Diverse syntrophic partnerships from-deep-sea methane vents revealed by direct cell capture and metagenomics

被引:212
作者
Pernthaler, Annelie [1 ]
Dekas, Anne E. [1 ]
Brown, C. Titus [2 ]
Goffredi, Shana K. [1 ]
Embaye, Tsegereda [1 ]
Orphan, Victoria J. [1 ,2 ]
机构
[1] CALTECH, Div Geol & Planetary Sci, Pasadena, CA 91125 USA
[2] CALTECH, Div Biol, Pasadena, CA 91125 USA
关键词
beta proteobacteria; methanotrophy; nitrogen fixation; syntrophy;
D O I
10.1073/pnas.0711303105
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner, The detection of nitrogenase genes within the metagenome and subsequent demonstration of (15)N(2) incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages.
引用
收藏
页码:7052 / 7057
页数:6
相关论文
共 39 条
[1]   PHYLOGENETIC IDENTIFICATION AND IN-SITU DETECTION OF INDIVIDUAL MICROBIAL-CELLS WITHOUT CULTIVATION [J].
AMANN, RI ;
LUDWIG, W ;
SCHLEIFER, KH .
MICROBIOLOGICAL REVIEWS, 1995, 59 (01) :143-169
[2]   Optical trapping and manipulation of neutral particles using lasers [J].
Ashkin, A .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (10) :4853-4860
[3]  
BINGA EK, 2008, ISME J, P1
[4]   A marine microbial consortium apparently mediating anaerobic oxidation of methane [J].
Boetius, A ;
Ravenschlag, K ;
Schubert, CJ ;
Rickert, D ;
Widdel, F ;
Gieseke, A ;
Amann, R ;
Jorgensen, BB ;
Witte, U ;
Pfannkuche, O .
NATURE, 2000, 407 (6804) :623-626
[5]   Heterotrophic bacteria growing in association with Methylococcus capsulatus (Bath) in a single cell protein production process [J].
Bothe, H ;
Jensen, KM ;
Mergel, A ;
Larsen, J ;
Jorgensen, C ;
Bothe, H ;
Jorgensen, L .
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2002, 59 (01) :33-39
[6]   Genomic perspectives in microbial oceanography [J].
DeLong, EF ;
Karl, DM .
NATURE, 2005, 437 (7057) :336-342
[7]   Using pyrosequencing to shed light on deep mine microbial ecology [J].
Edwards, Robert A. ;
Rodriguez-Brito, Beltran ;
Wegley, Linda ;
Haynes, Matthew ;
Breitbart, Mya ;
Peterson, Dean M. ;
Saar, Martin O. ;
Alexander, Scott ;
Alexander, E. Calvin, Jr. ;
Rohwer, Forest .
BMC GENOMICS, 2006, 7 (1)
[8]   The genome of M-acetivorans reveals extensive metabolic and physiological diversity [J].
Galagan, JE ;
Nusbaum, C ;
Roy, A ;
Endrizzi, MG ;
Macdonald, P ;
FitzHugh, W ;
Calvo, S ;
Engels, R ;
Smirnov, S ;
Atnoor, D ;
Brown, A ;
Allen, N ;
Naylor, J ;
Stange-Thomann, N ;
DeArellano, K ;
Johnson, R ;
Linton, L ;
McEwan, P ;
McKernan, K ;
Talamas, J ;
Tirrell, A ;
Ye, WJ ;
Zimmer, A ;
Barber, RD ;
Cann, I ;
Graham, DE ;
Grahame, DA ;
Guss, AM ;
Hedderich, R ;
Ingram-Smith, C ;
Kuettner, HC ;
Krzycki, JA ;
Leigh, JA ;
Li, WX ;
Liu, JF ;
Mukhopadhyay, B ;
Reeve, JN ;
Smith, K ;
Springer, TA ;
Umayam, LA ;
White, O ;
White, RH ;
de Macario, EC ;
Ferry, JG ;
Jarrell, KF ;
Jing, H ;
Macario, AJL ;
Paulsen, I ;
Pritchett, M ;
Sowers, KR .
GENOME RESEARCH, 2002, 12 (04) :532-542
[9]   Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor [J].
Girguis, PR ;
Cozen, AE ;
DeLong, EF .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2005, 71 (07) :3725-3733
[10]  
HALLAM SJ, 2004, SCIENCE, V305