217
Views
7
CrossRef citations to date
0
Altmetric
Original Articles

Using Stable Isotope Probing to Characterize Differences Between Free-Living and Sediment-Associated Microorganisms in the Subsurface

&
Pages 362-370 | Received 01 Sep 2011, Accepted 01 Apr 2012, Published online: 08 Feb 2013

References

  • Baker , M A , Valett , H M and Dahm , C N . 2000 . Organic carbon supply and metabolism in a shallow groundwater ecosystem . Ecology , 81 : 3133 – 3148 .
  • Barbeau , K , Moffett , J W , Caron , D A , Croot , P L and Erdner , D L . 1996 . Role of phytoplankton grazing in relieving iron limitation of phytoplankton . Nature , 380 : 61 – 64 .
  • Beck , A J , Tsukamoto , Y , Tovar-Sanchez , A , Huerta-Diaz , M , Bokuniewicz , H J and Sañudo-Wilhelmy , S A . 2007 . Importance of geochemical transformations in determining submarine groundwater discharge-derived trace metal and nutrient fluxes . Appl Geochem , 22 : 477 – 490 .
  • Blöthe , M and Roden , E E . 2009 . Microbial iron redox cycling in a circumneutral-pH groundwater seep . Appl Environ Microbiol , 75 : 468 – 473 .
  • Boschker , H TS , Nold , S C , Wellsbury , P , Bos , D , de Graaf , W , Pel , R , Parkes , R J and Cappenberg , T E . 1998 . Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers . Nature , 392 : 801 – 805 .
  • Campbell , L . 2001 . Methods in Microbiology , Edited by: Paul , J H . Vol. 30 , 317 – 343 . San Francisco , CA : Academic Press . editor
  • Caron , D A , Goldman , J C and Dennett , M R . 1988 . Experimental demonstration of the roles of bacteria and bacterivorous protozoa in plankton nutrient cycles . Hydrobiologia , 159 : 27 – 40 .
  • Chapelle , F H and Lovley , D R . 1990 . Rates of microbial metabolism in deep coastal plain aquifers . Appl Environ Microbiol , 56 : 1865 – 1874 .
  • Chapelle , F H , Zelibor , J L Jr , Grimes , D J and Knobel , L L . 1987 . Bacteria in deep coastal plain sediments of Maryland: A possible source of CO2 to groundwater . Water Resour Res , 23 : 1625 – 1632 .
  • Charette , M A and Sholkovitz , E R . 2006 . Trace element cycling in a subterranean estuary: Part 2. Geochemistry of the pore water . Geochim Cosmochim Acta , 70 : 811 – 826 .
  • DeFlaun , M F , Fuller , M E , Zhang , P , Johnson , W P , Mailloux , B J , Holben , W E , Kovacik , W P , Balkwill , D L and Onstott , T C . 2001 . Comparison of methods for monitoring bacterial transport in the subsurface . J Microbiol Meth , 47 : 219 – 231 .
  • DeLeo , P C and Baveye , P . 1997 . Factors affecting protozoa predation of bacteria clogging laboratory aquifer microcosms . Geomicrobiol J , 14 : 127 – 149 .
  • Dumont , M G and Murrell , J C . 2005 . Stable isotope probing - linking microbial identity to function . Nat Rev Micro , 3 : 499 – 504 .
  • Flynn , T M , Sanford , R A and Bethke , C M . 2008 . Attached and suspended microbial communities in a pristine confined aquifer . Water Resour Res , 44 : W07425
  • Freitag , T E , Chang , L and Prosser , J I . 2006 . Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient . Environ Microbiol , 8 : 684 – 696 .
  • Ghiorse , W C and Wilson , J T . 1988 . Microbial ecology of the terrestrial subsurface . Adv Appl Microbiol , 33 : 107 – 172 .
  • Goldscheider , N , Hunkeler , D and Rossi , P . 2006 . Review: Microbial biocenoses in pristine aquifers and an assessment of investigative methods . Hydrogeol J , 14 : 926 – 941 .
  • Griebler , C and Lueders , T . 2009 . Microbial biodiversity in groundwater ecosystems . Freshw Biol , 54 : 649 – 677 .
  • Griffiths , R I , Whiteley , A S , O’Donnell , A G and Bailey , M J . 2000 . Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition . Appl Environ Microbiol , 66 : 5488 – 5491 .
  • Gruber , D F , Simjouw , J P , Seitzinger , S P and Taghon , G L . 2006 . Dynamics and characterization of refractory dissolved organic matter produced by a pure bacterial culture in an experimental predator-prey system . Appl Environ Microbiol , 72 : 4184 – 4191 .
  • Haack , S K , Fogarty , L R , West , T G , Alm , E W , McGuire , J T , Long , D T , Hyndman , D W and Forney , L J . 2004 . Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer . Environ Microbiol , 6 : 438 – 448 .
  • Huber , T , Faulkner , G and Hugenholtz , P . 2004 . Bellerophon: a program to detect chimeric sequences in multiple sequence alignments . Bioinformatics , 20 : 2317 – 2319 .
  • Jezbera , J , Hornák , K and Šimek , K . 2005 . Food selection by bacterivorous protists: insight from the analysis of the food vacuole content by means of fluorescence in situ hybridization . FEMS Microbiol Ecol , 52 : 351 – 363 .
  • Jürgens , K and Matz , C . 2002 . Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria . Antonie Leeuwen , 81 : 413 – 434 .
  • Kato , K . 1984 . Functional difference in the utilization of phytoplankton cell materials and dissolved organic compounds in free-living and particulate-associated bacteria in an aquatic system . Archiv Hydrobiologie , 100 : 521 – 532 .
  • Kinner , N E , Harvey , R W , Shay , D M , Metge , D W and Warren , A . 2002 . Field evidence for a protistan role in an organically-contaminated aquifer . Environ Sci Technol , 36 : 4312 – 4318 .
  • Kruskal , J B . 1964 . Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis . Psychometrika , 29 : 1 – 27 .
  • Kujawinski , E B , Del Vecchio , R , Blough , N V , Klein , G C and Marshall , A G . 2004 . Probing molecular-level transformations of dissolved organic matter: insights on photochemical degradation and protozoan modification of DOM from electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry . Mar Chem , 92 : 23 – 37 .
  • Lehman , R M , O’Connell , S P , Banta , A , Fredrickson , J K , Reysenbach , A-L , Kieft , T L and Colwell , F S . 2004 . Microbiological comparison of core and groundwater samples collected from a fractured basalt aquifer with that of dialysis chambers incubated in situ . Geomicrobiol J , 21 : 169 – 182 .
  • Lehman , R M , Roberto , F F , Earley , D , Bruhn , D F , Brink , S E , O’Connell , S P , Delwiche , M E and Colwell , F S . 2001 . Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer . Appl Environ Microbiol , 67 : 2095 – 2106 .
  • Longnecker , K , Da Costa , A , Bhatia , M and Kujawinski , E B . 2009 . Effect of carbon addition and predation on acetate-assimilating bacterial cells in groundwater . FEMS Microbiol Ecol , 70 : 456 – 470 .
  • Longnecker , K and Kujawinski , E B . 2011 . Composition of dissolved organic matter in groundwater . Geochim Cosmochim Acta , 75 : 2752 – 2761 .
  • López-Archilla , A I , Moreira , D , Velasco , S and López-García , P . 2007 . Archaeal and bacterial community composition of a pristine coastal aquifer in Doñana National Park, Spain . Aquat Microb Ecol , 47 : 123 – 139 .
  • Madsen , E L and Ghiorse , W C . 1993 . Aquatic Microbiology , Edited by: Ford , T E . p167 – 213 . Boston , MA : Blackwell Scientific Publications . editor
  • Madsen , E L , Sinclair , J L and Ghiorse , W C . 1991 . In situ biodegradation: microbiological patterns in a contaminated aquifer . Science , 252 : 830 – 833 .
  • Mather , PM. 1976 . London : J. Wiley & Sons .
  • Mattison , R G , Taki , H and Harayama , S . 2002 . The bacterivorous soil flagellate Heteromita globosa reduces bacterial clogging under denitrifying conditions in sand-filled aquifer columns . Appl Environ Microbiol , 68 : 4539 – 4545 .
  • Matz , C and Kjelleberg , S . 2005 . Off the hook—How bacteria survive protozoan grazing . Trends Microbiol , 13 : 302 – 307 .
  • Moore , WS. 1999 . The subterranean estuary: A reaction zone of ground water and sea water . Mar Chem , 65 : 111 – 125 .
  • Nagaosa , K , Maruyama , T , Welikala , N , Yamashita , Y , Saito , Y , Kato , K , Fortin , D , Nanba , K , Miyasaka , I and Fukunaga , S . 2008 . Active bacterial populations and grazing impact revealed by an in situ experiment in a shallow aquifer . Geomicrobiol J , 25 : 131 – 141 .
  • Novarino , G , Warren , A , Butler , H , Lambourne , G , Boxshall , A , Bateman , J , Kinner , N E , Harvey , R W , Mossee , R A and Teltsche , B . 1997 . Protistan communities in aquifers: a review . FEMS Microbiol Rev , 20 : 261 – 275 .
  • Padmanabhan , P , Padmanabhan , S , DeRito , C , Gray , A , Gannon , D , Snape , J R , Tsai , C S , Park , W , Jeon , C and Madsen , E L . 2003 . Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA . Appl Environ Microbiol , 69 : 1614 – 1622 .
  • Peacock , A D , Chang , Y-J , Istok , J D , Krumholz , L , Geyer , R , Kinsall , B , Watson , D , Sublette , K L and White , D C . 2004 . Utilization of microbial biofilms as monitors of bioremediation . Microb Ecol , 47 : 284 – 292 .
  • Pedersen , K , Arlinger , J , Eriksson , S , Hallbeck , A , Hallbeck , L and Johansson , J . 2008 . Numbers, biomass and cultivable diversity of microbial populations relate to depth and borehole-specific conditions in groundwater from depths of 4–450 m in Olkiluoto, Finland . ISME J , 2 : 760 – 775 .
  • Pombo , S A , Kleikemper , J , Schroth , M H and Zeyer , J . 2005 . Field-scale isotopic labeling of phospholipid fatty acids from acetate-degrading sulfate-reducing bacteria . FEMS Microbiol Ecol , 51 : 197 – 207 .
  • Pombo , S A , Pelz , O , Schroth , M H and Zeyer , J . 2002 . Field-scale 13C-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic carbon: tracing acetate assimilation and mineralization in a petroleum hydrocarbon-contaminated aquifer . FEMS Microbiol Ecol , 41 : 259 – 267 .
  • Radajewski , S , Webster , G , Reay , D S , Morris , S A , Ineson , P , Nedwell , D B , Prosser , J I and Murrell , J C . 2002 . Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing . Microbiology , 148 : 2331 – 2342 .
  • Routh , J , Grossman , E L , Ulrich , G A and Suflita , J M . 2001 . Volatile organic acids and microbial processes in the Yegua formation, east-central Texas . Appl Geochem , 16 : 183 – 195 .
  • Sambrook , J , Fritsch , E F and Maniatus , T . 1989 . Plainview , NY : Cold Spring Harbor Laboratory Press .
  • Sherr , E B , Caron , D A and Sherr , B F . 1993 . Handbook of Methods in Aquatic Microbial Ecology , Edited by: Kemp , P F , Sherr , B F , Sherr , E B and Cole , J J . p213 – 228 . Boca Raton , FL : Lewis Publishers . editors
  • Shi , Y , Zwolinski , M D , Schreiber , M E , Bahr , J M , Sewell , G W and Hickey , W J . 1999 . Molecular analysis of microbial community structures in pristine and contaminated aquifers: Field and laboratory microcosm experiments . Appl Environ Microbiol , 65 : 2143 – 2150 .
  • Tso , S-F and Taghon , G . 2006 . Protozoan grazing increases mineralization of naphthalene in marine sediment . Microb Ecol , 51 : 460 – 469 .
  • Valiela , I , Costa , J , Foreman , K , Teal , J M , Howes , B and Aubrey , D . 1990 . Transport of groundwater-borne nutrients from watersheds and their effects on coastal waters . Biogeochemistry , 10 : 177 – 197 .
  • Valster , R M , Wullings , B A , Bakker , G , Smidt , H and van der Kooij , D . 2009 . Free-living protozoa in two unchlorinated drinking water supplies, identified by phylogenic analysis of 18S rRNA gene sequences . Appl Environ Microbiol , 75 : 4736 – 4746 .
  • Velasco Ayuso , S , Guerrero , M C , Montes , C and López-Archilla , A I . 2009 . Spatiotemporal distribution of microbial communities in a coastal, sandy aquifer system (Doñana, SW Spain) . Geobiology , 7 : 66 – 81 .
  • Wu , D , Hartman , A , Ward , N and Eisen , J A . 2008 . An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP) . PLoS ONE , 3 : e2566

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.