PMID- 22425347
OWN - NLM
STAT- MEDLINE
DCOM- 20130503
LR  - 20121203
IS  - 1618-0984 (Electronic)
IS  - 0723-2020 (Linking)
VI  - 35
IP  - 8
DP  - 2012 Dec
TI  - Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon 
      contaminated aquifer sediment samples.
PG  - 526-32
LID - S0723-2020(12)00026-4 [pii]
LID - 10.1016/j.syapm.2012.01.004 [doi]
AB  - Groundwater ecosystems are the most important sources of drinking water worldwide 
      but they are threatened by contamination and overexploitation. Petroleum spills 
      account for the most common source of contamination and the high carbon load 
      results in anoxia and steep geochemical gradients. Microbes play a major role in 
      the transformation of petroleum hydrocarbons into less toxic substances. To 
      investigate microbial populations at the single cell level, fluorescence in situ 
      hybridization (FISH) is now a well-established technique. Recently, however, 
      catalyzed reporter deposition (CARD)-FISH has been introduced for the detection 
      of microbes from oligotrophic environments. Nevertheless, petroleum contaminated 
      aquifers present a worst case scenario for FISH techniques due to the combination 
      of high background fluorescence of hydrocarbons and the presence of small 
      microbial cells caused by the low turnover rates characteristic of groundwater 
      ecosystems. It is therefore not surprising that studies of microorganisms from 
      such sites are mostly based on cultivation techniques, fingerprinting, and 
      amplicon sequencing. However, to reveal the population dynamics and interspecies 
      relationships of the key participants of contaminant degradation, FISH is an 
      indispensable tool. In this study, a protocol for FISH was developed in 
      combination with cell quantification using an automated counting microscope. The 
      protocol includes the separation and purification of microbial cells from 
      sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave 
      oven. As a proof of principle, the distribution of Archaea and Bacteria was shown 
      in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, 
      Germany), which has been heavily contaminated with several ten-thousand tonnes of 
      petroleum hydrocarbons since World War II.
CI  - Copyright (c) 2012 Elsevier GmbH. All rights reserved.
FAU - Tischer, Karolin
AU  - Tischer K
AD  - Helmholtz Centre for Environmental Research, Department of Environmental 
      Microbiology, Permoserstr. 15, 04318 Leipzig, Germany.
FAU - Zeder, Michael
AU  - Zeder M
FAU - Klug, Rebecca
AU  - Klug R
FAU - Pernthaler, Jakob
AU  - Pernthaler J
FAU - Schattenhofer, Martha
AU  - Schattenhofer M
FAU - Harms, Hauke
AU  - Harms H
FAU - Wendeberg, Annelie
AU  - Wendeberg A
LA  - eng
PT  - Journal Article
DEP - 20120316
PL  - Germany
TA  - Syst Appl Microbiol
JT  - Systematic and applied microbiology
JID - 8306133
RN  - 0 (Hydrocarbons)
RN  - 0 (Water Pollutants, Chemical)
SB  - IM
MH  - Archaea/genetics/isolation & purification
MH  - Bacteria/genetics/isolation & purification
MH  - *Biodiversity
MH  - Germany
MH  - Groundwater/*chemistry/*microbiology
MH  - Hydrocarbons/*analysis
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Water Pollutants, Chemical/*analysis
EDAT- 2012/03/20 06:00
MHDA- 2013/05/04 06:00
CRDT- 2012/03/20 06:00
PHST- 2011/09/30 00:00 [received]
PHST- 2012/01/11 00:00 [revised]
PHST- 2012/01/24 00:00 [accepted]
PHST- 2012/03/20 06:00 [entrez]
PHST- 2012/03/20 06:00 [pubmed]
PHST- 2013/05/04 06:00 [medline]
AID - S0723-2020(12)00026-4 [pii]
AID - 10.1016/j.syapm.2012.01.004 [doi]
PST - ppublish
SO  - Syst Appl Microbiol. 2012 Dec;35(8):526-32. doi: 10.1016/j.syapm.2012.01.004. 
      Epub 2012 Mar 16.