 (2014).
    • (2014) PLoS ONE , vol.9
    • Zhang, X.1    Barberán, A.2    Zhu, X.3    Zhang, G.4    Han, X.5
  • 28
    • 84951161269 scopus 로고    scopus 로고
    • Key edaphic properties largely explain temporal and geographic variation in soil microbial communities across four biomes
    • Docherty, K. M. et al. Key edaphic properties largely explain temporal and geographic variation in soil microbial communities across four biomes. PLoS ONE 10, e0135352 (2015).
    • (2015) PLoS ONE , vol.10
    • Docherty, K.M.1
  • 29
    • 84962621347 scopus 로고    scopus 로고
    • Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment
    • Bond-Lamberty, B. et al. Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment. PLoS ONE 11, e0150599 (2016).
    • (2016) PLoS ONE , vol.11
    • Bond-Lamberty, B.1
  • 30
    • 84897492912 scopus 로고    scopus 로고
    • Tackling soil diversity with the assembly of large, complex metagenomes
    • Howe, A. C. et al. Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl Acad. Sci. USA 111, 4904-4909 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 4904-4909
    • Howe, A.C.1
  • 31
    • 84908132133 scopus 로고    scopus 로고
    • Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally
    • Ramirez, K. S. et al. Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally. Proc. R. Soc. B 281, 20141988 (2014).
    • (2014) Proc. R. Soc. B , vol.281 , pp. 20141988
    • Ramirez, K.S.1
  • 32
    • 25844519572 scopus 로고    scopus 로고
    • Extracellular DNA plays a key role in deep-sea ecosystem functioning
    • Dell'Anno, A. & Danovaro, R. Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 309, 2179-2179 (2005).
    • (2005) Science , vol.309 , pp. 2179
    • Dell'Anno, A.1    Danovaro, R.2
  • 33
    • 84878150357 scopus 로고    scopus 로고
    • Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene
    • Coolen, M. J. L. et al. Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene. Proc. Natl Acad. Sci. USA 110, 8609-8614 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 8609-8614
    • Coolen, M.J.L.1
  • 34
    • 18144401354 scopus 로고    scopus 로고
    • Microbial survival: The paleome: A sedimentary genetic record of past microbial communities
    • Inagaki, F., Okada, H., Tsapin, A. I. & Nealson, K. H. Microbial survival: the paleome: a sedimentary genetic record of past microbial communities. Astrobiology 5, 141-153 (2005).
    • (2005) Astrobiology , vol.5 , pp. 141-153
    • Inagaki, F.1    Okada, H.2    Tsapin, A.I.3    Nealson, K.H.4
  • 36
    • 84902959036 scopus 로고    scopus 로고
    • Evaluation of viability-qPCR detection system on viable and dead Salmonella serovar Enteritidis
    • Barbau-Piednoir, E. et al. Evaluation of viability-qPCR detection system on viable and dead Salmonella serovar Enteritidis. J. Microbiol. Methods 103, 131-137 (2014).
    • (2014) J. Microbiol. Methods , vol.103 , pp. 131-137
    • Barbau-Piednoir, E.1
  • 37
    • 84969972576 scopus 로고    scopus 로고
    • Evaluation of the propidium monoazide-quantitative polymerase chain reaction method for the detection of viable Enterococcus faecalis
    • Pinheiro, E. T., Neves, V. D., Reis, C. C., Longo, P. L. & Mayer, M. P. Evaluation of the propidium monoazide-quantitative polymerase chain reaction method for the detection of viable Enterococcus faecalis. J. Endod. 42, 1089-1092 (2016).
    • (2016) J. Endod. , vol.42 , pp. 1089-1092
    • Pinheiro, E.T.1    Neves, V.D.2    Reis, C.C.3    Longo, P.L.4    Mayer, M.P.5
  • 38
    • 84926505310 scopus 로고    scopus 로고
    • Limitations of using propidium monoazide with qPCR to discriminate between live and dead Legionella in biofilm samples
    • Taylor, M. J., Bentham, R. H. & Ross, K. E. Limitations of using propidium monoazide with qPCR to discriminate between live and dead Legionella in biofilm samples. Microbiol. Insights 2014, 15-24 (2014).
    • (2014) Microbiol. Insights , vol.2014 , pp. 15-24
    • Taylor, M.J.1    Bentham, R.H.2    Ross, K.E.3
  • 39
    • 84886725824 scopus 로고    scopus 로고
    • Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses
    • Blazewicz, S. J., Barnard, R. L., Daly, R. A. & Firestone, M. K. Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J. 7, 2061-2068 (2013).
    • (2013) ISME J. , vol.7 , pp. 2061-2068
    • Blazewicz, S.J.1    Barnard, R.L.2    Daly, R.A.3    Firestone, M.K.4
  • 40
    • 41549115091 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coliDH10B: Insights into the biology of a laboratory workhorse
    • Durfee, T. et al. The complete genome sequence of Escherichia coliDH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190, 2597-2606 (2008).
    • (2008) J. Bacteriol. , vol.190 , pp. 2597-2606
    • Durfee, T.1
  • 41
    • 66149104807 scopus 로고    scopus 로고
    • Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus
    • Herrera, M. L., Vallor, A. C., Gelfond, J. A., Patterson, T. F. & Wickes, B. L. Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus. J. Clin. Microbiol. 47, 1325-1332 (2009).
    • (2009) J. Clin. Microbiol. , vol.47 , pp. 1325-1332
    • Herrera, M.L.1    Vallor, A.C.2    Gelfond, J.A.3    Patterson, T.F.4    Wickes, B.L.5
  • 42
    • 84941008535 scopus 로고    scopus 로고
    • Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
    • Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl Acad. Sci. USA 112, 10967-10972 (2015).
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. 10967-10972
    • Leff, J.W.1
  • 43
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate OTU sequences from microbial amplicon reads
    • Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996-998 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 44
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 45
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618 (2011).
    • (2011) ISME J. , vol.6 , pp. 610-618
    • McDonald, D.1
  • 46
    • 77954748234 scopus 로고    scopus 로고
    • The UNITE database for molecular identification of fungi - Recent updates and future perspectives
    • Abarenkov, K. et al. The UNITE database for molecular identification of fungi - recent updates and future perspectives. New Phytol. 186, 281-285 (2010).
    • (2010) New Phytol. , vol.186 , pp. 281-285
    • Abarenkov, K.1
  • 47
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007).
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 49
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey, J. D. A direct approach to false discovery rates. J. R. Stat. Soc. B 64, 479-498 (2002).
    • (2002) J. R. Stat. Soc. B , vol.64 , pp. 479-498
    • Storey, J.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.