메뉴 건너뛰기




Volumn 14, Issue 1, 2014, Pages

Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological

Author keywords

Bacterial ecology; Bacterial speciation; Biodiversity; Black queen hypothesis; Cooperation; Ecological networks; Ecological null models; Habitat filtering; Syntrophy

Indexed keywords

ARTICLE; COMMUNITY STRUCTURE; ECOLOGY; FILTRATION; MICROBIAL COMMUNITY; MICROHABITAT; NONHUMAN; ORGANISMAL INTERACTION; PHYLOGENY; SPECIES DIFFERENTIATION; BACTERIUM; BIOTA; CLASSIFICATION; MICROBIOLOGY;

EID: 84923927034     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-014-0284-5     Document Type: Article
Times cited : (21)

References (76)
  • 1
    • 0001281379 scopus 로고
    • Homage to Santa Rosalia or why are there so many kinds of animals?
    • Hutchinson GE: Homage to Santa Rosalia or why are there so many kinds of animals? The American Naturalist 1959, 93:145-159.
    • (1959) The American Naturalist , vol.93 , pp. 145-159
    • Hutchinson, G.E.1
  • 6
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • The Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
    • (2012) Nature , vol.486 , pp. 207-214
    • The Human Microbiome Project Consortium1
  • 9
    • 33747174849 scopus 로고    scopus 로고
    • Spatial scaling ofmicrobial biodiversity
    • Green J, Bohannan BJM: Spatial scaling ofmicrobial biodiversity. Trends Ecol Evol 2006, 21:501-507.
    • (2006) Trends Ecol Evol , vol.21 , pp. 501-507
    • Green, J.1    Bohannan, B.J.M.2
  • 11
    • 1642376424 scopus 로고    scopus 로고
    • Microbial biogeography along an estuarine salinity gradient: Combined influences of bacterial growth and residence time
    • Hopkinson CS, Sogin ML, Hobbie JE, Crump BC: Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol 2004, 70:1494-1505.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 1494-1505
    • Hopkinson, C.S.1    Sogin, M.L.2    Hobbie, J.E.3    Crump, B.C.4
  • 12
    • 33847327474 scopus 로고    scopus 로고
    • Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology and evolution
    • Ramette A, Tiedje JM: Biogeography: An emerging cornerstone for understanding prokaryotic diversity, ecology and evolution. Microb Ecol 2006, 53:197-207.
    • (2006) Microb Ecol , vol.53 , pp. 197-207
    • Ramette, A.1    Tiedje, J.M.2
  • 14
    • 77952803493 scopus 로고    scopus 로고
    • Conceptual synthesis in community ecology
    • Vellend M: Conceptual synthesis in community ecology. Q Rev Biol 2010, 85:183-206.
    • (2010) Q Rev Biol , vol.85 , pp. 183-206
    • Vellend, M.1
  • 15
    • 77954241658 scopus 로고    scopus 로고
    • The large-scale organization of the bacterial network of ecological co-occurrence interactions
    • Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E: The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucl Ac Res 2010, 38:3857-68.
    • (2010) Nucl Ac Res , vol.38 , pp. 3857-3868
    • Freilich, S.1    Kreimer, A.2    Meilijson, I.3    Gophna, U.4    Sharan, R.5    Ruppin, E.6
  • 17
    • 77954238817 scopus 로고    scopus 로고
    • A global network of coexisting microbes from environmental and whole-genome sequence data
    • Chaffron S, Rehrauer H, Pernthaler J, von Mering C: A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 2010, 20:947-959.
    • (2010) Genome Res , vol.20 , pp. 947-959
    • Chaffron, S.1    Rehrauer, H.2    Pernthaler, J.3    Von Mering, C.4
  • 19
    • 84855949949 scopus 로고    scopus 로고
    • Using network analysis to explore co-occurrence patterns in soil microbial communities
    • Barberán A, Bates ST, Casamayor EO, Fierer N: Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 2012, 6:343-51.
    • (2012) ISME J , vol.6 , pp. 343-351
    • Barberán, A.1    Bates, S.T.2    Casamayor, E.O.3    Fierer, N.4
  • 22
    • 84861990785 scopus 로고    scopus 로고
    • Predicting bacterial community assemblages using an artificial neural network apprach
    • Larsen PE, Field D, Gilbert JA: Predicting bacterial community assemblages using an artificial neural network apprach. Nat Methods 2012, 9:621-625.
    • (2012) Nat Methods , vol.9 , pp. 621-625
    • Larsen, P.E.1    Field, D.2    Gilbert, J.A.3
  • 23
    • 84867161176 scopus 로고    scopus 로고
    • Identifying genomic andmetabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
    • Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R: Identifying genomic andmetabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res 2012, 22:1974-1984.
    • (2012) Genome Res , vol.22 , pp. 1974-1984
    • Lozupone, C.1    Faust, K.2    Raes, J.3    Faith, J.J.4    Frank, D.N.5    Zaneveld, J.6    Gordon, J.I.7    Knight, R.8
  • 25
    • 84863920287 scopus 로고    scopus 로고
    • Microbial interactions: From networks tomodels
    • Faust K, Raes J: Microbial interactions: from networks tomodels. Nat Rev Microbiol 2012, 10:538-550.
    • (2012) Nat Rev Microbiol , vol.10 , pp. 538-550
    • Faust, K.1    Raes, J.2
  • 27
    • 70349865248 scopus 로고    scopus 로고
    • Null model analyses of presence-absencematrices need a definition of independence
    • Navarro-Alberto JA, Manly BFJ: Null model analyses of presence-absencematrices need a definition of independence. Popul Ecol 2009, 51:505-512.
    • (2009) Popul Ecol , vol.51 , pp. 505-512
    • Navarro-Alberto, J.A.1    Manly, B.F.J.2
  • 30
    • 42349106001 scopus 로고    scopus 로고
    • Syntrophism among prokaryotes
    • Edited by Dworkin M New York: Springer
    • Schink B, Stams AJM: Syntrophism among prokaryotes. In The Prokaryotes. Edited by Dworkin M. vol. 2. New York: Springer; 2006:309-335.
    • (2006) The Prokaryotes , vol.2 , pp. 309-335
    • Schink, B.1    Stams, A.J.M.2
  • 32
    • 42049111815 scopus 로고    scopus 로고
    • Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing
    • Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA, Wolcott RD: Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMCMicrobiol 2008, 8:43.
    • (2008) BMCMicrobiol , vol.8 , pp. 43
    • Dowd, S.E.1    Sun, Y.2    Secor, P.R.3    Rhoads, D.D.4    Wolcott, B.M.5    James, G.A.6    Wolcott, R.D.7
  • 37
    • 33846704237 scopus 로고    scopus 로고
    • Evolution of species interactions in a biofilm community
    • Hansen SK, Rainey PB, Haagensen JA, Molin S: Evolution of species interactions in a biofilm community. Nature 2007, 445:533-536.
    • (2007) Nature , vol.445 , pp. 533-536
    • Hansen, S.K.1    Rainey, P.B.2    Haagensen, J.A.3    Molin, S.4
  • 38
    • 33846820191 scopus 로고    scopus 로고
    • Diversity study of nitrifying bacteria in full-scalemunicipal wastewater treatment plants
    • Siripong S, Rittmann BE: Diversity study of nitrifying bacteria in full-scalemunicipal wastewater treatment plants. Water Res 2007, 41:1110-1120.
    • (2007) Water Res , vol.41 , pp. 1110-1120
    • Siripong, S.1    Rittmann, B.E.2
  • 40
    • 84879495314 scopus 로고    scopus 로고
    • Microbial diversity and its relationship to physicochemical characteristics of the water in two extreme acidic pit lakes from the iberian pyrite belt (SW Spain)
    • Santofimia E, Gonzàlez-Toril E, López-Pamo E, Gomariz M, Amils R, Aguilera A: Microbial diversity and its relationship to physicochemical characteristics of the water in two extreme acidic pit lakes from the iberian pyrite belt (SW Spain). PLoS ONE 2013, 8(6):e66746.
    • (2013) PLoS ONE , vol.8 , Issue.6 , pp. e66746
    • Santofimia, E.1    Gonzàlez-Toril, E.2    López-Pamo, E.3    Gomariz, M.4    Amils, R.5    Aguilera, A.6
  • 41
    • 58549094275 scopus 로고    scopus 로고
    • Complementary cooperation between two syntrophic bacteria in pesticide degradation
    • Katsuyama C, Nakaoka S, Takeuchi Y, Tago K, Hayatsu M, Kato K: Complementary cooperation between two syntrophic bacteria in pesticide degradation. J Theor Biol 2009, 256:644-654.
    • (2009) J Theor Biol , vol.256 , pp. 644-654
    • Katsuyama, C.1    Nakaoka, S.2    Takeuchi, Y.3    Tago, K.4    Hayatsu, M.5    Kato, K.6
  • 42
    • 4644322856 scopus 로고    scopus 로고
    • Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: Genome evolution, interactions and adaptation
    • Eberl L, Tümmler B: Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: genome evolution, interactions and adaptation. Int J Med Microbiol 2004, 294:123-131.
    • (2004) Int J Med Microbiol , vol.294 , pp. 123-131
    • Eberl, L.1    Tümmler, B.2
  • 46
    • 85166916238 scopus 로고    scopus 로고
    • Gephi: An open source software for exploring and manipulating networks
    • Association for the Advancement of Artificial Intelligence
    • Bastian M, Heymann S, Jacomy M: Gephi: an open source software for exploring and manipulating networks. In International AAAI Conference on Weblogs and Social Media; 2009. Association for the Advancement of Artificial Intelligence (www.aaai.org).
    • International AAAI Conference on Weblogs and Social Media; 2009
    • Bastian, M.1    Heymann, S.2    Jacomy, M.3
  • 48
    • 84903464596 scopus 로고    scopus 로고
    • Successional patterns of community assembly and functional ecology during gut microbiota development in an infant birth cohort
    • Aceptado en PloS Genetics
    • Vallès Y, Artacho A, Pascual-García A, Ferrús ML, Gosalbes MJ, Abellán JJ, Francino MP: Successional patterns of community assembly and functional ecology during gut microbiota development in an infant birth cohort. PLoS Genetics 2014, 10:e1004406. Aceptado en PloS Genetics
    • (2014) PLoS Genetics , vol.10 , pp. e1004406
    • Vallès, Y.1    Artacho, A.2    Pascual-García, A.3    Ferrús, M.L.4    Gosalbes, M.J.5    Abellán, J.J.6    Francino, M.P.7
  • 51
    • 0031981808 scopus 로고    scopus 로고
    • Santa Rosalia revisited:Why are there so many species of bacteria?
    • Dykhuizen DE: Santa Rosalia revisited:Why are there so many species of bacteria? Antonie Leeuwenhaek 1998, 73:25-33.
    • (1998) Antonie Leeuwenhaek , vol.73 , pp. 25-33
    • Dykhuizen, D.E.1
  • 54
    • 33751258603 scopus 로고    scopus 로고
    • The bacterial species dilemma and the genomic-phylogenetic species concept
    • Staley JT: The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 2006, 361:1899-1909.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , pp. 1899-1909
    • Staley, J.T.1
  • 55
    • 0036407157 scopus 로고    scopus 로고
    • What are bacterial species?
    • Cohan FM: What are bacterial species? Annu Rev Microbiol 2002, 56:457-487.
    • (2002) Annu Rev Microbiol , vol.56 , pp. 457-487
    • Cohan, F.M.1
  • 57
  • 58
    • 84894300674 scopus 로고    scopus 로고
    • Species matter: The role of competition in the assembly of congeneric bacteria
    • Koeppel AF, Wu M: Species matter: the role of competition in the assembly of congeneric bacteria. ISME J 2014, 8:531-540.
    • (2014) ISME J , vol.8 , pp. 531-540
    • Koeppel, A.F.1    Wu, M.2
  • 59
    • 0025622072 scopus 로고
    • The checkerboard score and species distribution
    • Stone L, Roberts A: The checkerboard score and species distribution. Oecologia 1990, 85:74-79.
    • (1990) Oecologia , vol.85 , pp. 74-79
    • Stone, L.1    Roberts, A.2
  • 60
    • 74449083073 scopus 로고    scopus 로고
    • The empirical bayes approach as a tool to identify non-random species associations
    • Gotelli NJ, Ulrich W: The empirical bayes approach as a tool to identify non-random species associations. Oecologia 2010, 162:463-477.
    • (2010) Oecologia , vol.162 , pp. 463-477
    • Gotelli, N.J.1    Ulrich, W.2
  • 61
    • 84881110826 scopus 로고    scopus 로고
    • Metabolicmodeling of species interaction in the humanmicrobiome elucidates community-level assembly rules
    • Levy R, Borenstein E: Metabolicmodeling of species interaction in the humanmicrobiome elucidates community-level assembly rules. Proc Natl Acad Sci USA 2013, 110:12804-12809.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 12804-12809
    • Levy, R.1    Borenstein, E.2
  • 63
    • 78649677586 scopus 로고    scopus 로고
    • Environments that induce synthetic microbial ecosystems
    • Klitgord N, Segré D: Environments that induce synthetic microbial ecosystems. PLoS Comp Biol 2010, 6:e1001002.
    • (2010) PLoS Comp Biol , vol.6 , pp. e1001002
    • Klitgord, N.1    Segré, D.2
  • 64
    • 84867405105 scopus 로고    scopus 로고
    • Competition, not cooperation, dominates interactions among culturable microbial species
    • Foster KR, Bell T: Competition, not cooperation, dominates interactions among culturable microbial species. Curr Biol 2012, 22:1845-1850.
    • (2012) Curr Biol , vol.22 , pp. 1845-1850
    • Foster, K.R.1    Bell, T.2
  • 65
    • 67649697839 scopus 로고    scopus 로고
    • Microbes and the dissipation of energy and respiration: From cells to ecosystems
    • Carlson CA, del Giorgio PA, Herndl GJ: Microbes and the dissipation of energy and respiration: from cells to ecosystems. Oceanography 2007, 20(2):89100.
    • (2007) Oceanography , vol.20 , Issue.2 , pp. 89100
    • Carlson, C.A.1    Del Giorgio, P.A.2    Herndl, G.J.3
  • 68
    • 0041909446 scopus 로고    scopus 로고
    • Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus
    • Velicer GJ, Yu YN: Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus. Nature 2003, 425:75-78.
    • (2003) Nature , vol.425 , pp. 75-78
    • Velicer, G.J.1    Yu, Y.N.2
  • 69
    • 78349245948 scopus 로고    scopus 로고
    • Novel cooperation experimentally evolved between species
    • Harcombe W: Novel cooperation experimentally evolved between species. Evolution 2010, 64:2166-2172.
    • (2010) Evolution , vol.64 , pp. 2166-2172
    • Harcombe, W.1
  • 71
    • 84869774396 scopus 로고    scopus 로고
    • Adaptation to a new environment allows cooperators to purge cheaters stochastically
    • Waite AJ, Shou W: Adaptation to a new environment allows cooperators to purge cheaters stochastically. Proc Natl Acad Sci U S A 2012, 109:19079-19086.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 19079-19086
    • Waite, A.J.1    Shou, W.2
  • 73
    • 84860511582 scopus 로고    scopus 로고
    • The Black Queen Hypothesis: Evolution of dependencies through adaptive gene loss
    • Morris JJ, Lenski RE, Zinser ER: The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio 2012, 3(2):e00036-12. doi:10.1128/mBio.00036-12.
    • (2012) MBio , vol.3 , Issue.2 , pp. e00036-e00112
    • Morris, J.J.1    Lenski, R.E.2    Zinser, E.R.3
  • 74
    • 84863495875 scopus 로고    scopus 로고
    • The origins of cooperative bacterial communities
    • Sachs JL, Hollowell AC: The origins of cooperative bacterial communities. MBio 2012, 3(3):e00099-12. doi:10.1128/mBio.00099-12.
    • (2012) MBio , vol.3 , Issue.3 , pp. e00099-e00112
    • Sachs, J.L.1    Hollowell, A.C.2
  • 76
    • 0002723108 scopus 로고
    • Factors contributing to non-randomness in species co-occurrences on islands
    • Gilpin ME, Diamond JM: Factors contributing to non-randomness in species co-occurrences on islands. Oecologia 1982, 52:75-84.
    • (1982) Oecologia , vol.52 , pp. 75-84
    • Gilpin, M.E.1    Diamond, J.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.